PDBx ontology
The OWL ontology for PDB/RDF, generated from the PDBML Schema.
Category
Abstract class for category holders.
CategoryElement
Abstract class for category elements.
categoryItem
Abstract datatype property for category items.
Abstract property for cross-references within PDBML.
Abstract property for cross-references between categories.
Abstract property for cross-references between categories.
Abstract property for external links.
Abstract property for external RDF links.
Abstract property for external HTML links.
link to PDBML-all file.
link to PDBML-noatom file.
link to PDBML-extatom file.
link to related PDB entry.
link to associated wwPDB validation report.
link to split PDB entry.
link to associated BMRB entry.
link to associated EMDB entry.
link to associated SASBDB entry.
external link to PubMed.
external link to sequence databases.
external link to UniProt.
external link to GenBank.
external link to EMBL.
external link to NORINE.
external link to PIR.
external link to RefSeq.
external link to glycoinfo.org.
external link to KEGG Compound.
external link to KEGG Drug.
external link to Novel Antibiotics Data Base.
external link to ORCiD (Open Researcher and Contributor ID).
external link to DOI (digital object identifier).
external link to NCBI taxonomy.
external link to NCBI taxonomy (source organism).
external link to NCBI taxonomy (host organism).
external link to EC (enzyme commission) number.
external link to GO (gene ontology).
external link to InterPro.
external link to Pfam.
external link to CATH.
external link to SCOP, SCOP2, and SCOP2B.
external link to Ensembl (Eukaryotic Genome).
external link to chemical component in CCD.
external link to parental chemical component in CCD.
external link to peptide reference in PRD (a part of BIRD, Biologically Interesting molecules Reference Dictionary).
external link to CCDC (Cambridge Crystallographic Data Centre).
external link to PubChem Substance.
external link to ChemSpider.
external link to CAS.
external link to ChEBI.
external link to MeSH.
external link to ChemIDplus.
external link to ChEMBL.
external link to BindingDB.
external link to DrugBank.
external link to ChemDB.
datablock
The datablock class holds all categories of PDB data.
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PDBML Schema translated from the PDBx/mmCIF Dictionary v5.389:
http://mmcif.wwpdb.org/dictionaries/ascii/mmcif_pdbx_v50.dic
Abstract property pointing to category.
Abstract property pointing to category element.
link_to_datablock
Link to the base datablock of category elements.
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array_data
Data items in the ARRAY_DATA category are the containers for
the array data items described in the category ARRAY_STRUCTURE.
It is recognized that the data in this category need to be used in
two distinct ways. During a data collection the lack of ancillary
data and timing constraints in processing data may dictate the
need to make a 'miniCBF', nothing more than an essential minimum
of information to record the results of the data collection. In that
case it is proper to use the ARRAY_DATA category as a
container for just a single image and a compacted, beamline-dependent
list of data collection parameter values. In such
a case, only the tags '_array_data.header_convention',
'_array_data.header_contents' and '_array_data.data' need be
populated.
For full processing and archiving, most of the tags in this
dictionary will need to be populated.
Example 1.
This example shows two binary data blocks. The first one
was compressed by the CBF_CANONICAL compression algorithm and is
presented as hexadecimal data. The first character 'H' on the
data lines means hexadecimal. It could have been 'O' for octal
or 'D' for decimal. The second character on the line shows
the number of bytes in each word (in this case '4'), which then
requires eight hexadecimal digits per word. The third character
gives the order of octets within a word, in this case '<'
for the ordering 4321 (i.e. 'big-endian'). Alternatively, the
character '>' could have been used for the ordering 1234
(i.e. 'little-endian'). The block has a 'message digest'
to check the integrity of the data.
The second block is similar, but uses CBF_PACKED compression
and BASE64 encoding. Note that the size and the digest are
different.
<PDBx:array_dataCategory>
<PDBx:array_data array_id="image_1" binary_id="1">
<PDBx:data> --CIF-BINARY-FORMAT-SECTION-- Content-Type: application/octet-stream; conversions="X-CBF_CANONICAL" Content-Transfer-Encoding: X-BASE16 X-Binary-Size: 3927126 X-Binary-ID: 1 Content-MD5: u2sTJEovAHkmkDjPi+gWsg== # Hexadecimal encoding, byte 0, byte order ...21 # H4< 0050B810 00000000 00000000 00000000 000F423F 00000000 00000000 ... .... --CIF-BINARY-FORMAT-SECTION----</PDBx:data>
</PDBx:array_data>
<PDBx:array_data array_id="image_2" binary_id="2">
<PDBx:data> --CIF-BINARY-FORMAT-SECTION-- Content-Type: application/octet-stream; conversions="X-CBF-PACKED" Content-Transfer-Encoding: BASE64 X-Binary-Size: 3745758 X-Binary-ID: 2 Content-MD5: 1zsJjWPfol2GYl2V+QSXrw== ELhQAAAAAAAA... ... --CIF-BINARY-FORMAT-SECTION----</PDBx:data>
</PDBx:array_data>
</PDBx:array_dataCategory>
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array_dataCategory
This property indicates that datablock
has a category holder array_dataCategory.
array_dataCategory
This property indicates that array_dataCategory.
has a category array_data.
array_dataItem
Abstract datatype property for array_data items.
reference_to_array_data
cross-reference to array_data.
referenced_by_array_data
cross-reference from array_data.
array_data.data
The value of attribute data in category array_data contains the array data
encapsulated in a STAR string. The value of this item is
required unless a value is given for
attribute external_data_id in category array_data instead, in which
case, a null value of '.' should be given here.
The representation used is a variant on the
Multipurpose Internet Mail Extensions (MIME) specified
in RFC 2045-2049 by N. Freed et al. The boundary
delimiter used in writing an imgCIF or CBF is
\n--CIF-BINARY-FORMAT-SECTION-- (including the
required initial \n--, where \n represents the system
newline character(s)).
The Content-Type may be any of the discrete types permitted
in RFC 2045; 'application/octet-stream' is recommended
for diffraction images in the ARRAY_DATA category.
Note: When appropriate in other categories, e.g. for
photographs of crystals, more precise types, such as
'image/jpeg', 'image/tiff', 'image/png', etc. should be used.
If an octet stream was compressed, the compression should
be specified by the parameter
conversions="X-CBF_PACKED"
or the parameter
conversions="X-CBF_CANONICAL"
or the parameter
conversions="X-CBF_BYTE_OFFSET"
or the parameter
conversions="X-CBF_BACKGROUND_OFFSET_DELTA"
If the parameter
conversions="X-CBF_PACKED"
is given it may be further modified with the parameters
uncorrelated_sections
or
flat
(e.g. conversions="X-CBF_PACKED flat").
In such cases the attribute compression_type_flag
in category array_structure should also be present with the corresponding value.
If the "uncorrelated_sections" parameter is
given, each section will be compressed without using
the prior section for averaging.
If the "flat" parameter is given, each
image will be treated as one long row.
Note that X-CBF_CANONICAL and X-CBF_PACKED are
slower but more efficient compressions than the others.
The X-CBF_BYTE_OFFSET compression is a good compromise
between speed and efficiency for ordinary diffraction
images. The X-CBF_BACKGROUND_OFFSET_DELTA compression
is oriented towards sparse data, such as masks and
tables of replacement pixel values for images with
overloaded spots.
The Content-Transfer-Encoding may be 'BASE64',
'Quoted-Printable', 'X-BASE8', 'X-BASE10',
'X-BASE16' or 'X-BASE32K', for an imgCIF or 'BINARY'
for a CBF. The octal, decimal and hexadecimal transfer
encodings are provided for convenience in debugging and
are not recommended for archiving and data interchange.
In a CIF, one of the parameters 'charset=us-ascii',
'charset=utf-8' or 'charset=utf-16' may be used on the
Content-Transfer-Encoding to specify the character set
used for the external presentation of the encoded data.
If no charset parameter is given, the character set of
the enclosing CIF is assumed. In any case, if a BOM
flag is detected (FE FF for big-endian UTF-16, FF FE for
little-endian UTF-16 or EF BB BF for UTF-8) is detected,
the indicated charset will be assumed until the end of the
encoded data or the detection of a different BOM. The
charset of the Content-Transfer-Encoding is not the character
set of the encoded data, only the character set of the
presentation of the encoded data and should be respecified
for each distinct STAR string.
In an imgCIF file, the encoded binary data begin after
the empty line terminating the header. In an imgCIF file,
the encoded binary data ends with the terminating boundary
delimiter '\n--CIF-BINARY-FORMAT-SECTION----'
in the currently effective charset or with the '\n;'
that terminates the STAR string.
In a CBF, the raw binary data begin after an empty line
terminating the header and after the sequence:
Octet Hex Decimal Purpose
0 0C 12 Ctrl-L: page break
1 1A 26 Ctrl-Z: stop listings, MS-DOS
2 04 04 Ctrl-D: stop listings, UNIX
3 D5 213 binary section begins
None of these octets are included in the calculation of
the message size or in the calculation of the
message digest.
The X-Binary-Size header specifies the size of the
equivalent binary data in octets. If compression was
used, this size is the size after compression, including
any book-keeping fields. An adjustment is made for
the deprecated binary formats in which eight bytes of binary
header are used for the compression type. In this case,
the eight bytes used for the compression type are subtracted
from the size, so that the same size will be reported
if the compression type is supplied in the MIME header.
Use of the MIME header is the recommended way to
supply the compression type. In general, no portion of
the binary header is included in the calculation of the size.
The X-Binary-Element-Type header specifies the type of
binary data in the octets, using the same descriptive
phrases as in attribute encoding_type in category array_structure. The default
value is 'unsigned 32-bit integer'.
An MD5 message digest may, optionally, be used. The 'RSA Data
Security, Inc. MD5 Message-Digest Algorithm' should be used.
No portion of the header is included in the calculation of the
message digest.
If the Transfer Encoding is 'X-BASE8', 'X-BASE10' or
'X-BASE16', the data are presented as octal, decimal or
hexadecimal data organized into lines or words. Each word
is created by composing octets of data in fixed groups of
2, 3, 4, 6 or 8 octets, either in the order ...4321 ('big-
endian') or 1234... ('little-endian'). If there are fewer
than the specified number of octets to fill the last word,
then the missing octets are presented as '==' for each
missing octet. Exactly two equal signs are used for each
missing octet even for octal and decimal encoding.
The format of lines is:
rnd xxxxxx xxxxxx xxxxxx
where r is 'H', 'O' or 'D' for hexadecimal, octal or
decimal, n is the number of octets per word and d is '<'
or '>' for the '...4321' and '1234...' octet orderings,
respectively. The '==' padding for the last word should
be on the appropriate side to correspond to the missing
octets, e.g.
H4< FFFFFFFF FFFFFFFF 07FFFFFF ====0000
or
H3> FF0700 00====
For these hexadecimal, octal and decimal formats only,
comments beginning with '#' are permitted to improve
readability.
BASE64 encoding follows MIME conventions. Octets are
in groups of three: c1, c2, c3. The resulting 24 bits
are broken into four six-bit quantities, starting with
the high-order six bits (c1 >> 2) of the first octet, then
the low-order two bits of the first octet followed by the
high-order four bits of the second octet [(c1 & 3)<<4 | (c2>>4)],
then the bottom four bits of the second octet followed by the
high-order two bits of the last octet [(c2 & 15)<<2 | (c3>>6)],
then the bottom six bits of the last octet (c3 & 63). Each
of these four quantities is translated into an ASCII character
using the mapping:
1 2 3 4 5 6
0123456789012345678901234567890123456789012345678901234567890123
| | | | | | |
ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789+/
with short groups of octets padded on the right with one '='
if c3 is missing, and with '==' if both c2 and c3 are missing.
X-BASE32K encoding is similar to BASE64 encoding, except that
sets of 15 octets are encoded as sets of 8 16-bit Unicode
characters, by breaking the 120 bits into 8 15-bit quantities.
256 is added to each 15-bit quantity to bring it into a
printable Unicode range. When encoding, zero padding is used
to fill out the last 15-bit quantity. If 8 or more bits of
padding are used, a single equals sign (hexadecimal 003D) is
appended. Embedded whitespace and newlines are introduced
to produce lines of no more than 80 characters each. On
decoding, all printable ASCII characters and ASCII whitespace
characters are ignored except for any trailing equals signs.
The number of trailing equals signs indicated the number of
trailing octets to be trimmed from the end of the decoded data
(see Darakev et al., 2006).
QUOTED-PRINTABLE encoding also follows MIME conventions, copying
octets without translation if their ASCII values are 32...38,
42, 48...57, 59, 60, 62, 64...126 and the octet is not a ';'
in column 1. All other characters are translated to =nn, where
nn is the hexadecimal encoding of the octet. All lines are
'wrapped' with a terminating '=' (i.e. the MIME conventions
for an implicit line terminator are never used).
The 'X-Binary-Element-Byte-Order' can specify either
'BIG_ENDIAN' or 'LITTLE_ENDIAN' byte order of the image
data. Only LITTLE_ENDIAN is recommended. Processors
may treat BIG_ENDIAN as a warning of data that can
only be processed by special software.
The 'X-Binary-Number-of-Elements' specifies the number of
elements (not the number of octets) in the decompressed,
decoded image.
The optional 'X-Binary-Size-Fastest-Dimension' specifies the
number of elements (not the number of octets) in one row of the
fastest changing dimension of the binary data array. This
information must be in the MIME header for proper operation of
some of the decompression algorithms.
The optional 'X-Binary-Size-Second-Dimension' specifies the
number of elements (not the number of octets) in one column of
the second-fastest changing dimension of the binary data array.
This information must be in the MIME header for proper operation
of some of the decompression algorithms.
The optional 'X-Binary-Size-Third-Dimension' specifies the
number of sections for the third-fastest changing dimension of
the binary data array.
The optional 'X-Binary-Size-Padding' specifies the size in
octets of an optional padding after the binary array data and
before the closing flags for a binary section.
Reference:
Darakev, G., Litchev, V., Mitev, K. Z. & Bernstein, H. J. (2006).
'Efficient Support of Binary Data in the XML Implementation of
the NeXus File Format', abstract W0165, ACA Summer Meeting,
Honolulu, HI, USA, July 2006.
array_data.external_data_id
This item is a pointer to attribute id in category array_data_external_data in the
ARRAY_DATA_EXTERNAL_DATA category.
If not given, then the actual array data should be specified as
the value of attribute data in category array_data. If
both values are given, the value on attribute data in category array_data takes
precedence, and a warning of a possible conflict should be issued.
array_data.header_contents
This item is a text field for use in minimal CBF files to carry
essential header information to be kept with image data
in attribute data in category array_data when the tags that normally carry the
structured metadata for the image have not been populated.
Normally this data item should not appear when the full set
of tags has been populated and attribute details
in category diffrn_data_frame appears.
array_data.header_convention
This item is an identifier for the convention followed in
constructing the contents of attribute header_contents
in category array_data
The permitted values are of an image creator identifier
followed by an underscore and a version string. To avoid
confusion about conventions, all creator identifiers
should be registered with the IUCr and the conventions
for all identifiers and versions should be posted on
the MEDSBIO.org web site.
array_data.array_id
This item is a pointer to attribute id in category array_structure in the
ARRAY_STRUCTURE category.
If not given, it defaults to 1.
array_data.binary_id
This item is an integer identifier which, along with
attribute array_id in category array_data, should uniquely identify the
particular block of array data.
If attribute binary_id in category array_data is not explicitly given,
it defaults to 1.
The value of attribute binary_id in category array_data distinguishes
among multiple sets of data with the same array
structure.
If the MIME header of the data array specifies a
value for X-Binary-ID, the value of attribute binary_id
in category array_data should be equal to the value given for X-Binary-ID.
0
array_intensities
Data items in the ARRAY_INTENSITIES category record the
information required to recover the intensity data from
the set of data values stored in the ARRAY_DATA category.
The detector may have a complex relationship
between the raw intensity values and the number of
incident photons. In most cases, the number stored
in the final array will have a simple linear relationship
to the actual number of incident photons, given by
attribute gain in category array_intensities. If raw, uncorrected values
are presented (e.g. for calibration experiments), the
value of attribute linearity in category array_intensities will be 'raw'
and attribute gain in category array_intensities will not be used.
Example 1
<PDBx:array_intensitiesCategory>
<PDBx:array_intensities array_id="image_1">
<PDBx:gain>1.2</PDBx:gain>
<PDBx:linearity>linear</PDBx:linearity>
<PDBx:overload>655535</PDBx:overload>
<PDBx:pixel_binning_method>hardware</PDBx:pixel_binning_method>
<PDBx:pixel_fast_bin_size>2</PDBx:pixel_fast_bin_size>
<PDBx:pixel_slow_bin_size>2</PDBx:pixel_slow_bin_size>
<PDBx:undefined_value>0</PDBx:undefined_value>
</PDBx:array_intensities>
</PDBx:array_intensitiesCategory>
0
1
1
1
1
1
1
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
1
array_intensitiesCategory
This property indicates that datablock
has a category holder array_intensitiesCategory.
array_intensitiesCategory
This property indicates that array_intensitiesCategory.
has a category array_intensities.
array_intensitiesItem
Abstract datatype property for array_intensities items.
reference_to_array_intensities
cross-reference to array_intensities.
referenced_by_array_intensities
cross-reference from array_intensities.
array_intensities.details
A description of special aspects of the calculation of array
intensities.
Gain_setting: low gain (vrf = -0.300)
array_intensities.gain
Detector 'gain'. The factor by which linearized
intensity count values should be divided to produce
true photon counts.
array_intensities.gain_esd
The standard uncertainty (estimated standard deviation, e.s.d.)
of detector 'gain'.
linear
offset
scaling
scaling_offset
sqrt_scaled
logarithmic_scaled
raw
The intensity linearity scaling method used to convert
from the raw intensity to the stored element value:
'linear' is linear.
'offset' means that the value defined by
attribute offset in category array_intensities should be added to each
element value.
'scaling' means that the value defined by
attribute scaling in category array_intensities should be multiplied with each
element value.
'scaling_offset' is the combination of the two previous cases,
with the scale factor applied before the offset value.
'sqrt_scaled' means that the square root of raw
intensities multiplied by attribute scaling in category array_intensities is
calculated and stored, perhaps rounded to the nearest
integer. Thus, linearization involves dividing the stored
values by attribute scaling in category array_intensities and squaring the
result.
'logarithmic_scaled' means that the logarithm base 10 of
raw intensities multiplied by attribute scaling
in category array_intensities is calculated and stored, perhaps rounded to the nearest
integer. Thus, linearization involves dividing the stored
values by attribute scaling in category array_intensities and calculating 10
to the power of this number.
'raw' means that the data are a set of raw values straight
from the detector.
array_intensities.offset
Offset value to add to array element values in the manner
described by the item attribute linearity in category array_intensities.
array_intensities.overload
The saturation intensity level for this data array, i.e. the
value above which correct intensities may not be recorded.
The valid pixel values are those less than
attribute overload in category array_intensities and greater than or equal to
attribute underload in category array_intensities
hardware
software
combined
none
unspecified
The value of attribute pixel_binning_method in category array_intensities specifies
the method used to derive array elements from multiple pixels.
array_intensities.pixel_fast_bin_size
The value of attribute pixel_fast_bin_size in category array_intensities specifies
the number of pixels that compose one element in the direction
of the most rapidly varying array dimension.
Typical values are 1, 2, 4 or 8. When there is 1 pixel per
array element in both directions, the value given for
attribute pixel_binning_method in category array_intensities normally should be
'none'.
It is specified as a float to allow for binning algorithms that
create array elements that are not integer multiples of the
detector pixel size.
array_intensities.pixel_slow_bin_size
The value of attribute pixel_slow_bin_size in category array_intensities specifies
the number of pixels that compose one element in the direction
of the second most rapidly varying array dimension.
Typical values are 1, 2, 4 or 8. When there is 1 pixel per
array element in both directions, the value given for
attribute pixel_binning_method in category array_intensities normally should be
'none'.
It is specified as a float to allow for binning algorithms that
create array elements that are not integer multiples of the
detector pixel size.
array_intensities.scaling
Multiplicative scaling value to be applied to array data
in the manner described by the item
attribute linearity in category array_intensities.
array_intensities.undefined_value
A value to be substituted for undefined values in
the data array.
array_intensities.underload
The lowest value at which pixels for this detector are
measured.
The valid pixel values are those less than
attribute overload in category array_intensities and greater than or equal to
attribute underload in category array_intensities
array_intensities.array_id
This item is a pointer to attribute id in category array_structure in the
ARRAY_STRUCTURE category.
array_intensities.binary_id
This item is a pointer to attribute binary_id in category array_data in the
ARRAY_DATA category.
0
array_structure
Data items in the ARRAY_STRUCTURE category record the organization and
encoding of array data that may be stored in the ARRAY_DATA category.
Example 1.
<PDBx:array_structureCategory>
<PDBx:array_structure id="image_1">
<PDBx:byte_order>little_endian</PDBx:byte_order>
<PDBx:compression_type>none</PDBx:compression_type>
<PDBx:encoding_type>unsigned 16-bit integer</PDBx:encoding_type>
</PDBx:array_structure>
</PDBx:array_structureCategory>
1
1
0
1
0
1
1
1
1
array_structureCategory
This property indicates that datablock
has a category holder array_structureCategory.
array_structureCategory
This property indicates that array_structureCategory.
has a category array_structure.
array_structureItem
Abstract datatype property for array_structure items.
reference_to_array_structure
cross-reference to array_structure.
referenced_by_array_structure
cross-reference from array_structure.
big_endian
little_endian
The order of bytes for integer values which require more
than 1 byte.
(IBM-PCs and compatibles, and DEC VAXs use low-byte-first
ordered integers, whereas Hewlett Packard 700
series, Sun-4 and Silicon Graphics use high-byte-first
ordered integers. DEC Alphas can produce/use either
depending on a compiler switch.)
byte_offset
canonical
nibble_offset
none
packed
packed_v2
Type of data-compression method used to compress the array
data.
uncorrelated_sections
flat
Flags modifying the type of data-compression method used to
compress the arraydata.
unsigned 1-bit integer
unsigned 8-bit integer
signed 8-bit integer
unsigned 16-bit integer
signed 16-bit integer
unsigned 32-bit integer
signed 32-bit integer
signed 32-bit real IEEE
signed 64-bit real IEEE
signed 32-bit complex IEEE
Data encoding of a single element of array data.
The type 'unsigned 1-bit integer' is used for
packed Boolean arrays for masks. Each element
of the array corresponds to a single bit
packed in unsigned 8-bit data.
In several cases, the IEEE format is referenced.
See IEEE Standard 754-1985 (IEEE, 1985).
Reference: IEEE (1985). IEEE Standard for Binary Floating-Point
Arithmetic. ANSI/IEEE Std 754-1985. New York: Institute of
Electrical and Electronics Engineers.
array_structure.id
The value of attribute id in category array_structure must uniquely identify
each item of array data.
This item has been made implicit and given a default value of 1
as a convenience in writing miniCBF files. Normally an
explicit name with useful content should be used.
0
array_structure_list
Data items in the ARRAY_STRUCTURE_LIST category record the size
and organization of each array dimension.
The relationship to physical axes may be given.
Example 1. An image array of 1300 x 1200 elements. The raster
order of the image is left to right (increasing) in the
first dimension and bottom to top (decreasing) in
the second dimension.
<PDBx:array_structure_listCategory>
<PDBx:array_structure_list array_id="image_1" index="1">
<PDBx:axis_set_id>ELEMENT_X</PDBx:axis_set_id>
<PDBx:dimension>1300</PDBx:dimension>
<PDBx:direction>increasing</PDBx:direction>
<PDBx:precedence>1</PDBx:precedence>
</PDBx:array_structure_list>
<PDBx:array_structure_list array_id="image_1" index="2">
<PDBx:axis_set_id>ELEMENY_Y</PDBx:axis_set_id>
<PDBx:dimension>1200</PDBx:dimension>
<PDBx:direction>decreasing</PDBx:direction>
<PDBx:precedence>2</PDBx:precedence>
</PDBx:array_structure_list>
</PDBx:array_structure_listCategory>
0
1
1
1
1
1
1
1
1
1
1
1
array_structure_listCategory
This property indicates that datablock
has a category holder array_structure_listCategory.
array_structure_listCategory
This property indicates that array_structure_listCategory.
has a category array_structure_list.
array_structure_listItem
Abstract datatype property for array_structure_list items.
reference_to_array_structure_list
cross-reference to array_structure_list.
referenced_by_array_structure_list
cross-reference from array_structure_list.
array_structure_list.array_section_id
This item is a pointer to attribute id in category array_structure_list_section in the
ARRAY_STRUCTURE_LIST_SECTION category.
array_structure_list.axis_set_id
This is a descriptor for the physical axis or set of axes
corresponding to an array index.
This data item is related to the axes of the detector
itself given in DIFFRN_DETECTOR_AXIS, but usually differs
in that the axes in this category are the axes of the
coordinate system of reported data points, while the axes in
DIFFRN_DETECTOR_AXIS are the physical axes
of the detector describing the 'poise' of the detector as an
overall physical object.
If there is only one axis in the set, the identifier of
that axis should be used as the identifier of the set.
array_structure_list.dimension
The number of elements stored in the array structure in
this dimension.
increasing
decreasing
Identifies the direction in which this array index changes.
array_structure_list.precedence
Identifies the rank order in which this array index changes
with respect to other array indices. The precedence of 1
indicates the index which changes fastest.
array_structure_list.array_id
This item is a pointer to attribute id in category array_structure in the
ARRAY_STRUCTURE category.
array_structure_list.index
Identifies the one-based index of the row or column in the
array structure.
0
array_structure_list_axis
Data items in the ARRAY_STRUCTURE_LIST_AXIS category describe
the physical settings of sets of axes for the centres of pixels that
correspond to data points described in the
ARRAY_STRUCTURE_LIST category.
In the simplest cases, the physical increments of a single axis correspond
to the increments of a single array index. More complex organizations,
e.g. spiral scans, may require coupled motions along multiple axes.
Note that a spiral scan uses two coupled axes: one for the angular
direction and one for the radial direction. This differs from a
cylindrical scan for which the two axes are not coupled into one
set.
Axes may be specified either for an entire array or for just a section
of an array.
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
1
array_structure_list_axisCategory
This property indicates that datablock
has a category holder array_structure_list_axisCategory.
array_structure_list_axisCategory
This property indicates that array_structure_list_axisCategory.
has a category array_structure_list_axis.
array_structure_list_axisItem
Abstract datatype property for array_structure_list_axis items.
reference_to_array_structure_list_axis
cross-reference to array_structure_list_axis.
referenced_by_array_structure_list_axis
cross-reference from array_structure_list_axis.
array_structure_list_axis.angle
The setting of the specified axis in degrees for the first
data point of the array index with the corresponding value
of attribute axis_set_id in category array_structure_list. If the index is
specified as 'increasing', this will be the centre of the
pixel with index value 1. If the index is specified as
'decreasing', this will be the centre of the pixel with
maximum index value.
array_structure_list_axis.angle_increment
The pixel-centre-to-pixel-centre increment in the angular
setting of the specified axis in degrees. This is not
meaningful in the case of 'constant velocity' spiral scans
and should not be specified for this case.
See attribute angular_pitch in category array_structure_list_axis.
array_structure_list_axis.angular_pitch
The pixel-centre-to-pixel-centre distance for a one-step
change in the setting of the specified axis in millimetres.
This is meaningful only for 'constant velocity' spiral scans
or for uncoupled angular scans at a constant radius
(cylindrical scans) and should not be specified for cases
in which the angle between pixels (rather than the distance
between pixels) is uniform.
See attribute angle_increment in category array_structure_list_axis.
array_structure_list_axis.displacement
The setting of the specified axis in millimetres for the first
data point of the array index with the corresponding value
of attribute axis_set_id in category array_structure_list. If the index is
specified as 'increasing', this will be the centre of the
pixel with index value 1. If the index is specified as
'decreasing', this will be the centre of the pixel with
maximum index value.
array_structure_list_axis.displacement_increment
The pixel-centre-to-pixel-centre increment for the displacement
setting of the specified axis in millimetres.
array_structure_list_axis.fract_displacement
The setting of the specified axis as a decimal fraction of
the axis unit vector for the first data point of the array
index with the corresponding value of
attribute axis_set_id.
in category array_structure_list
If the index is specified as 'increasing', this will be the
centre of the pixel with index value 1. If the index is
specified as 'decreasing', this will be the centre of the
pixel with maximum index value.
array_structure_list_axis.fract_displacement_increment
The pixel-centre-to-pixel-centre increment for the displacement
setting of the specified axis as a decimal fraction of the
axis unit vector.
array_structure_list_axis.radial_pitch
The radial distance from one 'cylinder' of pixels to the
next in millimetres. If the scan is a 'constant velocity'
scan with differing angular displacements between pixels,
the value of this item may differ significantly from the
value of attribute displacement_increment in category array_structure_list_axis.
array_structure_list_axis.reference_angle
The value of attribute reference_angle
in category array_structure_list_axis specifies the setting of the angle of this axis used for
determining a reference beam centre and a reference detector
distance. It is normally expected to be identical to the
value of attribute angle in category array_structure_list_axis.
array_structure_list_axis.reference_displacement
The value of attribute reference_displacement
in category array_structure_list_axis specifies the setting of the displacement of this axis used
for determining a reference beam centre and a reference detector
distance. It is normally expected to be identical to the value
of attribute displacement in category array_structure_list_axis.
array_structure_list_axis.axis_id
The value of this data item is the identifier of one of
the axes in the set of axes for which settings are being
specified.
Multiple axes may be specified for the same value of
attribute axis_set_id.
in category array_structure_list_axis
This item is a pointer to attribute id in category axis in the
AXIS category.
array_structure_list_axis.axis_set_id
The value of this data item is the identifier of the
set of axes for which axis settings are being specified.
Multiple axes may be specified for the same value of
attribute axis_set_id.
in category array_structure_list_axis
This item is a pointer to
attribute axis_set_id
in category array_structure_list in the ARRAY_STRUCTURE_LIST category.
If this item is not specified, it defaults to the corresponding
axis identifier.
0
array_structure_list_section
Data items in the ARRAY_STRUCTURE_LIST_SECTION category identify
the dimension-by-dimension start, end and stride of each section of an
array that is to be referenced.
For any array with identifier ARRAYID, array section ids of the form
ARRAYID(start1:end1:stride1,start2:end2:stride2, ...) are defined
by default.
For the given index, the elements in the section are of indices:
attribute start,
in category array_structure_list_section _array_structure_list_section.start + _array_structure_list_section.stride,
attribute start in category array_structure_list_section + 2*_array_structure_list_section.stride,
...
stopping either when the indices leave the limits of the indices
of that dimension or
[min(_array_structure_list_section.start, attribute end),
in category array_structure_list_section max(_array_structure_list_section.start, attribute end)].
in category array_structure_list_section
The ordering of these elements is determined by the overall ordering of
attribute array_id in category array_structure_list_section and not by the ordering implied
by the stride.
Example 1. An image array, myarray, of 1300 x 1200 elements, and
700 frames is defined in ARRAY_STRUCTURE_LIST, and
the array section identifier
"myarray(101:1200,101:1100,1:700:10)"
is explicitly defined taking every 10th frame and
removing a 100 pixel border. Note that even though
the slow index high is 700, the last frame that
will actually be included is only 691.
<PDBx:array_structure_listCategory>
<PDBx:array_structure_list array_id="myarray" index="1">
<PDBx:axis_set_id>ELEMENT_X</PDBx:axis_set_id>
<PDBx:dimension>1300</PDBx:dimension>
<PDBx:direction>increasing</PDBx:direction>
<PDBx:precedence>1</PDBx:precedence>
</PDBx:array_structure_list>
<PDBx:array_structure_list array_id="myarray" index="2">
<PDBx:axis_set_id>ELEMENT_Y</PDBx:axis_set_id>
<PDBx:dimension>1200</PDBx:dimension>
<PDBx:direction>increasing</PDBx:direction>
<PDBx:precedence>2</PDBx:precedence>
</PDBx:array_structure_list>
<PDBx:array_structure_list array_id="myarray" index="3">
<PDBx:axis_set_id>FRAME_NO</PDBx:axis_set_id>
<PDBx:dimension>700</PDBx:dimension>
<PDBx:direction>increasing</PDBx:direction>
<PDBx:precedence>3</PDBx:precedence>
</PDBx:array_structure_list>
</PDBx:array_structure_listCategory>
<PDBx:array_structure_list_sectionCategory>
<PDBx:array_structure_list_section array_id="myarray" id="myarray(101:1200,101:1100,1:700:10)" index="1">
<PDBx:end>1200</PDBx:end>
<PDBx:start>101</PDBx:start>
<PDBx:stride xsi:nil="true" />
</PDBx:array_structure_list_section>
<PDBx:array_structure_list_section array_id="myarray" id="myarray(101:1200,101:1100,1:700:10)" index="2">
<PDBx:end>1100</PDBx:end>
<PDBx:start>101</PDBx:start>
<PDBx:stride xsi:nil="true" />
</PDBx:array_structure_list_section>
<PDBx:array_structure_list_section array_id="myarray" id="myarray(101:1200,101:1100,1:700:10)" index="3">
<PDBx:end>700</PDBx:end>
<PDBx:start>1</PDBx:start>
<PDBx:stride>10</PDBx:stride>
</PDBx:array_structure_list_section>
</PDBx:array_structure_list_sectionCategory>
0
1
0
1
0
1
1
1
1
array_structure_list_sectionCategory
This property indicates that datablock
has a category holder array_structure_list_sectionCategory.
array_structure_list_sectionCategory
This property indicates that array_structure_list_sectionCategory.
has a category array_structure_list_section.
array_structure_list_sectionItem
Abstract datatype property for array_structure_list_section items.
reference_to_array_structure_list_section
cross-reference to array_structure_list_section.
referenced_by_array_structure_list_section
cross-reference from array_structure_list_section.
array_structure_list_section.end
Identifies the ending ordinal, numbered from 1, for an array
element of index attribute index in category array_structure_list_section in the
section.
The value defaults to the dimension for index
attribute index
in category array_structure_list_section of the array.
Note that this agrees with the Fortran convention, rather than
the Python convention in that, if compatible with the stride,
the end element is included in the section as in Fortran, rather
than being one beyond the section as in Python.
array_structure_list_section.start
Identifies the starting ordinal, numbered from 1,
for an array element of index attribute index
in category array_structure_list_section in the section.
The value defaults to 1. For the given index, the elements in
the section are of indices:
attribute start,
in category array_structure_list_section attribute start
in category array_structure_list_section + attribute stride,
in category array_structure_list_section attribute start
in category array_structure_list_section + 2*_array_structure_list_section.stride,
...
stopping either when the indices leave the limits of the indices
of that dimension or
[min(_array_structure_list_section.start,
attribute end in category array_structure_list_section ),
max(_array_structure_list_section.start,
attribute end in category array_structure_list_section )].
The ordering of these elements is determined by the overall
ordering of attribute array_id in category array_structure_list_section and not by
the ordering implied by the stride.
array_structure_list_section.stride
Identifies the incremental steps to be taken when moving
element to element in the section in that particular
dimension. The value of attribute stride
in category array_structure_list_section may be positive or negative. If the stride is zero, the section
is just defined by attribute start in category array_structure_list_section.
array_structure_list_section.array_id
This item is a pointer to attribute id in category array_structure in the
ARRAY_STRUCTURE category.
array_structure_list_section.id
Uniquely identifies the array section chosen.
To avoid confusion array section IDs that contain parentheses
should conform to the default syntax
ARRAYID(start1:end1:stride1,start2:end2:stride2, ...)
array_structure_list_section.index
This item is a pointer to attribute index
in category array_structure_list in the ARRAY_STRUCTURE_LIST category.
Identifies the one-based index of the row, column, sheet ...
the ARRAY_STRUCTURE_LIST category.
For a multidimensional array, a value must be explicitly given.
If an index is omitted from a section then all elements for that
index are assumed to be included in the section.
0
atom_site
Data items in the ATOM_SITE category record details about
the atom sites in a macromolecular crystal structure, such as
the positional coordinates, atomic displacement parameters,
magnetic moments and directions.
The data items for describing anisotropic atomic
displacement factors are only used if the corresponding items
are not given in the ATOM_SITE_ANISOTROP category.
wwPDB recommends wwPDB-assigned residue number, residue ID,
and chain ID, _atom_site.auth_seq_id _atom_site.auth_comp_id, and
attribute auth_asym_id in category atom_site, respectively, to be used for publication
materials.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:atom_siteCategory>
<PDBx:atom_site id="1">
<PDBx:B_iso_or_equiv>17.93</PDBx:B_iso_or_equiv>
<PDBx:Cartn_x>25.369</PDBx:Cartn_x>
<PDBx:Cartn_y>30.691</PDBx:Cartn_y>
<PDBx:Cartn_z>11.795</PDBx:Cartn_z>
<PDBx:auth_seq_id>11</PDBx:auth_seq_id>
<PDBx:footnote_id xsi:nil="true" />
<PDBx:group_PDB>ATOM</PDBx:group_PDB>
<PDBx:label_alt_id xsi:nil="true" />
<PDBx:label_asym_id>A</PDBx:label_asym_id>
<PDBx:label_atom_id>N</PDBx:label_atom_id>
<PDBx:label_comp_id>VAL</PDBx:label_comp_id>
<PDBx:label_seq_id>11</PDBx:label_seq_id>
<PDBx:occupancy>1.00</PDBx:occupancy>
<PDBx:type_symbol>N</PDBx:type_symbol>
</PDBx:atom_site>
<PDBx:atom_site id="2">
<PDBx:B_iso_or_equiv>17.75</PDBx:B_iso_or_equiv>
<PDBx:Cartn_x>25.970</PDBx:Cartn_x>
<PDBx:Cartn_y>31.965</PDBx:Cartn_y>
<PDBx:Cartn_z>12.332</PDBx:Cartn_z>
<PDBx:auth_seq_id>11</PDBx:auth_seq_id>
<PDBx:footnote_id xsi:nil="true" />
<PDBx:group_PDB>ATOM</PDBx:group_PDB>
<PDBx:label_alt_id xsi:nil="true" />
<PDBx:label_asym_id>A</PDBx:label_asym_id>
<PDBx:label_atom_id>CA</PDBx:label_atom_id>
<PDBx:label_comp_id>VAL</PDBx:label_comp_id>
<PDBx:label_seq_id>11</PDBx:label_seq_id>
<PDBx:occupancy>1.00</PDBx:occupancy>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:atom_site>
<PDBx:atom_site id="3">
<PDBx:B_iso_or_equiv>17.83</PDBx:B_iso_or_equiv>
<PDBx:Cartn_x>25.569</PDBx:Cartn_x>
<PDBx:Cartn_y>32.010</PDBx:Cartn_y>
<PDBx:Cartn_z>13.808</PDBx:Cartn_z>
<PDBx:auth_seq_id>11</PDBx:auth_seq_id>
<PDBx:footnote_id xsi:nil="true" />
<PDBx:group_PDB>ATOM</PDBx:group_PDB>
<PDBx:label_alt_id xsi:nil="true" />
<PDBx:label_asym_id>A</PDBx:label_asym_id>
<PDBx:label_atom_id>C</PDBx:label_atom_id>
<PDBx:label_comp_id>VAL</PDBx:label_comp_id>
<PDBx:label_seq_id>11</PDBx:label_seq_id>
<PDBx:occupancy>1.00</PDBx:occupancy>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:atom_site>
<PDBx:atom_site id="4">
<PDBx:B_iso_or_equiv>17.53</PDBx:B_iso_or_equiv>
<PDBx:Cartn_x>24.735</PDBx:Cartn_x>
<PDBx:Cartn_y>31.190</PDBx:Cartn_y>
<PDBx:Cartn_z>14.167</PDBx:Cartn_z>
<PDBx:auth_seq_id>11</PDBx:auth_seq_id>
<PDBx:footnote_id xsi:nil="true" />
<PDBx:group_PDB>ATOM</PDBx:group_PDB>
<PDBx:label_alt_id xsi:nil="true" />
<PDBx:label_asym_id>A</PDBx:label_asym_id>
<PDBx:label_atom_id>O</PDBx:label_atom_id>
<PDBx:label_comp_id>VAL</PDBx:label_comp_id>
<PDBx:label_seq_id>11</PDBx:label_seq_id>
<PDBx:occupancy>1.00</PDBx:occupancy>
<PDBx:type_symbol>O</PDBx:type_symbol>
</PDBx:atom_site>
<PDBx:atom_site id="5">
<PDBx:B_iso_or_equiv>17.66</PDBx:B_iso_or_equiv>
<PDBx:Cartn_x>25.379</PDBx:Cartn_x>
<PDBx:Cartn_y>33.146</PDBx:Cartn_y>
<PDBx:Cartn_z>11.540</PDBx:Cartn_z>
<PDBx:auth_seq_id>11</PDBx:auth_seq_id>
<PDBx:footnote_id xsi:nil="true" />
<PDBx:group_PDB>ATOM</PDBx:group_PDB>
<PDBx:label_alt_id xsi:nil="true" />
<PDBx:label_asym_id>A</PDBx:label_asym_id>
<PDBx:label_atom_id>CB</PDBx:label_atom_id>
<PDBx:label_comp_id>VAL</PDBx:label_comp_id>
<PDBx:label_seq_id>11</PDBx:label_seq_id>
<PDBx:occupancy>1.00</PDBx:occupancy>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:atom_site>
<PDBx:atom_site id="6">
<PDBx:B_iso_or_equiv>18.86</PDBx:B_iso_or_equiv>
<PDBx:Cartn_x>25.584</PDBx:Cartn_x>
<PDBx:Cartn_y>33.034</PDBx:Cartn_y>
<PDBx:Cartn_z>10.030</PDBx:Cartn_z>
<PDBx:auth_seq_id>11</PDBx:auth_seq_id>
<PDBx:footnote_id xsi:nil="true" />
<PDBx:group_PDB>ATOM</PDBx:group_PDB>
<PDBx:label_alt_id xsi:nil="true" />
<PDBx:label_asym_id>A</PDBx:label_asym_id>
<PDBx:label_atom_id>CG1</PDBx:label_atom_id>
<PDBx:label_comp_id>VAL</PDBx:label_comp_id>
<PDBx:label_seq_id>11</PDBx:label_seq_id>
<PDBx:occupancy>1.00</PDBx:occupancy>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:atom_site>
<PDBx:atom_site id="7">
<PDBx:B_iso_or_equiv>17.12</PDBx:B_iso_or_equiv>
<PDBx:Cartn_x>23.933</PDBx:Cartn_x>
<PDBx:Cartn_y>33.309</PDBx:Cartn_y>
<PDBx:Cartn_z>11.872</PDBx:Cartn_z>
<PDBx:auth_seq_id>11</PDBx:auth_seq_id>
<PDBx:footnote_id xsi:nil="true" />
<PDBx:group_PDB>ATOM</PDBx:group_PDB>
<PDBx:label_alt_id xsi:nil="true" />
<PDBx:label_asym_id>A</PDBx:label_asym_id>
<PDBx:label_atom_id>CG2</PDBx:label_atom_id>
<PDBx:label_comp_id>VAL</PDBx:label_comp_id>
<PDBx:label_seq_id>11</PDBx:label_seq_id>
<PDBx:occupancy>1.00</PDBx:occupancy>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:atom_site>
<PDBx:atom_site id="8">
<PDBx:B_iso_or_equiv>18.97</PDBx:B_iso_or_equiv>
<PDBx:Cartn_x>26.095</PDBx:Cartn_x>
<PDBx:Cartn_y>32.930</PDBx:Cartn_y>
<PDBx:Cartn_z>14.590</PDBx:Cartn_z>
<PDBx:auth_seq_id>12</PDBx:auth_seq_id>
<PDBx:footnote_id>4</PDBx:footnote_id>
<PDBx:group_PDB>ATOM</PDBx:group_PDB>
<PDBx:label_alt_id xsi:nil="true" />
<PDBx:label_asym_id>A</PDBx:label_asym_id>
<PDBx:label_atom_id>N</PDBx:label_atom_id>
<PDBx:label_comp_id>THR</PDBx:label_comp_id>
<PDBx:label_seq_id>12</PDBx:label_seq_id>
<PDBx:occupancy>1.00</PDBx:occupancy>
<PDBx:type_symbol>N</PDBx:type_symbol>
</PDBx:atom_site>
<PDBx:atom_site id="9">
<PDBx:B_iso_or_equiv>19.80</PDBx:B_iso_or_equiv>
<PDBx:Cartn_x>25.734</PDBx:Cartn_x>
<PDBx:Cartn_y>32.995</PDBx:Cartn_y>
<PDBx:Cartn_z>16.032</PDBx:Cartn_z>
<PDBx:auth_seq_id>12</PDBx:auth_seq_id>
<PDBx:footnote_id>4</PDBx:footnote_id>
<PDBx:group_PDB>ATOM</PDBx:group_PDB>
<PDBx:label_alt_id xsi:nil="true" />
<PDBx:label_asym_id>A</PDBx:label_asym_id>
<PDBx:label_atom_id>CA</PDBx:label_atom_id>
<PDBx:label_comp_id>THR</PDBx:label_comp_id>
<PDBx:label_seq_id>12</PDBx:label_seq_id>
<PDBx:occupancy>1.00</PDBx:occupancy>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:atom_site>
<PDBx:atom_site id="10">
<PDBx:B_iso_or_equiv>20.92</PDBx:B_iso_or_equiv>
<PDBx:Cartn_x>24.695</PDBx:Cartn_x>
<PDBx:Cartn_y>34.106</PDBx:Cartn_y>
<PDBx:Cartn_z>16.113</PDBx:Cartn_z>
<PDBx:auth_seq_id>12</PDBx:auth_seq_id>
<PDBx:footnote_id>4</PDBx:footnote_id>
<PDBx:group_PDB>ATOM</PDBx:group_PDB>
<PDBx:label_alt_id xsi:nil="true" />
<PDBx:label_asym_id>A</PDBx:label_asym_id>
<PDBx:label_atom_id>C</PDBx:label_atom_id>
<PDBx:label_comp_id>THR</PDBx:label_comp_id>
<PDBx:label_seq_id>12</PDBx:label_seq_id>
<PDBx:occupancy>1.00</PDBx:occupancy>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:atom_site>
<PDBx:atom_site id="11">
<PDBx:B_iso_or_equiv>21.84</PDBx:B_iso_or_equiv>
<PDBx:Cartn_x>24.869</PDBx:Cartn_x>
<PDBx:Cartn_y>35.118</PDBx:Cartn_y>
<PDBx:Cartn_z>15.421</PDBx:Cartn_z>
<PDBx:auth_seq_id>12</PDBx:auth_seq_id>
<PDBx:footnote_id>4</PDBx:footnote_id>
<PDBx:group_PDB>ATOM</PDBx:group_PDB>
<PDBx:label_alt_id xsi:nil="true" />
<PDBx:label_asym_id>A</PDBx:label_asym_id>
<PDBx:label_atom_id>O</PDBx:label_atom_id>
<PDBx:label_comp_id>THR</PDBx:label_comp_id>
<PDBx:label_seq_id>12</PDBx:label_seq_id>
<PDBx:occupancy>1.00</PDBx:occupancy>
<PDBx:type_symbol>O</PDBx:type_symbol>
</PDBx:atom_site>
<PDBx:atom_site id="12">
<PDBx:B_iso_or_equiv>20.51</PDBx:B_iso_or_equiv>
<PDBx:Cartn_x>26.911</PDBx:Cartn_x>
<PDBx:Cartn_y>33.346</PDBx:Cartn_y>
<PDBx:Cartn_z>17.018</PDBx:Cartn_z>
<PDBx:auth_seq_id>12</PDBx:auth_seq_id>
<PDBx:footnote_id>4</PDBx:footnote_id>
<PDBx:group_PDB>ATOM</PDBx:group_PDB>
<PDBx:label_alt_id xsi:nil="true" />
<PDBx:label_asym_id>A</PDBx:label_asym_id>
<PDBx:label_atom_id>CB</PDBx:label_atom_id>
<PDBx:label_comp_id>THR</PDBx:label_comp_id>
<PDBx:label_seq_id>12</PDBx:label_seq_id>
<PDBx:occupancy>1.00</PDBx:occupancy>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:atom_site>
<PDBx:atom_site id="13">
<PDBx:B_iso_or_equiv>20.29</PDBx:B_iso_or_equiv>
<PDBx:Cartn_x>27.946</PDBx:Cartn_x>
<PDBx:Cartn_y>33.921</PDBx:Cartn_y>
<PDBx:Cartn_z>16.183</PDBx:Cartn_z>
<PDBx:auth_seq_id>12</PDBx:auth_seq_id>
<PDBx:footnote_id>4</PDBx:footnote_id>
<PDBx:group_PDB>ATOM</PDBx:group_PDB>
<PDBx:label_alt_id>3</PDBx:label_alt_id>
<PDBx:label_asym_id>A</PDBx:label_asym_id>
<PDBx:label_atom_id>OG1</PDBx:label_atom_id>
<PDBx:label_comp_id>THR</PDBx:label_comp_id>
<PDBx:label_seq_id>12</PDBx:label_seq_id>
<PDBx:occupancy>0.50</PDBx:occupancy>
<PDBx:type_symbol>O</PDBx:type_symbol>
</PDBx:atom_site>
<PDBx:atom_site id="14">
<PDBx:B_iso_or_equiv>20.59</PDBx:B_iso_or_equiv>
<PDBx:Cartn_x>27.769</PDBx:Cartn_x>
<PDBx:Cartn_y>32.142</PDBx:Cartn_y>
<PDBx:Cartn_z>17.103</PDBx:Cartn_z>
<PDBx:auth_seq_id>12</PDBx:auth_seq_id>
<PDBx:footnote_id>4</PDBx:footnote_id>
<PDBx:group_PDB>ATOM</PDBx:group_PDB>
<PDBx:label_alt_id>4</PDBx:label_alt_id>
<PDBx:label_asym_id>A</PDBx:label_asym_id>
<PDBx:label_atom_id>OG1</PDBx:label_atom_id>
<PDBx:label_comp_id>THR</PDBx:label_comp_id>
<PDBx:label_seq_id>12</PDBx:label_seq_id>
<PDBx:occupancy>0.50</PDBx:occupancy>
<PDBx:type_symbol>O</PDBx:type_symbol>
</PDBx:atom_site>
<PDBx:atom_site id="15">
<PDBx:B_iso_or_equiv>20.47</PDBx:B_iso_or_equiv>
<PDBx:Cartn_x>27.418</PDBx:Cartn_x>
<PDBx:Cartn_y>32.181</PDBx:Cartn_y>
<PDBx:Cartn_z>17.878</PDBx:Cartn_z>
<PDBx:auth_seq_id>12</PDBx:auth_seq_id>
<PDBx:footnote_id>4</PDBx:footnote_id>
<PDBx:group_PDB>ATOM</PDBx:group_PDB>
<PDBx:label_alt_id>3</PDBx:label_alt_id>
<PDBx:label_asym_id>A</PDBx:label_asym_id>
<PDBx:label_atom_id>CG2</PDBx:label_atom_id>
<PDBx:label_comp_id>THR</PDBx:label_comp_id>
<PDBx:label_seq_id>12</PDBx:label_seq_id>
<PDBx:occupancy>0.50</PDBx:occupancy>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:atom_site>
<PDBx:atom_site id="16">
<PDBx:B_iso_or_equiv>20.00</PDBx:B_iso_or_equiv>
<PDBx:Cartn_x>26.489</PDBx:Cartn_x>
<PDBx:Cartn_y>33.778</PDBx:Cartn_y>
<PDBx:Cartn_z>18.426</PDBx:Cartn_z>
<PDBx:auth_seq_id>12</PDBx:auth_seq_id>
<PDBx:footnote_id>4</PDBx:footnote_id>
<PDBx:group_PDB>ATOM</PDBx:group_PDB>
<PDBx:label_alt_id>4</PDBx:label_alt_id>
<PDBx:label_asym_id>A</PDBx:label_asym_id>
<PDBx:label_atom_id>CG2</PDBx:label_atom_id>
<PDBx:label_comp_id>THR</PDBx:label_comp_id>
<PDBx:label_seq_id>12</PDBx:label_seq_id>
<PDBx:occupancy>0.50</PDBx:occupancy>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:atom_site>
<PDBx:atom_site id="17">
<PDBx:B_iso_or_equiv>22.08</PDBx:B_iso_or_equiv>
<PDBx:Cartn_x>23.664</PDBx:Cartn_x>
<PDBx:Cartn_y>33.855</PDBx:Cartn_y>
<PDBx:Cartn_z>16.884</PDBx:Cartn_z>
<PDBx:auth_seq_id>13</PDBx:auth_seq_id>
<PDBx:footnote_id xsi:nil="true" />
<PDBx:group_PDB>ATOM</PDBx:group_PDB>
<PDBx:label_alt_id xsi:nil="true" />
<PDBx:label_asym_id>A</PDBx:label_asym_id>
<PDBx:label_atom_id>N</PDBx:label_atom_id>
<PDBx:label_comp_id>ILE</PDBx:label_comp_id>
<PDBx:label_seq_id>13</PDBx:label_seq_id>
<PDBx:occupancy>1.00</PDBx:occupancy>
<PDBx:type_symbol>N</PDBx:type_symbol>
</PDBx:atom_site>
<PDBx:atom_site id="18">
<PDBx:B_iso_or_equiv>23.44</PDBx:B_iso_or_equiv>
<PDBx:Cartn_x>22.623</PDBx:Cartn_x>
<PDBx:Cartn_y>34.850</PDBx:Cartn_y>
<PDBx:Cartn_z>17.093</PDBx:Cartn_z>
<PDBx:auth_seq_id>13</PDBx:auth_seq_id>
<PDBx:footnote_id xsi:nil="true" />
<PDBx:group_PDB>ATOM</PDBx:group_PDB>
<PDBx:label_alt_id xsi:nil="true" />
<PDBx:label_asym_id>A</PDBx:label_asym_id>
<PDBx:label_atom_id>CA</PDBx:label_atom_id>
<PDBx:label_comp_id>ILE</PDBx:label_comp_id>
<PDBx:label_seq_id>13</PDBx:label_seq_id>
<PDBx:occupancy>1.00</PDBx:occupancy>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:atom_site>
<PDBx:atom_site id="19">
<PDBx:B_iso_or_equiv>25.77</PDBx:B_iso_or_equiv>
<PDBx:Cartn_x>22.657</PDBx:Cartn_x>
<PDBx:Cartn_y>35.113</PDBx:Cartn_y>
<PDBx:Cartn_z>18.610</PDBx:Cartn_z>
<PDBx:auth_seq_id>13</PDBx:auth_seq_id>
<PDBx:footnote_id xsi:nil="true" />
<PDBx:group_PDB>ATOM</PDBx:group_PDB>
<PDBx:label_alt_id xsi:nil="true" />
<PDBx:label_asym_id>A</PDBx:label_asym_id>
<PDBx:label_atom_id>C</PDBx:label_atom_id>
<PDBx:label_comp_id>ILE</PDBx:label_comp_id>
<PDBx:label_seq_id>13</PDBx:label_seq_id>
<PDBx:occupancy>1.00</PDBx:occupancy>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:atom_site>
<PDBx:atom_site id="20">
<PDBx:B_iso_or_equiv>26.28</PDBx:B_iso_or_equiv>
<PDBx:Cartn_x>23.123</PDBx:Cartn_x>
<PDBx:Cartn_y>34.250</PDBx:Cartn_y>
<PDBx:Cartn_z>19.406</PDBx:Cartn_z>
<PDBx:auth_seq_id>13</PDBx:auth_seq_id>
<PDBx:footnote_id xsi:nil="true" />
<PDBx:group_PDB>ATOM</PDBx:group_PDB>
<PDBx:label_alt_id xsi:nil="true" />
<PDBx:label_asym_id>A</PDBx:label_asym_id>
<PDBx:label_atom_id>O</PDBx:label_atom_id>
<PDBx:label_comp_id>ILE</PDBx:label_comp_id>
<PDBx:label_seq_id>13</PDBx:label_seq_id>
<PDBx:occupancy>1.00</PDBx:occupancy>
<PDBx:type_symbol>O</PDBx:type_symbol>
</PDBx:atom_site>
<PDBx:atom_site id="21">
<PDBx:B_iso_or_equiv>22.67</PDBx:B_iso_or_equiv>
<PDBx:Cartn_x>21.236</PDBx:Cartn_x>
<PDBx:Cartn_y>34.463</PDBx:Cartn_y>
<PDBx:Cartn_z>16.492</PDBx:Cartn_z>
<PDBx:auth_seq_id>13</PDBx:auth_seq_id>
<PDBx:footnote_id xsi:nil="true" />
<PDBx:group_PDB>ATOM</PDBx:group_PDB>
<PDBx:label_alt_id xsi:nil="true" />
<PDBx:label_asym_id>A</PDBx:label_asym_id>
<PDBx:label_atom_id>CB</PDBx:label_atom_id>
<PDBx:label_comp_id>ILE</PDBx:label_comp_id>
<PDBx:label_seq_id>13</PDBx:label_seq_id>
<PDBx:occupancy>1.00</PDBx:occupancy>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:atom_site>
<PDBx:atom_site id="22">
<PDBx:B_iso_or_equiv>22.14</PDBx:B_iso_or_equiv>
<PDBx:Cartn_x>20.478</PDBx:Cartn_x>
<PDBx:Cartn_y>33.469</PDBx:Cartn_y>
<PDBx:Cartn_z>17.371</PDBx:Cartn_z>
<PDBx:auth_seq_id>13</PDBx:auth_seq_id>
<PDBx:footnote_id xsi:nil="true" />
<PDBx:group_PDB>ATOM</PDBx:group_PDB>
<PDBx:label_alt_id xsi:nil="true" />
<PDBx:label_asym_id>A</PDBx:label_asym_id>
<PDBx:label_atom_id>CG1</PDBx:label_atom_id>
<PDBx:label_comp_id>ILE</PDBx:label_comp_id>
<PDBx:label_seq_id>13</PDBx:label_seq_id>
<PDBx:occupancy>1.00</PDBx:occupancy>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:atom_site>
<PDBx:atom_site id="23">
<PDBx:B_iso_or_equiv>21.75</PDBx:B_iso_or_equiv>
<PDBx:Cartn_x>21.357</PDBx:Cartn_x>
<PDBx:Cartn_y>33.986</PDBx:Cartn_y>
<PDBx:Cartn_z>15.016</PDBx:Cartn_z>
<PDBx:auth_seq_id>13</PDBx:auth_seq_id>
<PDBx:footnote_id xsi:nil="true" />
<PDBx:group_PDB>ATOM</PDBx:group_PDB>
<PDBx:label_alt_id xsi:nil="true" />
<PDBx:label_asym_id>A</PDBx:label_asym_id>
<PDBx:label_atom_id>CG2</PDBx:label_atom_id>
<PDBx:label_comp_id>ILE</PDBx:label_comp_id>
<PDBx:label_seq_id>13</PDBx:label_seq_id>
<PDBx:occupancy>1.00</PDBx:occupancy>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:atom_site>
<PDBx:atom_site id="101">
<PDBx:B_iso_or_equiv>17.27</PDBx:B_iso_or_equiv>
<PDBx:Cartn_x>4.171</PDBx:Cartn_x>
<PDBx:Cartn_y>29.012</PDBx:Cartn_y>
<PDBx:Cartn_z>7.116</PDBx:Cartn_z>
<PDBx:auth_seq_id>300</PDBx:auth_seq_id>
<PDBx:footnote_id>1</PDBx:footnote_id>
<PDBx:group_PDB>HETATM</PDBx:group_PDB>
<PDBx:label_alt_id>1</PDBx:label_alt_id>
<PDBx:label_asym_id>C</PDBx:label_asym_id>
<PDBx:label_atom_id>C1</PDBx:label_atom_id>
<PDBx:label_comp_id>APS</PDBx:label_comp_id>
<PDBx:label_seq_id xsi:nil="true" />
<PDBx:occupancy>0.58</PDBx:occupancy>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:atom_site>
<PDBx:atom_site id="102">
<PDBx:B_iso_or_equiv>16.95</PDBx:B_iso_or_equiv>
<PDBx:Cartn_x>4.949</PDBx:Cartn_x>
<PDBx:Cartn_y>27.758</PDBx:Cartn_y>
<PDBx:Cartn_z>6.793</PDBx:Cartn_z>
<PDBx:auth_seq_id>300</PDBx:auth_seq_id>
<PDBx:footnote_id>1</PDBx:footnote_id>
<PDBx:group_PDB>HETATM</PDBx:group_PDB>
<PDBx:label_alt_id>1</PDBx:label_alt_id>
<PDBx:label_asym_id>C</PDBx:label_asym_id>
<PDBx:label_atom_id>C2</PDBx:label_atom_id>
<PDBx:label_comp_id>APS</PDBx:label_comp_id>
<PDBx:label_seq_id xsi:nil="true" />
<PDBx:occupancy>0.58</PDBx:occupancy>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:atom_site>
<PDBx:atom_site id="103">
<PDBx:B_iso_or_equiv>16.85</PDBx:B_iso_or_equiv>
<PDBx:Cartn_x>4.800</PDBx:Cartn_x>
<PDBx:Cartn_y>26.678</PDBx:Cartn_y>
<PDBx:Cartn_z>7.393</PDBx:Cartn_z>
<PDBx:auth_seq_id>300</PDBx:auth_seq_id>
<PDBx:footnote_id>1</PDBx:footnote_id>
<PDBx:group_PDB>HETATM</PDBx:group_PDB>
<PDBx:label_alt_id>1</PDBx:label_alt_id>
<PDBx:label_asym_id>C</PDBx:label_asym_id>
<PDBx:label_atom_id>O3</PDBx:label_atom_id>
<PDBx:label_comp_id>APS</PDBx:label_comp_id>
<PDBx:label_seq_id xsi:nil="true" />
<PDBx:occupancy>0.58</PDBx:occupancy>
<PDBx:type_symbol>O</PDBx:type_symbol>
</PDBx:atom_site>
<PDBx:atom_site id="104">
<PDBx:B_iso_or_equiv>16.43</PDBx:B_iso_or_equiv>
<PDBx:Cartn_x>5.930</PDBx:Cartn_x>
<PDBx:Cartn_y>27.841</PDBx:Cartn_y>
<PDBx:Cartn_z>5.869</PDBx:Cartn_z>
<PDBx:auth_seq_id>300</PDBx:auth_seq_id>
<PDBx:footnote_id>1</PDBx:footnote_id>
<PDBx:group_PDB>HETATM</PDBx:group_PDB>
<PDBx:label_alt_id>1</PDBx:label_alt_id>
<PDBx:label_asym_id>C</PDBx:label_asym_id>
<PDBx:label_atom_id>N4</PDBx:label_atom_id>
<PDBx:label_comp_id>APS</PDBx:label_comp_id>
<PDBx:label_seq_id xsi:nil="true" />
<PDBx:occupancy>0.58</PDBx:occupancy>
<PDBx:type_symbol>N</PDBx:type_symbol>
</PDBx:atom_site>
</PDBx:atom_siteCategory>
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1
atom_siteCategory
This property indicates that datablock
has a category holder atom_siteCategory.
atom_siteCategory
This property indicates that atom_siteCategory.
has a category atom_site.
atom_siteItem
Abstract datatype property for atom_site items.
reference_to_atom_site
cross-reference to atom_site.
referenced_by_atom_site
cross-reference from atom_site.
atom_site.B_equiv_geom_mean
Equivalent isotropic atomic displacement parameter, B~eq~,
in angstroms squared, calculated as the geometric mean of
the anisotropic atomic displacement parameters.
B~eq~ = (B~i~ B~j~ B~k~)^1/3^
B~n~ = the principal components of the orthogonalized B^ij^
The IUCr Commission on Nomenclature recommends against the use
of B for reporting atomic displacement parameters. U, being
directly proportional to B, is preferred.
atom_site.B_equiv_geom_mean_esd
The standard uncertainty (estimated standard deviation)
of attribute B_equiv_geom_mean in category atom_site.
atom_site.B_iso_or_equiv
Isotropic atomic displacement parameter, or equivalent isotropic
atomic displacement parameter, B~eq~, calculated from the
anisotropic displacement parameters.
B~eq~ = (1/3) sum~i~[sum~j~(B^ij^ A~i~ A~j~ a*~i~ a*~j~)]
A = the real space cell lengths
a* = the reciprocal space cell lengths
B^ij^ = 8 pi^2^ U^ij^
Ref: Fischer, R. X. & Tillmanns, E. (1988). Acta Cryst. C44,
775-776.
The IUCr Commission on Nomenclature recommends against the use
of B for reporting atomic displacement parameters. U, being
directly proportional to B, is preferred.
Note -
The particular type of ADP stored in this item is qualified
by item attribute pdbx_adp_type in category refine.
atom_site.B_iso_or_equiv_esd
The standard uncertainty (estimated standard deviation)
of attribute B_iso_or_equiv in category atom_site.
atom_site.Cartn_x
The x atom-site coordinate in angstroms specified according to
a set of orthogonal Cartesian axes related to the cell axes as
specified by the description given in
attribute Cartn_transform_axes in category atom_sites.
atom_site.Cartn_x_esd
The standard uncertainty (estimated standard deviation)
of attribute Cartn_x in category atom_site.
atom_site.Cartn_y
The y atom-site coordinate in angstroms specified according to
a set of orthogonal Cartesian axes related to the cell axes as
specified by the description given in
attribute Cartn_transform_axes in category atom_sites.
atom_site.Cartn_y_esd
The standard uncertainty (estimated standard deviation)
of attribute Cartn_y in category atom_site.
atom_site.Cartn_z
The z atom-site coordinate in angstroms specified according to
a set of orthogonal Cartesian axes related to the cell axes as
specified by the description given in
attribute Cartn_transform_axes in category atom_sites.
atom_site.Cartn_z_esd
The standard uncertainty (estimated standard deviation)
of attribute Cartn_z in category atom_site.
atom_site.U_equiv_geom_mean
Equivalent isotropic atomic displacement parameter, U~eq~,
in angstroms squared, calculated as the geometric mean of
the anisotropic atomic displacement parameters.
U~eq~ = (U~i~ U~j~ U~k~)^1/3^
U~n~ = the principal components of the orthogonalized U^ij^
atom_site.U_equiv_geom_mean_esd
The standard uncertainty (estimated standard deviation)
of attribute U_equiv_geom_mean in category atom_site.
atom_site.U_iso_or_equiv
Isotropic atomic displacement parameter, or equivalent isotropic
atomic displacement parameter, U~eq~, calculated from
anisotropic atomic displacement parameters.
U~eq~ = (1/3) sum~i~[sum~j~(U^ij^ A~i~ A~j~ a*~i~ a*~j~)]
A = the real space cell lengths
a* = the reciprocal space cell lengths
Ref: Fischer, R. X. & Tillmanns, E. (1988). Acta Cryst. C44,
775-776.
atom_site.U_iso_or_equiv_esd
The standard uncertainty (estimated standard deviation)
of attribute U_iso_or_equiv in category atom_site.
atom_site.Wyckoff_symbol
The Wyckoff symbol (letter) as listed in the space-group tables
of International Tables for Crystallography, Vol. A (2002).
Uani
Uiso
Uovl
Umpe
Bani
Biso
Bovl
A standard code used to describe the type of atomic displacement
parameters used for the site.
atom_site.aniso_B11
The [1][1] element of the anisotropic atomic displacement
matrix B, which appears in the structure-factor term as:
T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]}
h = the Miller indices
a* = the reciprocal space cell lengths
These matrix elements may appear with atomic coordinates
in the ATOM_SITE category, or they may appear in the separate
ATOM_SITE_ANISOTROP category, but they may not appear in both
places. Similarly, anisotropic displacements may appear as
either B's or U's, but not as both.
The unique elements of the real symmetric matrix are
entered by row.
The IUCr Commission on Nomenclature recommends against the use
of B for reporting atomic displacement parameters. U, being
directly proportional to B, is preferred.
atom_site.aniso_B11_esd
The standard uncertainty (estimated standard deviation)
of attribute aniso_B[1][1] in category atom_site.
atom_site.aniso_B12
The [1][2] element of the anisotropic atomic displacement
matrix B, which appears in the structure-factor term as:
T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]}
h = the Miller indices
a* = the reciprocal space cell lengths
These matrix elements may appear with atomic coordinates
in the ATOM_SITE category, or they may appear in the separate
ATOM_SITE_ANISOTROP category, but they may not appear in both
places. Similarly, anisotropic displacements may appear as
either B's or U's, but not as both.
The unique elements of the real symmetric matrix are
entered by row.
The IUCr Commission on Nomenclature recommends against the use
of B for reporting atomic displacement parameters. U, being
directly proportional to B, is preferred.
atom_site.aniso_B12_esd
The standard uncertainty (estimated standard deviation)
of attribute aniso_B[1][2] in category atom_site.
atom_site.aniso_B13
The [1][3] element of the anisotropic atomic displacement
matrix B, which appears in the structure-factor term as:
T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]}
h = the Miller indices
a* = the reciprocal space cell lengths
These matrix elements may appear with atomic coordinates
in the ATOM_SITE category, or they may appear in the separate
ATOM_SITE_ANISOTROP category, but they may not appear in both
places. Similarly, anisotropic displacements may appear as
either B's or U's, but not as both.
The unique elements of the real symmetric matrix are
entered by row.
The IUCr Commission on Nomenclature recommends against the use
of B for reporting atomic displacement parameters. U, being
directly proportional to B, is preferred.
atom_site.aniso_B13_esd
The standard uncertainty (estimated standard deviation)
of attribute aniso_B[1][3] in category atom_site.
atom_site.aniso_B22
The [2][2] element of the anisotropic atomic displacement
matrix B, which appears in the structure-factor term as:
T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]}
h = the Miller indices
a* = the reciprocal space cell lengths
These matrix elements may appear with atomic coordinates
in the ATOM_SITE category, or they may appear in the separate
ATOM_SITE_ANISOTROP category, but they may not appear in both
places. Similarly, anisotropic displacements may appear as
either B's or U's, but not as both.
The unique elements of the real symmetric matrix are
entered by row.
The IUCr Commission on Nomenclature recommends against the use
of B for reporting atomic displacement parameters. U, being
directly proportional to B, is preferred.
atom_site.aniso_B22_esd
The standard uncertainty (estimated standard deviation)
of attribute aniso_B[2][2] in category atom_site.
atom_site.aniso_B23
The [2][3] element of the anisotropic atomic displacement
matrix B, which appears in the structure-factor term as:
T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]}
h = the Miller indices
a* = the reciprocal space cell lengths
These matrix elements may appear with atomic coordinates
in the ATOM_SITE category, or they may appear in the separate
ATOM_SITE_ANISOTROP category, but they may not appear in both
places. Similarly, anisotropic displacements may appear as
either B's or U's, but not as both.
The unique elements of the real symmetric matrix are
entered by row.
The IUCr Commission on Nomenclature recommends against the use
of B for reporting atomic displacement parameters. U, being
directly proportional to B, is preferred.
atom_site.aniso_B23_esd
The standard uncertainty (estimated standard deviation)
of attribute aniso_B[2][3] in category atom_site.
atom_site.aniso_B33
The [3][3] element of the anisotropic atomic displacement
matrix B, which appears in the structure-factor term as:
T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]}
h = the Miller indices
a* = the reciprocal space cell lengths
These matrix elements may appear with atomic coordinates
in the ATOM_SITE category, or they may appear in the separate
ATOM_SITE_ANISOTROP category, but they may not appear in both
places. Similarly, anisotropic displacements may appear as
either B's or U's, but not as both.
The unique elements of the real symmetric matrix are
entered by row.
The IUCr Commission on Nomenclature recommends against the use
of B for reporting atomic displacement parameters. U, being
directly proportional to B, is preferred.
atom_site.aniso_B33_esd
The standard uncertainty (estimated standard deviation)
of attribute aniso_B[3][3] in category atom_site.
atom_site.aniso_U11
The [1][1] element of the standard anisotropic atomic
displacement matrix U, which appears in the structure-factor
term as:
T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]}
h = the Miller indices
a* = the reciprocal space cell lengths
These matrix elements may appear with atomic coordinates
in the ATOM_SITE category, or they may appear in the separate
ATOM_SITE_ANISOTROP category, but they may not appear in both
places. Similarly, anisotropic displacements may appear as
either B's or U's, but not as both.
The unique elements of the real symmetric matrix are
entered by row.
atom_site.aniso_U11_esd
The standard uncertainty (estimated standard deviation)
of attribute aniso_U[1][1] in category atom_site.
atom_site.aniso_U12
The [1][2] element of the standard anisotropic atomic
displacement matrix U, which appears in the structure-factor
term as:
T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]}
h = the Miller indices
a* = the reciprocal space cell lengths
These matrix elements may appear with atomic coordinates
in the ATOM_SITE category, or they may appear in the separate
ATOM_SITE_ANISOTROP category, but they may not appear in both
places. Similarly, anisotropic displacements may appear as
either B's or U's, but not as both.
The unique elements of the real symmetric matrix are
entered by row.
atom_site.aniso_U12_esd
The standard uncertainty (estimated standard deviation)
of attribute aniso_U[1][2] in category atom_site.
atom_site.aniso_U13
The [1][3] element of the standard anisotropic atomic
displacement matrix U, which appears in the structure-factor
term as:
T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]}
h = the Miller indices
a* = the reciprocal space cell lengths
These matrix elements may appear with atomic coordinates
in the ATOM_SITE category, or they may appear in the separate
ATOM_SITE_ANISOTROP category, but they may not appear in both
places. Similarly, anisotropic displacements may appear as
either B's or U's, but not as both.
The unique elements of the real symmetric matrix are
entered by row.
atom_site.aniso_U13_esd
The standard uncertainty (estimated standard deviation)
of attribute aniso_U[1][3] in category atom_site.
atom_site.aniso_U22
The [2][2] element of the standard anisotropic atomic
displacement matrix U, which appears in the structure-factor
term as:
T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]}
h = the Miller indices
a* = the reciprocal space cell lengths
These matrix elements may appear with atomic coordinates
in the ATOM_SITE category, or they may appear in the separate
ATOM_SITE_ANISOTROP category, but they may not appear in both
places. Similarly, anisotropic displacements may appear as
either B's or U's, but not as both.
The unique elements of the real symmetric matrix are
entered by row.
atom_site.aniso_U22_esd
The standard uncertainty (estimated standard deviation)
of attribute aniso_U[2][2] in category atom_site.
atom_site.aniso_U23
The [2][3] element of the standard anisotropic atomic
displacement matrix U, which appears in the structure-factor
term as:
T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]}
h = the Miller indices
a* = the reciprocal space cell lengths
These matrix elements may appear with atomic coordinates
in the ATOM_SITE category, or they may appear in the separate
ATOM_SITE_ANISOTROP category, but they may not appear in both
places. Similarly, anisotropic displacements may appear as
either B's or U's, but not as both.
The unique elements of the real symmetric matrix are
entered by row.
atom_site.aniso_U23_esd
The standard uncertainty (estimated standard deviation)
of attribute aniso_U[2][3] in category atom_site.
atom_site.aniso_U33
The [3][3] element of the standard anisotropic atomic
displacement matrix U, which appears in the structure-factor
term as:
T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]}
h = the Miller indices
a* = the reciprocal space cell lengths
These matrix elements may appear with atomic coordinates
in the ATOM_SITE category, or they may appear in the separate
ATOM_SITE_ANISOTROP category, but they may not appear in both
places. Similarly, anisotropic displacements may appear as
either B's or U's, but not as both.
The unique elements of the real symmetric matrix are
entered by row.
atom_site.aniso_U33_esd
The standard uncertainty (estimated standard deviation)
of attribute aniso_U[3][3] in category atom_site.
atom_site.aniso_ratio
Ratio of the maximum to minimum principal axes of
displacement (thermal) ellipsoids.
atom_site.attached_hydrogens
The number of hydrogen atoms attached to the atom at this site
excluding any hydrogen atoms for which coordinates (measured or
calculated) are given.
water oxygen
2
hydroxyl oxygen
1
ammonium nitrogen
4
atom_site.auth_asym_id
An alternative identifier for attribute label_asym_id in category atom_site that
may be provided by an author in order to match the identification
used in the publication that describes the structure.
atom_site.auth_atom_id
An alternative identifier for attribute label_atom_id in category atom_site that
may be provided by an author in order to match the identification
used in the publication that describes the structure.
atom_site.auth_comp_id
An alternative identifier for attribute label_comp_id in category atom_site that
may be provided by an author in order to match the identification
used in the publication that describes the structure.
atom_site.auth_seq_id
An alternative identifier for attribute label_seq_id in category atom_site that
may be provided by an author in order to match the identification
used in the publication that describes the structure.
Note that this is not necessarily a number, that the values do
not have to be positive, and that the value does not have to
correspond to the value of attribute label_seq_id in category atom_site. The value
of attribute label_seq_id in category atom_site is required to be a sequential list
of positive integers.
The author may assign values to attribute auth_seq_id in category atom_site in any
desired way. For instance, the values may be used to relate
this structure to a numbering scheme in a homologous structure,
including sequence gaps or insertion codes. Alternatively, a
scheme may be used for a truncated polymer that maintains the
numbering scheme of the full length polymer. In all cases, the
scheme used here must match the scheme used in the publication
that describes the structure.
atom_site.calc_attached_atom
The attribute id in category atom_site of the atom site to which the
'geometry-calculated' atom site is attached.
d
calc
c
dum
A standard code to signal whether the site coordinates have been
determined from the intensities or calculated from the geometry
of surrounding sites, or have been assigned dummy values. The
abbreviation 'c' may be used in place of 'calc'.
atom_site.chemical_conn_number
This data item is a pointer to attribute number in category chemical_conn_atom in the
CHEMICAL_CONN_ATOM category.
atom_site.constraints
A description of the constraints applied to parameters at this
site during refinement. See also attribute refinement_flags
in category atom_site and attribute ls_number_constraints in category refine.
pop=1.0-pop(Zn3)
atom_site.details
A description of special aspects of this site. See also
attribute refinement_flags in category atom_site.
Ag/Si disordered
atom_site.disorder_assembly
A code which identifies a cluster of atoms that show long-range
positional disorder but are locally ordered. Within each such
cluster of atoms, attribute disorder_group in category atom_site is used to identify
the sites that are simultaneously occupied. This field is only
needed if there is more than one cluster of disordered atoms
showing independent local order.
*** This data item would not in general be used in a
macromolecular data block. ***
atom_site.disorder_group
A code which identifies a group of positionally disordered atom
sites that are locally simultaneously occupied. Atoms that are
positionally disordered over two or more sites (e.g. the hydrogen
atoms of a methyl group that exists in two orientations) can
be assigned to two or more groups. Sites belonging to the same
group are simultaneously occupied, but those belonging to
different groups are not. A minus prefix (e.g. '-1') is used to
indicate sites disordered about a special position.
*** This data item would not in general be used in a
macromolecular data block. ***
atom_site.footnote_id
The value of attribute footnote_id in category atom_site must match an ID
specified by attribute id in category atom_sites_footnote in the
ATOM_SITES_FOOTNOTE list.
atom_site.fract_x
The x coordinate of the atom-site position specified as a
fraction of attribute length_a in category cell.
atom_site.fract_x_esd
The standard uncertainty (estimated standard deviation)
of attribute fract_x in category atom_site.
atom_site.fract_y
The y coordinate of the atom-site position specified as a
fraction of attribute length_b in category cell.
atom_site.fract_y_esd
The standard uncertainty (estimated standard deviation)
of attribute fract_y in category atom_site.
atom_site.fract_z
The z coordinate of the atom-site position specified as a
fraction of attribute length_c in category cell.
atom_site.fract_z_esd
The standard uncertainty (estimated standard deviation)
of attribute fract_z in category atom_site.
ATOM
HETATM
The group of atoms to which the atom site belongs. This data
item is provided for compatibility with the original Protein
Data Bank format, and only for that purpose.
atom_site.label_alt_id
A place holder to indicate alternate conformation. The alternate conformation
can be an entire polymer chain, or several residues or
partial residue (several atoms within one residue). If
an atom is provided in more than one position, then a
non-blank alternate location indicator must be used for
each of the atomic positions.
atom_site.label_asym_id
A component of the identifier for this atom site.
For further details, see the definition of the STRUCT_ASYM
category.
This data item is a pointer to attribute id in category struct_asym in the
STRUCT_ASYM category.
atom_site.label_atom_id
A component of the identifier for this atom site.
This data item is a pointer to attribute atom_id in category chem_comp_atom in the
CHEM_COMP_ATOM category.
atom_site.label_comp_id
A component of the identifier for this atom site.
This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP
category.
atom_site.label_entity_id
This data item is a pointer to attribute id in category entity in the ENTITY category.
atom_site.label_seq_id
This data item is a pointer to attribute num in category entity_poly_seq in the
ENTITY_POLY_SEQ category.
atom_site.occupancy
The fraction of the atom type present at this site.
The sum of the occupancies of all the atom types at this site
may not exceed 1.0 unless it is a dummy site.
atom_site.occupancy_esd
The standard uncertainty (estimated standard deviation)
of attribute occupancy in category atom_site.
atom_site.pdbx_PDB_atom_name
PDB atom name.
atom_site.pdbx_PDB_ins_code
PDB insertion code.
atom_site.pdbx_PDB_model_num
PDB model number.
atom_site.pdbx_PDB_residue_name
PDB residue name.
atom_site.pdbx_PDB_residue_no
PDB residue number.
atom_site.pdbx_PDB_strand_id
PDB strand id.
atom_site.pdbx_atom_ambiguity
The optional value of attribute pdbx_atom_ambiguity in category atom_site atoms that differ only by stereochemistry but
are not stereospecifically assigned by the experiment.
HDx%
HDy%
H5x
H5y
atom_site.pdbx_atom_group
The ATOM group code used by the NDB.
atom_site.pdbx_auth_alt_id
Author's alternate location identifier.
atom_site.pdbx_auth_asym_id
Author's strand id.
atom_site.pdbx_auth_atom_name
Author's atom name.
atom_site.pdbx_auth_comp_id
Author's residue name.
atom_site.pdbx_auth_seq_id
Author's sequence identifier.
atom_site.pdbx_formal_charge
The net integer charge assigned to this atom. This is the
formal charge assignment normally found in chemical diagrams.
for an ammonium nitrogen
1
for a chloride ion
-1
atom_site.pdbx_group_NDB
The ATOM group code used by the NDB.
atom_site.pdbx_label_index
This data item is an ordinal which identifies distinct chemical components in the atom_site category, both
polymeric and non-polymeric.
atom_site.pdbx_label_seq_num
Sequential residue number used by NDB.
atom_site.pdbx_ncs_dom_id
The NCS domain to which the atom position is assigned.
The NCS group is defined in category struct_ncs_dom.
This item is a reference to attribute id in category struct_ncs_dom.
atom_site.pdbx_not_in_asym
Will identify with a 'Y' that this strand got generated.
atom_site.pdbx_sifts_xref_db_acc
The accession code related to the additional external database entry.
atom_site.pdbx_sifts_xref_db_name
The name of additional external databases with residue level mapping.
atom_site.pdbx_sifts_xref_db_num
The sequence position of the external database entry that corresponds
to the residue mapping defined by the SIFTS process.
atom_site.pdbx_sifts_xref_db_res
Describes the residue type of the given UniProt match
alanine
A
arginine
R
asparagine
N
aspartic acid
D
cysteine
C
glutamine
Q
glutamic acid
E
glycine
G
histidine
H
isoleucine
I
leucine
L
lysine
K
methionine
M
phenylalanine
F
proline
P
selenocysteine
U
serine
S
threonine
T
tryptophan
W
tyrosine
Y
valine
V
pyrrolysine
O
other
X
atom_site.pdbx_struct_group_id
The value of attribute pdbx_struct_group_id in category atom_site identifies the group or groups
assigned to this atom. This is a reference to the identifier for
group definition in category PDBX_STRUCT_GROUP_LIST.
Multiple groups identifiers are encoded as a comma separated list.
atom assigned to individual group C1
C1
atom assigned to multiple groups C1, C2 and C3
C1,C2,C3
atom_site.pdbx_tls_group_id
The TLS group to which the atom position is assigned.
The TLS group is defined in category pdbx_refine_tls.
This item is a reference to attribute id in category pdbx_refine_tls.
S
G
R
D
T
U
P
A concatenated series of single-letter codes which indicate the
refinement restraints or constraints applied to this site. This
item should not be used. It has been replaced by
attribute refinement_flags_posn in category atom_site, *_adp and *_occupancy. It is
retained in this dictionary only to provide compatibility with
old CIFs.
T
U
TU
A code which indicates the refinement restraints or constraints
applied to the atomic displacement parameters of this site.
P
A code which indicates that refinement restraints or
constraints were applied to the occupancy of this site.
D
G
R
S
DG
DR
DS
GR
GS
RS
DGR
DGS
DRS
GRS
DGRS
A code which indicates the refinement restraints or constraints
applied to the positional coordinates of this site.
atom_site.restraints
A description of restraints applied to specific parameters at
this site during refinement. See also attribute refinement_flags
in category atom_site and attribute ls_number_restraints in category refine.
restrained to planar ring
atom_site.symmetry_multiplicity
The multiplicity of a site due to the space-group symmetry as is
given in International Tables for Crystallography Vol. A (2002).
Uani
Uiso
Uovl
Umpe
Bani
Biso
Bovl
A standard code used to describe the type of atomic displacement
parameters used for the site.
atom_site.type_symbol
This data item is a pointer to attribute symbol in category atom_type in the
ATOM_TYPE category.
atom_site.id
The value of attribute id in category atom_site must uniquely identify a record in the
ATOM_SITE list.
Note that this item need not be a number; it can be any unique
identifier.
This data item was introduced to provide compatibility between
small-molecule and macromolecular CIFs. In a small-molecule
CIF, _atom_site_label is the identifier for the atom. In a
macromolecular CIF, the atom identifier is the aggregate of
_atom_site.label_alt_id, _atom_site.label_asym_id,
_atom_site.label_atom_id, _atom_site.label_comp_id and
attribute label_seq_id in category atom_site. For the two types of files to be
compatible, a formal identifier for the category had to be
introduced that was independent of the different modes of
identifying the atoms. For compatibility with older CIFs,
_atom_site_label is aliased to attribute id.
in category atom_site
In general, this aggregate identifier does not uniquely
identify an atom site as for non-polymers attribute label_seq_id
in category atom_site is '.'.
5
C12
Ca3g28
Fe3+17
H*251
boron2a
C_a_phe_83_a_0
Zn_Zn_301_A_0
0
atom_site_anisotrop
Data items in the ATOM_SITE_ANISOTROP category record details
about anisotropic displacement parameters.
If the ATOM_SITE_ANISOTROP category is used for storing these
data, the corresponding ATOM_SITE data items are not used.
Example 1 - based on NDB structure BDL005 of Holbrook, Dickerson &
Kim [Acta Cryst. (1985), B41, 255-262].
<PDBx:atom_site_anisotropCategory>
<PDBx:atom_site_anisotrop id="1">
<PDBx:U11>8642</PDBx:U11>
<PDBx:U12>4866</PDBx:U12>
<PDBx:U13>7299</PDBx:U13>
<PDBx:U22>-342</PDBx:U22>
<PDBx:U23>-258</PDBx:U23>
<PDBx:U33>-1427</PDBx:U33>
<PDBx:type_symbol>O</PDBx:type_symbol>
</PDBx:atom_site_anisotrop>
<PDBx:atom_site_anisotrop id="2">
<PDBx:U11>5174</PDBx:U11>
<PDBx:U12>4871</PDBx:U12>
<PDBx:U13>6243</PDBx:U13>
<PDBx:U22>-1885</PDBx:U22>
<PDBx:U23>-2051</PDBx:U23>
<PDBx:U33>-1377</PDBx:U33>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:atom_site_anisotrop>
<PDBx:atom_site_anisotrop id="3">
<PDBx:U11>6202</PDBx:U11>
<PDBx:U12>5020</PDBx:U12>
<PDBx:U13>4395</PDBx:U13>
<PDBx:U22>-1130</PDBx:U22>
<PDBx:U23>-556</PDBx:U23>
<PDBx:U33>-632</PDBx:U33>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:atom_site_anisotrop>
<PDBx:atom_site_anisotrop id="4">
<PDBx:U11>4224</PDBx:U11>
<PDBx:U12>4700</PDBx:U12>
<PDBx:U13>5046</PDBx:U13>
<PDBx:U22>1105</PDBx:U22>
<PDBx:U23>-161</PDBx:U23>
<PDBx:U33>345</PDBx:U33>
<PDBx:type_symbol>O</PDBx:type_symbol>
</PDBx:atom_site_anisotrop>
<PDBx:atom_site_anisotrop id="5">
<PDBx:U11>8684</PDBx:U11>
<PDBx:U12>4688</PDBx:U12>
<PDBx:U13>4171</PDBx:U13>
<PDBx:U22>-1850</PDBx:U22>
<PDBx:U23>-433</PDBx:U23>
<PDBx:U33>-292</PDBx:U33>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:atom_site_anisotrop>
<PDBx:atom_site_anisotrop id="6">
<PDBx:U11>11226</PDBx:U11>
<PDBx:U12>5255</PDBx:U12>
<PDBx:U13>3532</PDBx:U13>
<PDBx:U22>-341</PDBx:U22>
<PDBx:U23>2685</PDBx:U23>
<PDBx:U33>1328</PDBx:U33>
<PDBx:type_symbol>O</PDBx:type_symbol>
</PDBx:atom_site_anisotrop>
<PDBx:atom_site_anisotrop id="7">
<PDBx:U11>10214</PDBx:U11>
<PDBx:U12>2428</PDBx:U12>
<PDBx:U13>5614</PDBx:U13>
<PDBx:U22>-2610</PDBx:U22>
<PDBx:U23>-1940</PDBx:U23>
<PDBx:U33>902</PDBx:U33>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:atom_site_anisotrop>
<PDBx:atom_site_anisotrop id="8">
<PDBx:U11>4590</PDBx:U11>
<PDBx:U12>3488</PDBx:U12>
<PDBx:U13>5827</PDBx:U13>
<PDBx:U22>751</PDBx:U22>
<PDBx:U23>-770</PDBx:U23>
<PDBx:U33>986</PDBx:U33>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:atom_site_anisotrop>
<PDBx:atom_site_anisotrop id="9">
<PDBx:U11>5014</PDBx:U11>
<PDBx:U12>4434</PDBx:U12>
<PDBx:U13>3447</PDBx:U13>
<PDBx:U22>-17</PDBx:U22>
<PDBx:U23>-1593</PDBx:U23>
<PDBx:U33>539</PDBx:U33>
<PDBx:type_symbol>N</PDBx:type_symbol>
</PDBx:atom_site_anisotrop>
</PDBx:atom_site_anisotropCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
1
1
atom_site_anisotropCategory
This property indicates that datablock
has a category holder atom_site_anisotropCategory.
atom_site_anisotropCategory
This property indicates that atom_site_anisotropCategory.
has a category atom_site_anisotrop.
atom_site_anisotropItem
Abstract datatype property for atom_site_anisotrop items.
reference_to_atom_site_anisotrop
cross-reference to atom_site_anisotrop.
referenced_by_atom_site_anisotrop
cross-reference from atom_site_anisotrop.
atom_site_anisotrop.B11
The [1][1] element of the anisotropic atomic displacement
matrix B, which appears in the structure-factor term as:
T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]}
h = the Miller indices
a* = the reciprocal space cell lengths
These matrix elements may appear with atomic coordinates
in the ATOM_SITE category, or they may appear in the separate
ATOM_SITE_ANISOTROP category, but they may not appear in both
places. Similarly, anisotropic displacements may appear as
either B's or U's, but not as both.
The unique elements of the real symmetric matrix are
entered by row.
The IUCr Commission on Nomenclature recommends against the use
of B for reporting atomic displacement parameters. U, being
directly proportional to B, is preferred.
atom_site_anisotrop.B11_esd
The standard uncertainty (estimated standard deviation)
of attribute B[1][1] in category atom_site_anisotrop.
atom_site_anisotrop.B12
The [1][2] element of the anisotropic atomic displacement
matrix B, which appears in the structure-factor term as:
T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]}
h = the Miller indices
a* = the reciprocal space cell lengths
These matrix elements may appear with atomic coordinates
in the ATOM_SITE category, or they may appear in the separate
ATOM_SITE_ANISOTROP category, but they may not appear in both
places. Similarly, anisotropic displacements may appear as
either B's or U's, but not as both.
The unique elements of the real symmetric matrix are
entered by row.
The IUCr Commission on Nomenclature recommends against the use
of B for reporting atomic displacement parameters. U, being
directly proportional to B, is preferred.
atom_site_anisotrop.B12_esd
The standard uncertainty (estimated standard deviation)
of attribute B[1][2] in category atom_site_anisotrop.
atom_site_anisotrop.B13
The [1][3] element of the anisotropic atomic displacement
matrix B, which appears in the structure-factor term as:
T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]}
h = the Miller indices
a* = the reciprocal space cell lengths
These matrix elements may appear with atomic coordinates
in the ATOM_SITE category, or they may appear in the separate
ATOM_SITE_ANISOTROP category, but they may not appear in both
places. Similarly, anisotropic displacements may appear as
either B's or U's, but not as both.
The unique elements of the real symmetric matrix are
entered by row.
The IUCr Commission on Nomenclature recommends against the use
of B for reporting atomic displacement parameters. U, being
directly proportional to B, is preferred.
atom_site_anisotrop.B13_esd
The standard uncertainty (estimated standard deviation)
of attribute B[1][3] in category atom_site_anisotrop.
atom_site_anisotrop.B22
The [2][2] element of the anisotropic atomic displacement
matrix B, which appears in the structure-factor term as:
T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]}
h = the Miller indices
a* = the reciprocal space cell lengths
These matrix elements may appear with atomic coordinates
in the ATOM_SITE category, or they may appear in the separate
ATOM_SITE_ANISOTROP category, but they may not appear in both
places. Similarly, anisotropic displacements may appear as
either B's or U's, but not as both.
The unique elements of the real symmetric matrix are
entered by row.
The IUCr Commission on Nomenclature recommends against the use
of B for reporting atomic displacement parameters. U, being
directly proportional to B, is preferred.
atom_site_anisotrop.B22_esd
The standard uncertainty (estimated standard deviation)
of attribute B[2][2] in category atom_site_anisotrop.
atom_site_anisotrop.B23
The [2][3] element of the anisotropic atomic displacement
matrix B, which appears in the structure-factor term as:
T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]}
h = the Miller indices
a* = the reciprocal space cell lengths
These matrix elements may appear with atomic coordinates
in the ATOM_SITE category, or they may appear in the separate
ATOM_SITE_ANISOTROP category, but they may not appear in both
places. Similarly, anisotropic displacements may appear as
either B's or U's, but not as both.
The unique elements of the real symmetric matrix are
entered by row.
The IUCr Commission on Nomenclature recommends against the use
of B for reporting atomic displacement parameters. U, being
directly proportional to B, is preferred.
atom_site_anisotrop.B23_esd
The standard uncertainty (estimated standard deviation)
of attribute B[2][3] in category atom_site_anisotrop.
atom_site_anisotrop.B33
The [3][3] element of the anisotropic atomic displacement
matrix B, which appears in the structure-factor term as:
T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]}
h = the Miller indices
a* = the reciprocal space cell lengths
These matrix elements may appear with atomic coordinates
in the ATOM_SITE category, or they may appear in the separate
ATOM_SITE_ANISOTROP category, but they may not appear in both
places. Similarly, anisotropic displacements may appear as
either B's or U's, but not as both.
The unique elements of the real symmetric matrix are
entered by row.
The IUCr Commission on Nomenclature recommends against the use
of B for reporting atomic displacement parameters. U, being
directly proportional to B, is preferred.
atom_site_anisotrop.B33_esd
The standard uncertainty (estimated standard deviation)
of attribute B[3][3] in category atom_site_anisotrop.
atom_site_anisotrop.U11
The [1][1] element of the standard anisotropic atomic
displacement matrix U, which appears in the structure-factor
term as:
T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]}
h = the Miller indices
a* = the reciprocal space cell lengths
These matrix elements may appear with atomic coordinates
in the ATOM_SITE category, or they may appear in the separate
ATOM_SITE_ANISOTROP category, but they may not appear in both
places. Similarly, anisotropic displacements may appear as
either B's or U's, but not as both.
The unique elements of the real symmetric matrix are
entered by row.
atom_site_anisotrop.U11_esd
The standard uncertainty (estimated standard deviation)
of attribute U[1][1] in category atom_site_anisotrop.
atom_site_anisotrop.U12
The [1][2] element of the standard anisotropic atomic
displacement matrix U, which appears in the structure-factor
term as:
T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]}
h = the Miller indices
a* = the reciprocal space cell lengths
These matrix elements may appear with atomic coordinates
in the ATOM_SITE category, or they may appear in the separate
ATOM_SITE_ANISOTROP category, but they may not appear in both
places. Similarly, anisotropic displacements may appear as
either B's or U's, but not as both.
The unique elements of the real symmetric matrix are
entered by row.
atom_site_anisotrop.U12_esd
The standard uncertainty (estimated standard deviation)
of attribute U[1][2] in category atom_site_anisotrop.
atom_site_anisotrop.U13
The [1][3] element of the standard anisotropic atomic
displacement matrix U, which appears in the structure-factor
term as:
T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]}
h = the Miller indices
a* = the reciprocal space cell lengths
These matrix elements may appear with atomic coordinates
in the ATOM_SITE category, or they may appear in the separate
ATOM_SITE_ANISOTROP category, but they may not appear in both
places. Similarly, anisotropic displacements may appear as
either B's or U's, but not as both.
The unique elements of the real symmetric matrix are
entered by row.
atom_site_anisotrop.U13_esd
The standard uncertainty (estimated standard deviation)
of attribute U[1][3] in category atom_site_anisotrop.
atom_site_anisotrop.U22
The [2][2] element of the standard anisotropic atomic
displacement matrix U, which appears in the structure-factor
term as:
T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]}
h = the Miller indices
a* = the reciprocal space cell lengths
These matrix elements may appear with atomic coordinates
in the ATOM_SITE category, or they may appear in the separate
ATOM_SITE_ANISOTROP category, but they may not appear in both
places. Similarly, anisotropic displacements may appear as
either B's or U's, but not as both.
The unique elements of the real symmetric matrix are
entered by row.
atom_site_anisotrop.U22_esd
The standard uncertainty (estimated standard deviation)
of attribute U[2][2] in category atom_site_anisotrop.
atom_site_anisotrop.U23
The [2][3] element of the standard anisotropic atomic
displacement matrix U, which appears in the structure-factor
term as:
T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]}
h = the Miller indices
a* = the reciprocal space cell lengths
These matrix elements may appear with atomic coordinates
in the ATOM_SITE category, or they may appear in the separate
ATOM_SITE_ANISOTROP category, but they may not appear in both
places. Similarly, anisotropic displacements may appear as
either B's or U's, but not as both.
The unique elements of the real symmetric matrix are
entered by row.
atom_site_anisotrop.U23_esd
The standard uncertainty (estimated standard deviation)
of attribute U[2][3] in category atom_site_anisotrop.
atom_site_anisotrop.U33
The [3][3] element of the standard anisotropic atomic
displacement matrix U, which appears in the structure-factor
term as:
T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]}
h = the Miller indices
a* = the reciprocal space cell lengths
These matrix elements may appear with atomic coordinates
in the ATOM_SITE category, or they may appear in the separate
ATOM_SITE_ANISOTROP category, but they may not appear in both
places. Similarly, anisotropic displacements may appear as
either B's or U's, but not as both.
The unique elements of the real symmetric matrix are
entered by row.
atom_site_anisotrop.U33_esd
The standard uncertainty (estimated standard deviation)
of attribute U[3][3] in category atom_site_anisotrop.
atom_site_anisotrop.pdbx_PDB_atom_name
PDB atom name.
atom_site_anisotrop.pdbx_PDB_ins_code
Pointer to attribute pdbx_PDB_ins_code in category atom_site
atom_site_anisotrop.pdbx_PDB_model_num
Pointer to attribute pdbx_PDB_model_num in category atom_site
atom_site_anisotrop.pdbx_PDB_residue_name
PDB residue name.
atom_site_anisotrop.pdbx_PDB_residue_no
PDB residue number.
atom_site_anisotrop.pdbx_PDB_strand_id
PDB strand id.
atom_site_anisotrop.pdbx_auth_alt_id
Pointer to attribute pdbx_auth_alt_id in category atom_site.
atom_site_anisotrop.pdbx_auth_asym_id
Pointer to attribute auth_asym_id in category atom_site
atom_site_anisotrop.pdbx_auth_atom_id
Pointer to attribute auth_atom_id in category atom_site
atom_site_anisotrop.pdbx_auth_atom_name
Author's atom name.
atom_site_anisotrop.pdbx_auth_comp_id
Pointer to attribute auth_comp_id in category atom_site
atom_site_anisotrop.pdbx_auth_seq_id
Pointer to attribute auth_seq_id in category atom_site
atom_site_anisotrop.pdbx_label_alt_id
Pointer to attribute label_alt_id in category atom_site.
atom_site_anisotrop.pdbx_label_asym_id
Pointer to attribute label_asym_id in category atom_site
atom_site_anisotrop.pdbx_label_atom_id
Pointer to attribute label_atom_id in category atom_site
atom_site_anisotrop.pdbx_label_comp_id
Pointer to attribute label_comp_id in category atom_site
atom_site_anisotrop.pdbx_label_ins_code
NDB INSERTION CODE
atom_site_anisotrop.pdbx_label_seq_id
Pointer to attribute label_seq_id in category atom_site
atom_site_anisotrop.pdbx_not_in_asym
Will identify with a 'Y' that this strand got generated.
atom_site_anisotrop.ratio
Ratio of the maximum to minimum principal axes of
displacement (thermal) ellipsoids.
atom_site_anisotrop.type_symbol
This data item is a pointer to attribute symbol in category atom_type in the
ATOM_TYPE category.
atom_site_anisotrop.id
This data item is a pointer to attribute id in category atom_site in the ATOM_SITE
category.
0
atom_sites
Data items in the ATOM_SITES category record details about
the crystallographic cell and cell transformations, which are
common to all atom sites.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:atom_sitesCategory>
<PDBx:atom_sites entry_id="5HVP">
<PDBx:Cartn_transf_matrix11>58.39</PDBx:Cartn_transf_matrix11>
<PDBx:Cartn_transf_matrix12>0.00</PDBx:Cartn_transf_matrix12>
<PDBx:Cartn_transf_matrix13>0.00</PDBx:Cartn_transf_matrix13>
<PDBx:Cartn_transf_matrix21>0.00</PDBx:Cartn_transf_matrix21>
<PDBx:Cartn_transf_matrix22>86.70</PDBx:Cartn_transf_matrix22>
<PDBx:Cartn_transf_matrix23>0.00</PDBx:Cartn_transf_matrix23>
<PDBx:Cartn_transf_matrix31>0.00</PDBx:Cartn_transf_matrix31>
<PDBx:Cartn_transf_matrix32>0.00</PDBx:Cartn_transf_matrix32>
<PDBx:Cartn_transf_matrix33>46.27</PDBx:Cartn_transf_matrix33>
<PDBx:Cartn_transf_vector1>0.00</PDBx:Cartn_transf_vector1>
<PDBx:Cartn_transf_vector2>0.00</PDBx:Cartn_transf_vector2>
<PDBx:Cartn_transf_vector3>0.00</PDBx:Cartn_transf_vector3>
<PDBx:Cartn_transform_axes>c along z, astar along x, b along y</PDBx:Cartn_transform_axes>
</PDBx:atom_sites>
</PDBx:atom_sitesCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
atom_sitesCategory
This property indicates that datablock
has a category holder atom_sitesCategory.
atom_sitesCategory
This property indicates that atom_sitesCategory.
has a category atom_sites.
atom_sitesItem
Abstract datatype property for atom_sites items.
reference_to_atom_sites
cross-reference to atom_sites.
referenced_by_atom_sites
cross-reference from atom_sites.
atom_sites.Cartn_transf_matrix11
The [1][1] element of the 3x3 matrix used to transform
fractional coordinates in the ATOM_SITE category to Cartesian
coordinates in the same category. The axial alignments of this
transformation are described in attribute Cartn_transform_axes.
in category atom_sites The 3x1 translation is defined in
attribute Cartn_transf_vector[].
in category atom_sites
|x'| |11 12 13| |x| |1|
|y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2|
|z'| |31 32 33| |z| |3|
atom_sites.Cartn_transf_matrix12
The [1][2] element of the 3x3 matrix used to transform
fractional coordinates in the ATOM_SITE category to Cartesian
coordinates in the same category. The axial alignments of this
transformation are described in attribute Cartn_transform_axes.
in category atom_sites The 3x1 translation is defined in
attribute Cartn_transf_vector[].
in category atom_sites
|x'| |11 12 13| |x| |1|
|y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2|
|z'| |31 32 33| |z| |3|
atom_sites.Cartn_transf_matrix13
The [1][3] element of the 3x3 matrix used to transform
fractional coordinates in the ATOM_SITE category to Cartesian
coordinates in the same category. The axial alignments of this
transformation are described in attribute Cartn_transform_axes.
in category atom_sites The 3x1 translation is defined in
attribute Cartn_transf_vector[].
in category atom_sites
|x'| |11 12 13| |x| |1|
|y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2|
|z'| |31 32 33| |z| |3|
atom_sites.Cartn_transf_matrix21
The [2][1] element of the 3x3 matrix used to transform
fractional coordinates in the ATOM_SITE category to Cartesian
coordinates in the same category. The axial alignments of this
transformation are described in attribute Cartn_transform_axes.
in category atom_sites The 3x1 translation is defined in
attribute Cartn_transf_vector[].
in category atom_sites
|x'| |11 12 13| |x| |1|
|y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2|
|z'| |31 32 33| |z| |3|
atom_sites.Cartn_transf_matrix22
The [2][2] element of the 3x3 matrix used to transform
fractional coordinates in the ATOM_SITE category to Cartesian
coordinates in the same category. The axial alignments of this
transformation are described in attribute Cartn_transform_axes.
in category atom_sites The 3x1 translation is defined in
attribute Cartn_transf_vector[].
in category atom_sites
|x'| |11 12 13| |x| |1|
|y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2|
|z'| |31 32 33| |z| |3|
atom_sites.Cartn_transf_matrix23
The [2][3] element of the 3x3 matrix used to transform
fractional coordinates in the ATOM_SITE category to Cartesian
coordinates in the same category. The axial alignments of this
transformation are described in attribute Cartn_transform_axes.
in category atom_sites The 3x1 translation is defined in
attribute Cartn_transf_vector[].
in category atom_sites
|x'| |11 12 13| |x| |1|
|y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2|
|z'| |31 32 33| |z| |3|
atom_sites.Cartn_transf_matrix31
The [3][1] element of the 3x3 matrix used to transform
fractional coordinates in the ATOM_SITE category to Cartesian
coordinates in the same category. The axial alignments of this
transformation are described in attribute Cartn_transform_axes.
in category atom_sites The 3x1 translation is defined in
attribute Cartn_transf_vector[].
in category atom_sites
|x'| |11 12 13| |x| |1|
|y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2|
|z'| |31 32 33| |z| |3|
atom_sites.Cartn_transf_matrix32
The [3][2] element of the 3x3 matrix used to transform
fractional coordinates in the ATOM_SITE category to Cartesian
coordinates in the same category. The axial alignments of this
transformation are described in attribute Cartn_transform_axes.
in category atom_sites The 3x1 translation is defined in
attribute Cartn_transf_vector[].
in category atom_sites
|x'| |11 12 13| |x| |1|
|y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2|
|z'| |31 32 33| |z| |3|
atom_sites.Cartn_transf_matrix33
The [3][3] element of the 3x3 matrix used to transform
fractional coordinates in the ATOM_SITE category to Cartesian
coordinates in the same category. The axial alignments of this
transformation are described in attribute Cartn_transform_axes.
in category atom_sites The 3x1 translation is defined in
attribute Cartn_transf_vector[].
in category atom_sites
|x'| |11 12 13| |x| |1|
|y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2|
|z'| |31 32 33| |z| |3|
atom_sites.Cartn_transf_vector1
The [1] element of the three-element vector used to transform
fractional coordinates in the ATOM_SITE category to Cartesian
coordinates in the same category. The axial alignments of this
transformation are described in attribute Cartn_transform_axes.
in category atom_sites The rotation matrix is defined in
attribute Cartn_transf_matrix[][].
in category atom_sites
|x'| |11 12 13| |x| |1|
|y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2|
|z'| |31 32 33| |z| |3|
atom_sites.Cartn_transf_vector2
The [2] element of the three-element vector used to transform
fractional coordinates in the ATOM_SITE category to Cartesian
coordinates in the same category. The axial alignments of this
transformation are described in attribute Cartn_transform_axes.
in category atom_sites The rotation matrix is defined in
attribute Cartn_transf_matrix[][].
in category atom_sites
|x'| |11 12 13| |x| |1|
|y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2|
|z'| |31 32 33| |z| |3|
atom_sites.Cartn_transf_vector3
The [3] element of the three-element vector used to transform
fractional coordinates in the ATOM_SITE category to Cartesian
coordinates in the same category. The axial alignments of this
transformation are described in attribute Cartn_transform_axes.
in category atom_sites The rotation matrix is defined in
attribute Cartn_transf_matrix[][].
in category atom_sites
|x'| |11 12 13| |x| |1|
|y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2|
|z'| |31 32 33| |z| |3|
atom_sites.Cartn_transform_axes
A description of the relative alignment of the crystal cell
axes to the Cartesian orthogonal axes as applied in the
transformation matrix attribute Cartn_transf_matrix[][] in category atom_sites.
a parallel to x; b in the plane of y and z
atom_sites.fract_transf_matrix11
The [1][1] element of the 3x3 matrix used to transform Cartesian
coordinates in the ATOM_SITE category to fractional coordinates
in the same category. The axial alignments of this
transformation are described in attribute Cartn_transform_axes.
in category atom_sites The 3x1 translation is defined in
attribute fract_transf_vector[].
in category atom_sites
|x'| |11 12 13| |x| |1|
|y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2|
|z'| |31 32 33| |z| |3|
atom_sites.fract_transf_matrix12
The [1][2] element of the 3x3 matrix used to transform Cartesian
coordinates in the ATOM_SITE category to fractional coordinates
in the same category. The axial alignments of this
transformation are described in attribute Cartn_transform_axes.
in category atom_sites The 3x1 translation is defined in
attribute fract_transf_vector[].
in category atom_sites
|x'| |11 12 13| |x| |1|
|y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2|
|z'| |31 32 33| |z| |3|
atom_sites.fract_transf_matrix13
The [1][3] element of the 3x3 matrix used to transform Cartesian
coordinates in the ATOM_SITE category to fractional coordinates
in the same category. The axial alignments of this
transformation are described in attribute Cartn_transform_axes.
in category atom_sites The 3x1 translation is defined in
attribute fract_transf_vector[].
in category atom_sites
|x'| |11 12 13| |x| |1|
|y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2|
|z'| |31 32 33| |z| |3|
atom_sites.fract_transf_matrix21
The [2][1] element of the 3x3 matrix used to transform Cartesian
coordinates in the ATOM_SITE category to fractional coordinates
in the same category. The axial alignments of this
transformation are described in attribute Cartn_transform_axes.
in category atom_sites The 3x1 translation is defined in
attribute fract_transf_vector[].
in category atom_sites
|x'| |11 12 13| |x| |1|
|y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2|
|z'| |31 32 33| |z| |3|
atom_sites.fract_transf_matrix22
The [2][2] element of the 3x3 matrix used to transform Cartesian
coordinates in the ATOM_SITE category to fractional coordinates
in the same category. The axial alignments of this
transformation are described in attribute Cartn_transform_axes.
in category atom_sites The 3x1 translation is defined in
attribute fract_transf_vector[].
in category atom_sites
|x'| |11 12 13| |x| |1|
|y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2|
|z'| |31 32 33| |z| |3|
atom_sites.fract_transf_matrix23
The [2][3] element of the 3x3 matrix used to transform Cartesian
coordinates in the ATOM_SITE category to fractional coordinates
in the same category. The axial alignments of this
transformation are described in attribute Cartn_transform_axes.
in category atom_sites The 3x1 translation is defined in
attribute fract_transf_vector[].
in category atom_sites
|x'| |11 12 13| |x| |1|
|y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2|
|z'| |31 32 33| |z| |3|
atom_sites.fract_transf_matrix31
The [3][1] element of the 3x3 matrix used to transform Cartesian
coordinates in the ATOM_SITE category to fractional coordinates
in the same category. The axial alignments of this
transformation are described in attribute Cartn_transform_axes.
in category atom_sites The 3x1 translation is defined in
attribute fract_transf_vector[].
in category atom_sites
|x'| |11 12 13| |x| |1|
|y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2|
|z'| |31 32 33| |z| |3|
atom_sites.fract_transf_matrix32
The [3][2] element of the 3x3 matrix used to transform Cartesian
coordinates in the ATOM_SITE category to fractional coordinates
in the same category. The axial alignments of this
transformation are described in attribute Cartn_transform_axes.
in category atom_sites The 3x1 translation is defined in
attribute fract_transf_vector[].
in category atom_sites
|x'| |11 12 13| |x| |1|
|y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2|
|z'| |31 32 33| |z| |3|
atom_sites.fract_transf_matrix33
The [3][3] element of the 3x3 matrix used to transform Cartesian
coordinates in the ATOM_SITE category to fractional coordinates
in the same category. The axial alignments of this
transformation are described in attribute Cartn_transform_axes.
in category atom_sites The 3x1 translation is defined in
attribute fract_transf_vector[].
in category atom_sites
|x'| |11 12 13| |x| |1|
|y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2|
|z'| |31 32 33| |z| |3|
atom_sites.fract_transf_vector1
The [1] element of the three-element vector used to transform
Cartesian coordinates in the ATOM_SITE category to fractional
coordinates in the same category. The axial alignments of this
transformation are described in attribute Cartn_transform_axes.
in category atom_sites The 3x3 rotation is defined in
attribute fract_transf_matrix[][].
in category atom_sites
|x'| |11 12 13| |x| |1|
|y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2|
|z'| |31 32 33| |z| |3|
atom_sites.fract_transf_vector2
The [2] element of the three-element vector used to transform
Cartesian coordinates in the ATOM_SITE category to fractional
coordinates in the same category. The axial alignments of this
transformation are described in attribute Cartn_transform_axes.
in category atom_sites The 3x3 rotation is defined in
attribute fract_transf_matrix[][].
in category atom_sites
|x'| |11 12 13| |x| |1|
|y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2|
|z'| |31 32 33| |z| |3|
atom_sites.fract_transf_vector3
The [3] element of the three-element vector used to transform
Cartesian coordinates in the ATOM_SITE category to fractional
coordinates in the same category. The axial alignments of this
transformation are described in attribute Cartn_transform_axes.
in category atom_sites The 3x3 rotation is defined in
attribute fract_transf_matrix[][].
in category atom_sites
|x'| |11 12 13| |x| |1|
|y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2|
|z'| |31 32 33| |z| |3|
difmap
vecmap
heavy
direct
geom
disper
isomor
This code identifies the method used to locate the
hydrogen atoms.
*** This data item would not in general be used in a
macromolecular data block. ***
difmap
vecmap
heavy
direct
geom
disper
isomor
This code identifies the method used to locate the initial
atom sites.
*** This data item would not in general be used in a
macromolecular data block. ***
difmap
vecmap
heavy
direct
geom
disper
isomor
This code identifies the method used to locate the
non-hydrogen-atom sites not found by
attribute solution_primary.
in category atom_sites
*** This data item would not in general be used in a
macromolecular data block. ***
atom_sites.special_details
Additional information about the atomic coordinates not coded
elsewhere in the CIF.
atom_sites.entry_id
This data item is a pointer to attribute id in category entry in the ENTRY category.
0
atom_sites_alt
Data items in the ATOM_SITES_ALT category record details
about the structural ensembles that should be generated from
atom sites or groups of atom sites that are modelled in
alternative conformations in this data block.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:atom_sites_altCategory>
<PDBx:atom_sites_alt id="1">
<PDBx:details> Atom sites with the alternative ID set to 1 have been
modeled in alternative conformations with respect to atom
sites marked with alternative ID 2. The conformations of
amino-acid side chains and solvent atoms with alternative
ID set to 1 correlate with the conformation of the
inhibitor marked with alternative ID 1. They have been
given an occupancy of 0.58 to match the occupancy assigned
to the inhibitor.</PDBx:details>
</PDBx:atom_sites_alt>
<PDBx:atom_sites_alt id="2">
<PDBx:details> Atom sites with the alternative ID set to 2 have been
modeled in alternative conformations with respect to atom
sites marked with alternative ID 1. The conformations of
amino-acid side chains and solvent atoms with alternative
ID set to 2 correlate with the conformation of the
inhibitor marked with alternative ID 2. They have been
given an occupancy of 0.42 to match the occupancy assigned
to the inhibitor.</PDBx:details>
</PDBx:atom_sites_alt>
<PDBx:atom_sites_alt id="3">
<PDBx:details> Atom sites with the alternative ID set to 3 have been
modeled in alternative conformations with respect to
atoms marked with alternative ID 4. The conformations of
amino-acid side chains and solvent atoms with alternative
ID set to 3 do not correlate with the conformation of the
inhibitor. These atom sites have arbitrarily been given
an occupancy of 0.50.</PDBx:details>
</PDBx:atom_sites_alt>
<PDBx:atom_sites_alt id="4">
<PDBx:details> Atom sites with the alternative ID set to 4 have been
modeled in alternative conformations with respect to
atoms marked with alternative ID 3. The conformations of
amino-acid side chains and solvent atoms with alternative
ID set to 4 do not correlate with the conformation of the
inhibitor. These atom sites have arbitrarily been given
an occupancy of 0.50.</PDBx:details>
</PDBx:atom_sites_alt>
</PDBx:atom_sites_altCategory>
0
1
1
atom_sites_altCategory
This property indicates that datablock
has a category holder atom_sites_altCategory.
atom_sites_altCategory
This property indicates that atom_sites_altCategory.
has a category atom_sites_alt.
atom_sites_altItem
Abstract datatype property for atom_sites_alt items.
reference_to_atom_sites_alt
cross-reference to atom_sites_alt.
referenced_by_atom_sites_alt
cross-reference from atom_sites_alt.
atom_sites_alt.details
A description of special aspects of the modelling of atoms in
alternative conformations.
atom_sites_alt.id
The value of attribute id in category atom_sites_alt must uniquely identify
a record in the ATOM_SITES_ALT list.
Note that this item need not be a number; it can be any unique
identifier.
orientation 1
molecule abc
0
atom_sites_alt_ens
Data items in the ATOM_SITES_ALT_ENS category record details
about the ensemble structure generated from atoms with various
alternative conformation IDs.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:atom_sites_alt_ensCategory>
<PDBx:atom_sites_alt_ens id="Ensemble 1-A">
<PDBx:details> The inhibitor binds to the enzyme in two, roughly twofold
symmetric alternative conformations.
This conformational ensemble includes the more populated
conformation of the inhibitor (ID=1) and the amino-acid
side chains and solvent structure that correlate with this
inhibitor conformation.
Also included are one set (ID=3) of side chains with
alternative conformations when the conformations are not
correlated with the inhibitor conformation.</PDBx:details>
</PDBx:atom_sites_alt_ens>
<PDBx:atom_sites_alt_ens id="Ensemble 1-B">
<PDBx:details> The inhibitor binds to the enzyme in two, roughly twofold
symmetric alternative conformations.
This conformational ensemble includes the more populated
conformation of the inhibitor (ID=1) and the amino-acid
side chains and solvent structure that correlate with
this inhibitor conformation.
Also included are one set (ID=4) of side chains with
alternative conformations when the conformations are not
correlated with the inhibitor conformation.</PDBx:details>
</PDBx:atom_sites_alt_ens>
<PDBx:atom_sites_alt_ens id="Ensemble 2-A">
<PDBx:details> The inhibitor binds to the enzyme in two, roughly twofold
symmetric alternative conformations.
This conformational ensemble includes the less populated
conformation of the inhibitor (ID=2) and the amino-acid
side chains and solvent structure that correlate with this
inhibitor conformation.
Also included are one set (ID=3) of side chains with
alternative conformations when the conformations are not
correlated with the inhibitor conformation.</PDBx:details>
</PDBx:atom_sites_alt_ens>
<PDBx:atom_sites_alt_ens id="Ensemble 2-B">
<PDBx:details> The inhibitor binds to the enzyme in two, roughly twofold
symmetric alternative conformations.
This conformational ensemble includes the less populated
conformation of the inhibitor (ID=2) and the amino-acid
side chains and solvent structure that correlate with this
inhibitor conformation.
Also included are one set (ID=4) of side chains with
alternative conformations when the conformations are not
correlated with the inhibitor conformation.</PDBx:details>
</PDBx:atom_sites_alt_ens>
</PDBx:atom_sites_alt_ensCategory>
0
1
1
atom_sites_alt_ensCategory
This property indicates that datablock
has a category holder atom_sites_alt_ensCategory.
atom_sites_alt_ensCategory
This property indicates that atom_sites_alt_ensCategory.
has a category atom_sites_alt_ens.
atom_sites_alt_ensItem
Abstract datatype property for atom_sites_alt_ens items.
reference_to_atom_sites_alt_ens
cross-reference to atom_sites_alt_ens.
referenced_by_atom_sites_alt_ens
cross-reference from atom_sites_alt_ens.
atom_sites_alt_ens.details
A description of special aspects of the ensemble structure
generated from atoms with various alternative IDs.
atom_sites_alt_ens.id
The value of attribute id in category atom_sites_alt_ens must uniquely identify a
record in the ATOM_SITES_ALT_ENS list.
Note that this item need not be a number; it can be any unique
identifier.
0
atom_sites_alt_gen
Data items in the ATOM_SITES_ALT_GEN category record details
about the interpretation of multiple conformations in the
structure.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:atom_sites_alt_genCategory>
<PDBx:atom_sites_alt_gen alt_id="1" ens_id="Ensemble 1-A"></PDBx:atom_sites_alt_gen>
<PDBx:atom_sites_alt_gen alt_id="2" ens_id="Ensemble 1-A"></PDBx:atom_sites_alt_gen>
<PDBx:atom_sites_alt_gen alt_id="1" ens_id="Ensemble 1-B"></PDBx:atom_sites_alt_gen>
<PDBx:atom_sites_alt_gen alt_id="4" ens_id="Ensemble 1-B"></PDBx:atom_sites_alt_gen>
<PDBx:atom_sites_alt_gen alt_id="2" ens_id="Ensemble 2-A"></PDBx:atom_sites_alt_gen>
<PDBx:atom_sites_alt_gen alt_id="3" ens_id="Ensemble 2-A"></PDBx:atom_sites_alt_gen>
<PDBx:atom_sites_alt_gen alt_id="2" ens_id="Ensemble 2-B"></PDBx:atom_sites_alt_gen>
<PDBx:atom_sites_alt_gen alt_id="4" ens_id="Ensemble 2-B"></PDBx:atom_sites_alt_gen>
</PDBx:atom_sites_alt_genCategory>
1
1
atom_sites_alt_genCategory
This property indicates that datablock
has a category holder atom_sites_alt_genCategory.
atom_sites_alt_genCategory
This property indicates that atom_sites_alt_genCategory.
has a category atom_sites_alt_gen.
atom_sites_alt_genItem
Abstract datatype property for atom_sites_alt_gen items.
reference_to_atom_sites_alt_gen
cross-reference to atom_sites_alt_gen.
referenced_by_atom_sites_alt_gen
cross-reference from atom_sites_alt_gen.
atom_sites_alt_gen.alt_id
This data item is a pointer to attribute id in category atom_sites_alt in the
ATOM_SITES_ALT category.
atom_sites_alt_gen.ens_id
This data item is a pointer to attribute id in category atom_sites_alt_ens in the
ATOM_SITES_ALT_ENS category.
0
atom_sites_footnote
Data items in the ATOM_SITES_FOOTNOTE category record detailed
comments about an atom site or a group of atom sites.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:atom_sites_footnoteCategory>
<PDBx:atom_sites_footnote id="1">
<PDBx:text> The inhibitor binds to the enzyme in two alternative
orientations. The two orientations have been assigned
alternative IDs *1* and *2*.</PDBx:text>
</PDBx:atom_sites_footnote>
<PDBx:atom_sites_footnote id="2">
<PDBx:text> Side chains of these residues adopt alternative
orientations that correlate with the alternative
orientations of the inhibitor.
Side chains with alternative ID *1* and occupancy 0.58
correlate with inhibitor orientation *1*.
Side chains with alternative ID *2* and occupancy 0.42
correlate with inhibitor orientation *2*.</PDBx:text>
</PDBx:atom_sites_footnote>
<PDBx:atom_sites_footnote id="3">
<PDBx:text> The positions of these water molecules correlate with
the alternative orientations of the inhibitor.
Water molecules with alternative ID *1* and occupancy 0.58
correlate with inhibitor orientation *1*.
Water molecules with alternative ID *2* and occupancy 0.42
correlate with inhibitor orientation *2*.</PDBx:text>
</PDBx:atom_sites_footnote>
<PDBx:atom_sites_footnote id="4">
<PDBx:text> Side chains of these residues adopt alternative
orientations that do not correlate with the alternative
orientation of the inhibitor.</PDBx:text>
</PDBx:atom_sites_footnote>
<PDBx:atom_sites_footnote id="5">
<PDBx:text> The positions of these water molecules correlate with
alternative orientations of amino-acid side chains that
do not correlate with alternative orientations of the
inhibitor.</PDBx:text>
</PDBx:atom_sites_footnote>
</PDBx:atom_sites_footnoteCategory>
0
1
1
atom_sites_footnoteCategory
This property indicates that datablock
has a category holder atom_sites_footnoteCategory.
atom_sites_footnoteCategory
This property indicates that atom_sites_footnoteCategory.
has a category atom_sites_footnote.
atom_sites_footnoteItem
Abstract datatype property for atom_sites_footnote items.
reference_to_atom_sites_footnote
cross-reference to atom_sites_footnote.
referenced_by_atom_sites_footnote
cross-reference from atom_sites_footnote.
atom_sites_footnote.text
The text of the footnote. Footnotes are used to describe
an atom site or a group of atom sites in the ATOM_SITE list.
For example, footnotes may be used to indicate atoms for which
the electron density is very weak, or atoms for which static
disorder has been modelled.
atom_sites_footnote.id
A code that identifies the footnote.
a
b
1
2
0
atom_type
Data items in the ATOM_TYPE category record details about the
properties of the atoms that occupy the atom sites, such as the
atomic scattering factors.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:atom_typeCategory>
<PDBx:atom_type symbol="C">
<PDBx:oxidation_number>0</PDBx:oxidation_number>
<PDBx:scat_Cromer_Mann_a1>2.31000</PDBx:scat_Cromer_Mann_a1>
<PDBx:scat_Cromer_Mann_a2>1.58860</PDBx:scat_Cromer_Mann_a2>
<PDBx:scat_Cromer_Mann_a3>1.02000</PDBx:scat_Cromer_Mann_a3>
<PDBx:scat_Cromer_Mann_a4>0.865000</PDBx:scat_Cromer_Mann_a4>
<PDBx:scat_Cromer_Mann_b1>20.8439</PDBx:scat_Cromer_Mann_b1>
<PDBx:scat_Cromer_Mann_b2>0.568700</PDBx:scat_Cromer_Mann_b2>
<PDBx:scat_Cromer_Mann_b3>10.2075</PDBx:scat_Cromer_Mann_b3>
<PDBx:scat_Cromer_Mann_b4>51.6512</PDBx:scat_Cromer_Mann_b4>
<PDBx:scat_Cromer_Mann_c>0.21560</PDBx:scat_Cromer_Mann_c>
</PDBx:atom_type>
<PDBx:atom_type symbol="N">
<PDBx:oxidation_number>0</PDBx:oxidation_number>
<PDBx:scat_Cromer_Mann_a1>12.2126</PDBx:scat_Cromer_Mann_a1>
<PDBx:scat_Cromer_Mann_a2>3.13220</PDBx:scat_Cromer_Mann_a2>
<PDBx:scat_Cromer_Mann_a3>2.01250</PDBx:scat_Cromer_Mann_a3>
<PDBx:scat_Cromer_Mann_a4>1.166300</PDBx:scat_Cromer_Mann_a4>
<PDBx:scat_Cromer_Mann_b1>0.005700</PDBx:scat_Cromer_Mann_b1>
<PDBx:scat_Cromer_Mann_b2>9.893300</PDBx:scat_Cromer_Mann_b2>
<PDBx:scat_Cromer_Mann_b3>28.9975</PDBx:scat_Cromer_Mann_b3>
<PDBx:scat_Cromer_Mann_b4>0.582600</PDBx:scat_Cromer_Mann_b4>
<PDBx:scat_Cromer_Mann_c>-11.529</PDBx:scat_Cromer_Mann_c>
</PDBx:atom_type>
<PDBx:atom_type symbol="O">
<PDBx:oxidation_number>0</PDBx:oxidation_number>
<PDBx:scat_Cromer_Mann_a1>3.04850</PDBx:scat_Cromer_Mann_a1>
<PDBx:scat_Cromer_Mann_a2>2.28680</PDBx:scat_Cromer_Mann_a2>
<PDBx:scat_Cromer_Mann_a3>1.54630</PDBx:scat_Cromer_Mann_a3>
<PDBx:scat_Cromer_Mann_a4>0.867000</PDBx:scat_Cromer_Mann_a4>
<PDBx:scat_Cromer_Mann_b1>13.2771</PDBx:scat_Cromer_Mann_b1>
<PDBx:scat_Cromer_Mann_b2>5.70110</PDBx:scat_Cromer_Mann_b2>
<PDBx:scat_Cromer_Mann_b3>0.323900</PDBx:scat_Cromer_Mann_b3>
<PDBx:scat_Cromer_Mann_b4>32.9089</PDBx:scat_Cromer_Mann_b4>
<PDBx:scat_Cromer_Mann_c>0.250800</PDBx:scat_Cromer_Mann_c>
</PDBx:atom_type>
<PDBx:atom_type symbol="S">
<PDBx:oxidation_number>0</PDBx:oxidation_number>
<PDBx:scat_Cromer_Mann_a1>6.90530</PDBx:scat_Cromer_Mann_a1>
<PDBx:scat_Cromer_Mann_a2>5.20340</PDBx:scat_Cromer_Mann_a2>
<PDBx:scat_Cromer_Mann_a3>1.58630</PDBx:scat_Cromer_Mann_a3>
<PDBx:scat_Cromer_Mann_a4>1.43790</PDBx:scat_Cromer_Mann_a4>
<PDBx:scat_Cromer_Mann_b1>1.46790</PDBx:scat_Cromer_Mann_b1>
<PDBx:scat_Cromer_Mann_b2>22.2151</PDBx:scat_Cromer_Mann_b2>
<PDBx:scat_Cromer_Mann_b3>56.1720</PDBx:scat_Cromer_Mann_b3>
<PDBx:scat_Cromer_Mann_b4>0.253600</PDBx:scat_Cromer_Mann_b4>
<PDBx:scat_Cromer_Mann_c>0.866900</PDBx:scat_Cromer_Mann_c>
</PDBx:atom_type>
<PDBx:atom_type symbol="CL">
<PDBx:oxidation_number>-1</PDBx:oxidation_number>
<PDBx:scat_Cromer_Mann_a1>18.2915</PDBx:scat_Cromer_Mann_a1>
<PDBx:scat_Cromer_Mann_a2>7.20840</PDBx:scat_Cromer_Mann_a2>
<PDBx:scat_Cromer_Mann_a3>6.53370</PDBx:scat_Cromer_Mann_a3>
<PDBx:scat_Cromer_Mann_a4>2.33860</PDBx:scat_Cromer_Mann_a4>
<PDBx:scat_Cromer_Mann_b1>0.006600</PDBx:scat_Cromer_Mann_b1>
<PDBx:scat_Cromer_Mann_b2>1.17170</PDBx:scat_Cromer_Mann_b2>
<PDBx:scat_Cromer_Mann_b3>19.5424</PDBx:scat_Cromer_Mann_b3>
<PDBx:scat_Cromer_Mann_b4>60.4486</PDBx:scat_Cromer_Mann_b4>
<PDBx:scat_Cromer_Mann_c>-16.378</PDBx:scat_Cromer_Mann_c>
</PDBx:atom_type>
</PDBx:atom_typeCategory>
Example 2 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
<PDBx:atom_typeCategory>
<PDBx:atom_type symbol="C">
<PDBx:number_in_cell>72</PDBx:number_in_cell>
<PDBx:oxidation_number>0</PDBx:oxidation_number>
<PDBx:scat_dispersion_imag>.009</PDBx:scat_dispersion_imag>
<PDBx:scat_dispersion_real>.017</PDBx:scat_dispersion_real>
<PDBx:scat_source>International_Tables_Vol_IV_Table_2.2B</PDBx:scat_source>
</PDBx:atom_type>
<PDBx:atom_type symbol="H">
<PDBx:number_in_cell>100</PDBx:number_in_cell>
<PDBx:oxidation_number>0</PDBx:oxidation_number>
<PDBx:scat_dispersion_imag>0</PDBx:scat_dispersion_imag>
<PDBx:scat_dispersion_real>0</PDBx:scat_dispersion_real>
<PDBx:scat_source>International_Tables_Vol_IV_Table_2.2B</PDBx:scat_source>
</PDBx:atom_type>
<PDBx:atom_type symbol="O">
<PDBx:number_in_cell>12</PDBx:number_in_cell>
<PDBx:oxidation_number>0</PDBx:oxidation_number>
<PDBx:scat_dispersion_imag>.032</PDBx:scat_dispersion_imag>
<PDBx:scat_dispersion_real>.047</PDBx:scat_dispersion_real>
<PDBx:scat_source>International_Tables_Vol_IV_Table_2.2B</PDBx:scat_source>
</PDBx:atom_type>
<PDBx:atom_type symbol="N">
<PDBx:number_in_cell>4</PDBx:number_in_cell>
<PDBx:oxidation_number>0</PDBx:oxidation_number>
<PDBx:scat_dispersion_imag>.018</PDBx:scat_dispersion_imag>
<PDBx:scat_dispersion_real>.029</PDBx:scat_dispersion_real>
<PDBx:scat_source>International_Tables_Vol_IV_Table_2.2B</PDBx:scat_source>
</PDBx:atom_type>
</PDBx:atom_typeCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
atom_typeCategory
This property indicates that datablock
has a category holder atom_typeCategory.
atom_typeCategory
This property indicates that atom_typeCategory.
has a category atom_type.
atom_typeItem
Abstract datatype property for atom_type items.
reference_to_atom_type
cross-reference to atom_type.
referenced_by_atom_type
cross-reference from atom_type.
atom_type.analytical_mass_percent
Mass percentage of this atom type derived from chemical analysis.
atom_type.description
A description of the atom(s) designated by this atom type. In
most cases, this is the element name and oxidation state of
a single atom species. For disordered or nonstoichiometric
structures it will describe a combination of atom species.
deuterium
0.34Fe+0.66Ni
atom_type.number_in_cell
Total number of atoms of this atom type in the unit cell.
atom_type.oxidation_number
Formal oxidation state of this atom type in the structure.
atom_type.pdbx_N_electrons
Number of electrons in atom used in scattering factor
atom_type.pdbx_scat_Cromer_Mann_a5
Scattering-factor coefficient a5, used to calculate electron
elastic atomic scattering factors for the defined atom type.
Electron Elastic Scattering Factors Ref:
International Tables for X-ray Crystallography (2006).
Vol. C, Table 4.3.2.2, pp. 282-283.
Cromer_Mann equation Ref:
International Tables for X-ray Crystallography (1974).
Vol. IV, Table 2.2B
or: International Tables for Crystallography (2004). Vol. C,
Tables 6.1.1.4 and 6.1.1.5.
atom_type.pdbx_scat_Cromer_Mann_a6
Scattering-factor coefficient a6, used to calculate electron
elastic atomic scattering factors for the defined atom type.
Electron Elastic Scattering Factors Ref:
International Tables for X-ray Crystallography (2006).
Vol. C, Table 4.3.2.2, pp. 282-283.
Cromer_Mann equation Ref:
International Tables for X-ray Crystallography (1974).
Vol. IV, Table 2.2B
or: International Tables for Crystallography (2004). Vol. C,
Tables 6.1.1.4 and 6.1.1.5.
atom_type.pdbx_scat_Cromer_Mann_b5
Scattering-factor coefficient b5, used to calculate electron
elastic atomic scattering factors for the defined atom type.
Electron Elastic Scattering Factors Ref:
International Tables for X-ray Crystallography (2006).
Vol. C, Table 4.3.2.2, pp. 282-283.
Cromer_Mann equation Ref:
International Tables for X-ray Crystallography (1974).
Vol. IV, Table 2.2B
or: International Tables for Crystallography (2004). Vol. C,
Tables 6.1.1.4 and 6.1.1.5.
atom_type.pdbx_scat_Cromer_Mann_b6
Scattering-factor coefficient b6, used to calculate electron
elastic atomic scattering factors for the defined atom type.
Electron Elastic Scattering Factors Ref:
International Tables for X-ray Crystallography (2006).
Vol. C, Table 4.3.2.2, pp. 282-283.
Cromer_Mann equation Ref:
International Tables for X-ray Crystallography (1974).
Vol. IV, Table 2.2B
or: International Tables for Crystallography (2004). Vol. C,
Tables 6.1.1.4 and 6.1.1.5.
atom_type.pdbx_scat_Z
Atomic number of atom in scattering amplitude.
atom_type.radius_bond
The effective intramolecular bonding radius in angstroms
of this atom type.
atom_type.radius_contact
The effective intermolecular bonding radius in angstroms
of this atom type.
atom_type.scat_Cromer_Mann_a1
The Cromer-Mann scattering-factor coefficient a1 used to
calculate the scattering factors for this atom type.
Ref: International Tables for X-ray Crystallography (1974).
Vol. IV, Table 2.2B
or: International Tables for Crystallography (2004). Vol. C,
Tables 6.1.1.4 and 6.1.1.5.
atom_type.scat_Cromer_Mann_a2
The Cromer-Mann scattering-factor coefficient a2 used to
calculate the scattering factors for this atom type.
Ref: International Tables for X-ray Crystallography (1974).
Vol. IV, Table 2.2B
or: International Tables for Crystallography (2004). Vol. C,
Tables 6.1.1.4 and 6.1.1.5.
atom_type.scat_Cromer_Mann_a3
The Cromer-Mann scattering-factor coefficient a3 used to
calculate the scattering factors for this atom type.
Ref: International Tables for X-ray Crystallography (1974).
Vol. IV, Table 2.2B
or: International Tables for Crystallography (2004). Vol. C,
Tables 6.1.1.4 and 6.1.1.5.
atom_type.scat_Cromer_Mann_a4
The Cromer-Mann scattering-factor coefficient a4 used to
calculate the scattering factors for this atom type.
Ref: International Tables for X-ray Crystallography (1974).
Vol. IV, Table 2.2B
or: International Tables for Crystallography (2004). Vol. C,
Tables 6.1.1.4 and 6.1.1.5.
atom_type.scat_Cromer_Mann_b1
The Cromer-Mann scattering-factor coefficient b1 used to
calculate the scattering factors for this atom type.
Ref: International Tables for X-ray Crystallography (1974).
Vol. IV, Table 2.2B
or: International Tables for Crystallography (2004). Vol. C,
Tables 6.1.1.4 and 6.1.1.5.
atom_type.scat_Cromer_Mann_b2
The Cromer-Mann scattering-factor coefficient b2 used to
calculate the scattering factors for this atom type.
Ref: International Tables for X-ray Crystallography (1974).
Vol. IV, Table 2.2B
or: International Tables for Crystallography (2004). Vol. C,
Tables 6.1.1.4 and 6.1.1.5.
atom_type.scat_Cromer_Mann_b3
The Cromer-Mann scattering-factor coefficient b3 used to
calculate the scattering factors for this atom type.
Ref: International Tables for X-ray Crystallography (1974).
Vol. IV, Table 2.2B
or: International Tables for Crystallography (2004). Vol. C,
Tables 6.1.1.4 and 6.1.1.5.
atom_type.scat_Cromer_Mann_b4
The Cromer-Mann scattering-factor coefficient b4 used to
calculate the scattering factors for this atom type.
Ref: International Tables for X-ray Crystallography (1974).
Vol. IV, Table 2.2B
or: International Tables for Crystallography (2004). Vol. C,
Tables 6.1.1.4 and 6.1.1.5.
atom_type.scat_Cromer_Mann_c
The Cromer-Mann scattering-factor coefficient c used to
calculate the scattering factors for this atom type.
Ref: International Tables for X-ray Crystallography (1974).
Vol. IV, Table 2.2B
or: International Tables for Crystallography (2004). Vol. C,
Tables 6.1.1.4 and 6.1.1.5.
atom_type.scat_dispersion_imag
The imaginary component of the anomalous-dispersion
scattering factor, f'', in electrons for this atom type and
the radiation identified by attribute id in category diffrn_radiation_wavelength.
atom_type.scat_dispersion_real
The real component of the anomalous-dispersion
scattering factor, f', in electrons for this atom type and
the radiation identified by attribute id in category diffrn_radiation_wavelength.
atom_type.scat_dispersion_source
Reference to the source of the real and imaginary dispersion
corrections for scattering factors used for this atom type.
International Tables Vol. IV Table 2.3.1
atom_type.scat_length_neutron
The bound coherent scattering length in femtometres for the
atom type at the isotopic composition used for the diffraction
experiment.
atom_type.scat_source
Reference to the source of the scattering factors or scattering
lengths used for this atom type.
International Tables Vol. IV Table 2.4.6B
atom_type.scat_versus_stol_list
A table of scattering factors as a function of sin theta over
lambda. This table should be well commented to indicate the
items present. Regularly formatted lists are strongly
recommended.
atom_type.symbol
The code used to identify the atom species (singular or plural)
representing this atom type. Normally this code is the element
symbol. The code may be composed of any character except
an underscore with the additional proviso that digits designate
an oxidation state and must be followed by a + or - character.
C
Cu2+
H(SDS)
dummy
FeNi
0
audit
Data items in the AUDIT category record details about the
creation and subsequent updating of the data block.
Note that these items apply only to the creation and updating of
the data block, and should not be confused with the data items
in the JOURNAL category that record different stages in the
publication of the material in the data block.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:auditCategory>
<PDBx:audit revision_id="1">
<PDBx:creation_date>1992-12-08</PDBx:creation_date>
<PDBx:creation_method> Created by hand from PDB entry 5HVP, from the J. Biol.
Chem. paper describing this structure and from
laboratory records</PDBx:creation_method>
<PDBx:update_record> 1992-12-09 adjusted to reflect comments from B. McKeever
1992-12-10 adjusted to reflect comments from H. Berman
1992-12-12 adjusted to reflect comments from K. Watenpaugh</PDBx:update_record>
</PDBx:audit>
</PDBx:auditCategory>
Example 2 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
<PDBx:auditCategory>
<PDBx:audit revision_id="2">
<PDBx:creation_date>1991-03-20</PDBx:creation_date>
<PDBx:creation_method>from_xtal_archive_file_using_CIFIO</PDBx:creation_method>
<PDBx:update_record> 1991-04-09 text and data added by Tony Willis.
1991-04-15 rec'd by co-editor as manuscript HL0007.
1991-04-17 adjustments based on first referee report.
1991-04-18 adjustments based on second referee report.</PDBx:update_record>
</PDBx:audit>
</PDBx:auditCategory>
0
1
0
1
0
1
1
auditCategory
This property indicates that datablock
has a category holder auditCategory.
auditCategory
This property indicates that auditCategory.
has a category audit.
auditItem
Abstract datatype property for audit items.
reference_to_audit
cross-reference to audit.
referenced_by_audit
cross-reference from audit.
audit.creation_date
A date that the data block was created. The date format is
yyyy-mm-dd.
1990-07-12
audit.creation_method
A description of how data were entered into the data block.
spawned by the program QBEE
audit.update_record
A record of any changes to the data block. The update format is
a date (yyyy-mm-dd) followed by a description of the changes.
The latest update entry is added to the bottom of this record.
1990-07-15 Updated by the Co-editor
audit.revision_id
The value of attribute revision_id in category audit must uniquely identify a record
in the AUDIT list.
rev1
0
audit_author
Data items in the AUDIT_AUTHOR category record details about
the author(s) of the data block.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:audit_authorCategory>
<PDBx:audit_author pdbx_ordinal="1">
<PDBx:address> Department of Biophysical Chemistry
Merck Research Laboratories
P. O. Box 2000, Ry80M203
Rahway, New Jersey 07065
USA</PDBx:address>
<PDBx:name>Fitzgerald, Paula M.D.</PDBx:name>
</PDBx:audit_author>
<PDBx:audit_author pdbx_ordinal="2">
<PDBx:address> Department of Biophysical Chemistry
Merck Research Laboratories
P. O. Box 2000, Ry80M203
Rahway, New Jersey 07065
USA</PDBx:address>
<PDBx:name>McKeever, Brian M.</PDBx:name>
</PDBx:audit_author>
<PDBx:audit_author pdbx_ordinal="3">
<PDBx:address> Department of Biophysical Chemistry
Merck Research Laboratories
P. O. Box 2000, Ry80M203
Rahway, New Jersey 07065
USA</PDBx:address>
<PDBx:name>Van Middlesworth, J.F.</PDBx:name>
</PDBx:audit_author>
<PDBx:audit_author pdbx_ordinal="4">
<PDBx:address> Department of Biophysical Chemistry
Merck Research Laboratories
P. O. Box 2000, Ry80M203
Rahway, New Jersey 07065
USA</PDBx:address>
<PDBx:name>Springer, James P.</PDBx:name>
</PDBx:audit_author>
</PDBx:audit_authorCategory>
0
1
0
1
1
1
1
audit_authorCategory
This property indicates that datablock
has a category holder audit_authorCategory.
audit_authorCategory
This property indicates that audit_authorCategory.
has a category audit_author.
audit_authorItem
Abstract datatype property for audit_author items.
reference_to_audit_author
cross-reference to audit_author.
referenced_by_audit_author
cross-reference from audit_author.
audit_author.address
The address of an author of this data block. If there are
multiple authors, attribute address in category audit_author is looped with
attribute name in category audit_author.
Department
Institute
Street
City and postcode
COUNTRY
audit_author.identifier_ORCID
The Open Researcher and Contributor ID (ORCID).
0000-0002-6681-547X
audit_author.name
The name of an author of this data block. If there are multiple
authors, _audit_author.name is looped with _audit_author.address.
The family name(s), followed by a comma and including any
dynastic components, precedes the first name(s) or initial(s).
Bleary, Percival R.
O'Neil, F.K.
Van den Bossche, G.
Yang, D.-L.
Simonov, Yu.A
audit_author.pdbx_ordinal
This data item defines the order of the author's name in the
list of audit authors.
1
2
3
0
audit_conform
Data items in the AUDIT_CONFORM category describe the
dictionary versions against which the data names appearing in
the current data block are conformant.
Example 1 - any file conforming to the current CIF core dictionary.
<PDBx:audit_conformCategory>
<PDBx:audit_conform dict_name="cif_core.dic" dict_version="2.3.1">
<PDBx:dict_location>ftp://ftp.iucr.org/pub/cif_core.2.3.1.dic</PDBx:dict_location>
</PDBx:audit_conform>
</PDBx:audit_conformCategory>
0
1
1
1
audit_conformCategory
This property indicates that datablock
has a category holder audit_conformCategory.
audit_conformCategory
This property indicates that audit_conformCategory.
has a category audit_conform.
audit_conformItem
Abstract datatype property for audit_conform items.
reference_to_audit_conform
cross-reference to audit_conform.
referenced_by_audit_conform
cross-reference from audit_conform.
audit_conform.dict_location
A file name or uniform resource locator (URL) for the
dictionary to which the current data block conforms.
audit_conform.dict_name
The string identifying the highest-level dictionary defining
data names used in this file.
audit_conform.dict_version
The version number of the dictionary to which the current
data block conforms.
0
audit_contact_author
Data items in the AUDIT_CONTACT_AUTHOR category record details
about the name and address of the author to be contacted
concerning the content of this data block.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:audit_contact_authorCategory>
<PDBx:audit_contact_author name="Fitzgerald, Paula M.D.">
<PDBx:address> Department of Biophysical Chemistry
Merck Research Laboratories
PO Box 2000, Ry80M203
Rahway, New Jersey 07065
USA</PDBx:address>
<PDBx:email>paula_fitzgerald@merck.com</PDBx:email>
<PDBx:fax>1(908)5946645</PDBx:fax>
<PDBx:phone>1(908)5945510</PDBx:phone>
</PDBx:audit_contact_author>
</PDBx:audit_contact_authorCategory>
0
1
0
1
0
1
0
1
1
audit_contact_authorCategory
This property indicates that datablock
has a category holder audit_contact_authorCategory.
audit_contact_authorCategory
This property indicates that audit_contact_authorCategory.
has a category audit_contact_author.
audit_contact_authorItem
Abstract datatype property for audit_contact_author items.
reference_to_audit_contact_author
cross-reference to audit_contact_author.
referenced_by_audit_contact_author
cross-reference from audit_contact_author.
audit_contact_author.address
The mailing address of the author of the data block to whom
correspondence should be addressed.
Department
Institute
Street
City and postcode
COUNTRY
audit_contact_author.email
The electronic mail address of the author of the data block to
whom correspondence should be addressed, in a form recognizable
to international networks. The format of e-mail
addresses is given in Section 3.4, Address Specification, of
Internet Message Format, RFC 2822, P. Resnick (Editor),
Network Standards Group, April 2001.
name@host.domain.country
bm@iucr.org
audit_contact_author.fax
The facsimile telephone number of the author of the data
block to whom correspondence should be addressed.
The recommended style starts with the international dialing
prefix, followed by the area code in parentheses, followed by the
local number with no spaces.
12(34)9477334
12()349477334
audit_contact_author.phone
The telephone number of the author of the data block to whom
correspondence should be addressed.
The recommended style starts with the international dialing
prefix, followed by the area code in parentheses, followed by the
local number and any extension number prefixed by 'x',
with no spaces.
12(34)9477330
12()349477330
12(34)9477330x5543
audit_contact_author.name
The name of the author of the data block to whom correspondence
should be addressed.
The family name(s), followed by a comma and including any
dynastic components, precedes the first name(s) or initial(s).
Bleary, Percival R.
O'Neil, F.K.
Van den Bossche, G.
Yang, D.-L.
Simonov, Yu.A
0
audit_link
Data items in the AUDIT_LINK category record details about the
relationships between data blocks in the current CIF.
Example 1 - multiple structure paper, as illustrated
in A Guide to CIF for Authors (1995). IUCr: Chester.
<PDBx:audit_linkCategory>
<PDBx:audit_link block_code="morA_pub" block_description="discursive text of paper with two structures"></PDBx:audit_link>
<PDBx:audit_link block_code="morA_(1)" block_description="structure 1 of 2"></PDBx:audit_link>
<PDBx:audit_link block_code="morA_(2)" block_description="structure 2 of 2"></PDBx:audit_link>
</PDBx:audit_linkCategory>
Example 2 - example file for the one-dimensional incommensurately
modulated structure of K~2~SeO~4~.
<PDBx:audit_linkCategory>
<PDBx:audit_link block_code="KSE_PUB" block_description="publication details"></PDBx:audit_link>
<PDBx:audit_link block_code="KSE_COM" block_description="experimental data common to ref./mod. structures"></PDBx:audit_link>
<PDBx:audit_link block_code="KSE_REF" block_description="reference structure"></PDBx:audit_link>
<PDBx:audit_link block_code="KSE_MOD" block_description="modulated structure"></PDBx:audit_link>
</PDBx:audit_linkCategory>
1
1
audit_linkCategory
This property indicates that datablock
has a category holder audit_linkCategory.
audit_linkCategory
This property indicates that audit_linkCategory.
has a category audit_link.
audit_linkItem
Abstract datatype property for audit_link items.
reference_to_audit_link
cross-reference to audit_link.
referenced_by_audit_link
cross-reference from audit_link.
audit_link.block_code
The value of attribute code in category audit_block associated with a data block
in the current file related to the current data block. The
special value '.' may be used to refer to the current data
block for completeness.
audit_link.block_description
A textual description of the relationship of the referenced
data block to the current one.
0
cell
Data items in the CELL category record details about the
crystallographic cell parameters.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:cellCategory>
<PDBx:cell entry_id="5HVP">
<PDBx:angle_alpha>90.00</PDBx:angle_alpha>
<PDBx:angle_beta>90.00</PDBx:angle_beta>
<PDBx:angle_gamma>90.00</PDBx:angle_gamma>
<PDBx:details> The cell parameters were refined every twenty frames during
data integration. The cell lengths given are the mean of
55 such refinements; the esds given are the root mean
square deviations of these 55 observations from that mean.</PDBx:details>
<PDBx:length_a>58.39</PDBx:length_a>
<PDBx:length_a_esd>0.05</PDBx:length_a_esd>
<PDBx:length_b>86.70</PDBx:length_b>
<PDBx:length_b_esd>0.12</PDBx:length_b_esd>
<PDBx:length_c>46.27</PDBx:length_c>
<PDBx:length_c_esd>0.06</PDBx:length_c_esd>
<PDBx:volume>234237</PDBx:volume>
</PDBx:cell>
</PDBx:cellCategory>
Example 2 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
<PDBx:cellCategory>
<PDBx:cell entry_id="1TOZ">
<PDBx:angle_alpha>90.0</PDBx:angle_alpha>
<PDBx:angle_beta>90.0</PDBx:angle_beta>
<PDBx:angle_gamma>90.0</PDBx:angle_gamma>
<PDBx:length_a>5.959</PDBx:length_a>
<PDBx:length_a_esd>0.001</PDBx:length_a_esd>
<PDBx:length_b>14.956</PDBx:length_b>
<PDBx:length_b_esd>0.001</PDBx:length_b_esd>
<PDBx:length_c>19.737</PDBx:length_c>
<PDBx:length_c_esd>0.003</PDBx:length_c_esd>
<PDBx:volume>1759.0</PDBx:volume>
<PDBx:volume_esd>0.3</PDBx:volume_esd>
</PDBx:cell>
</PDBx:cellCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
cellCategory
This property indicates that datablock
has a category holder cellCategory.
cellCategory
This property indicates that cellCategory.
has a category cell.
cellItem
Abstract datatype property for cell items.
reference_to_cell
cross-reference to cell.
referenced_by_cell
cross-reference from cell.
cell.Z_PDB
The number of the polymeric chains in a unit cell. In the case
of heteropolymers, Z is the number of occurrences of the most
populous chain.
This data item is provided for compatibility with the original
Protein Data Bank format, and only for that purpose.
cell.angle_alpha
Unit-cell angle alpha of the reported structure in degrees.
cell.angle_alpha_esd
The standard uncertainty (estimated standard deviation)
of attribute angle_alpha in category cell.
cell.angle_beta
Unit-cell angle beta of the reported structure in degrees.
cell.angle_beta_esd
The standard uncertainty (estimated standard deviation)
of attribute angle_beta in category cell.
cell.angle_gamma
Unit-cell angle gamma of the reported structure in degrees.
cell.angle_gamma_esd
The standard uncertainty (estimated standard deviation)
of attribute angle_gamma in category cell.
cell.details
A description of special aspects of the cell choice, noting
possible alternative settings.
pseudo-orthorhombic
standard setting from 45 deg rotation around c
cell.formula_units_Z
The number of the formula units in the unit cell as specified
by _chemical_formula.structural, _chemical_formula.moiety or
attribute sum in category chemical_formula.
cell.length_a
Unit-cell length a corresponding to the structure reported in
angstroms.
cell.length_a_esd
The standard uncertainty (estimated standard deviation)
of attribute length_a in category cell.
cell.length_b
Unit-cell length b corresponding to the structure reported in
angstroms.
cell.length_b_esd
The standard uncertainty (estimated standard deviation)
of attribute length_b in category cell.
cell.length_c
Unit-cell length c corresponding to the structure reported in
angstroms.
cell.length_c_esd
The standard uncertainty (estimated standard deviation)
of attribute length_c in category cell.
single crystal
window
scan varying
propagated
population
refined
How the estimated standard deviation was determined.
cell.pdbx_unique_axis
To further identify unique axis if necessary. E.g., P 21 with
an unique C axis will have 'C' in this field.
cell.reciprocal_angle_alpha
The angle (recip-alpha) defining the reciprocal cell in degrees.
(recip-alpha), (recip-alpha) and (recip-alpha) related to the
angles in the real cell by:
cos(recip-alpha)
= [cos(beta)*cos(gamma) - cos(alpha)]/[sin(beta)*sin(gamma)]
cos(recip-beta)
= [cos(gamma)*cos(alpha) - cos(beta)]/[sin(gamma)*sin(alpha)]
cos(recip-gamma)
= [cos(alpha)*cos(beta) - cos(gamma)]/[sin(alpha)*sin(beta)]
Ref: Buerger, M. J. (1942). X-ray Crystallography, p. 360.
New York: John Wiley & Sons Inc.
cell.reciprocal_angle_alpha_esd
The estimated standard deviation of attribute reciprocal_angle_alpha in category cell.
cell.reciprocal_angle_beta
The angle (recip-beta) defining the reciprocal cell in degrees.
(recip-alpha), (recip-alpha) and (recip-alpha) related to the
angles in the real cell by:
cos(recip-alpha)
= [cos(beta)*cos(gamma) - cos(alpha)]/[sin(beta)*sin(gamma)]
cos(recip-beta)
= [cos(gamma)*cos(alpha) - cos(beta)]/[sin(gamma)*sin(alpha)]
cos(recip-gamma)
= [cos(alpha)*cos(beta) - cos(gamma)]/[sin(alpha)*sin(beta)]
Ref: Buerger, M. J. (1942). X-ray Crystallography, p. 360.
New York: John Wiley & Sons Inc.
cell.reciprocal_angle_beta_esd
The estimated standard deviation of attribute reciprocal_angle_beta in category cell.
cell.reciprocal_angle_gamma
The angle (recip-gamma) defining the reciprocal cell in degrees.
(recip-alpha), (recip-alpha) and (recip-alpha) related to the
angles in the real cell by:
cos(recip-alpha)
= [cos(beta)*cos(gamma) - cos(alpha)]/[sin(beta)*sin(gamma)]
cos(recip-beta)
= [cos(gamma)*cos(alpha) - cos(beta)]/[sin(gamma)*sin(alpha)]
cos(recip-gamma)
= [cos(alpha)*cos(beta) - cos(gamma)]/[sin(alpha)*sin(beta)]
Ref: Buerger, M. J. (1942). X-ray Crystallography, p. 360.
New York: John Wiley & Sons Inc.
cell.reciprocal_angle_gamma_esd
The estimated standard deviation of attribute reciprocal_angle_gamma in category cell.
cell.reciprocal_length_a
The reciprocal cell length (recip-a) in inverse angstroms.
(recip-a), (recip-b) and (recip-c) are related to the real cell
by the following equation:
recip-a = b*c*sin(alpha)/V
recip-b = c*a*sin(beta)/V
recip-c = a*b*sin(gamma)/V
where V is the cell volume.
Ref: Buerger, M. J. (1942). X-ray Crystallography, p. 360.
New York: John Wiley & Sons Inc.
cell.reciprocal_length_a_esd
The estimated standard deviation of attribute reciprocal_length_a in category cell.
cell.reciprocal_length_b
The reciprocal cell length (recip-b) in inverse angstroms.
(recip-a), (recip-b) and (recip-c) are related to the real cell
by the following equation:
recip-a = b*c*sin(alpha)/V
recip-b = c*a*sin(beta)/V
recip-c = a*b*sin(gamma)/V
where V is the cell volume.
Ref: Buerger, M. J. (1942). X-ray Crystallography, p. 360.
New York: John Wiley & Sons Inc.
cell.reciprocal_length_b_esd
The estimated standard deviation of attribute reciprocal_length_b in category cell.
cell.reciprocal_length_c
The reciprocal cell length (recip-c) in inverse angstroms.
(recip-a), (recip-b) and (recip-c) are related to the real cell
by the following equation:
recip-a = b*c*sin(alpha)/V
recip-b = c*a*sin(beta)/V
recip-c = a*b*sin(gamma)/V
where V is the cell volume.
Ref: Buerger, M. J. (1942). X-ray Crystallography, p. 360.
New York: John Wiley & Sons Inc.
cell.reciprocal_length_c_esd
The estimated standard deviation of attribute reciprocal_length_c in category cell.
cell.volume
Cell volume V in angstroms cubed.
V = a b c (1 - cos^2^~alpha~ - cos^2^~beta~ - cos^2^~gamma~
+ 2 cos~alpha~ cos~beta~ cos~gamma~)^1/2^
a = attribute length_a
in category cell b = attribute length_b
in category cell c = attribute length_c
in category cell alpha = attribute angle_alpha
in category cell beta = attribute angle_beta
in category cell gamma = attribute angle_gamma in category cell
cell.volume_esd
The standard uncertainty (estimated standard deviation)
of attribute volume in category cell.
cell.entry_id
This data item is a pointer to attribute id in category entry in the ENTRY category.
0
cell_measurement
Data items in the CELL_MEASUREMENT category record details
about the measurement of the crystallographic cell parameters.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:cell_measurementCategory>
<PDBx:cell_measurement entry_id="5HVP">
<PDBx:temp>293</PDBx:temp>
<PDBx:temp_esd>3</PDBx:temp_esd>
<PDBx:theta_max>31</PDBx:theta_max>
<PDBx:theta_min>11</PDBx:theta_min>
<PDBx:wavelength>1.54</PDBx:wavelength>
</PDBx:cell_measurement>
</PDBx:cell_measurementCategory>
Example 2 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
<PDBx:cell_measurementCategory>
<PDBx:cell_measurement entry_id="1TOZ">
<PDBx:reflns_used>25</PDBx:reflns_used>
<PDBx:temp>293</PDBx:temp>
<PDBx:theta_max>31</PDBx:theta_max>
<PDBx:theta_min>25</PDBx:theta_min>
</PDBx:cell_measurement>
</PDBx:cell_measurementCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
cell_measurementCategory
This property indicates that datablock
has a category holder cell_measurementCategory.
cell_measurementCategory
This property indicates that cell_measurementCategory.
has a category cell_measurement.
cell_measurementItem
Abstract datatype property for cell_measurement items.
reference_to_cell_measurement
cross-reference to cell_measurement.
referenced_by_cell_measurement
cross-reference from cell_measurement.
cell_measurement.pressure
The pressure in kilopascals at which the unit-cell parameters
were measured (not the pressure at which the sample was
synthesized).
cell_measurement.pressure_esd
The standard uncertainty (estimated standard deviation)
of attribute pressure in category cell_measurement.
cell_measurement.radiation
Description of the radiation used to measure the unit-cell data.
See also attribute wavelength in category cell_measurement.
neutron
Cu K\a
synchrotron
cell_measurement.reflns_used
The total number of reflections used to determine the unit cell.
These reflections may be specified as CELL_MEASUREMENT_REFLN
data items.
cell_measurement.temp
The temperature in kelvins at which the unit-cell parameters
were measured (not the temperature of synthesis).
cell_measurement.temp_esd
The standard uncertainty (estimated standard deviation)
of attribute temp in category cell_measurement.
cell_measurement.theta_max
The maximum theta angle of reflections used to measure
the unit cell in degrees.
cell_measurement.theta_min
The minimum theta angle of reflections used to measure
the unit cell in degrees.
cell_measurement.wavelength
The wavelength in angstroms of the radiation used to measure
the unit cell. If this is not specified, the wavelength is
assumed to be that specified in the category
DIFFRN_RADIATION_WAVELENGTH.
cell_measurement.entry_id
This data item is a pointer to attribute id in category entry in the ENTRY category.
0
cell_measurement_refln
Data items in the CELL_MEASUREMENT_REFLN category record
details about the reflections used to determine the
crystallographic cell parameters.
The CELL_MEASUREMENT_REFLN data items would in general be used
only for diffractometer data.
Example 1 - extracted from the CAD-4 listing of Rb~2~S~2~O~6~ at room
temperature (unpublished).
<PDBx:cell_measurement_reflnCategory>
<PDBx:cell_measurement_refln index_h="-2" index_k="4" index_l="1">
<PDBx:theta>8.67</PDBx:theta>
</PDBx:cell_measurement_refln>
<PDBx:cell_measurement_refln index_h="0" index_k="3" index_l="2">
<PDBx:theta>9.45</PDBx:theta>
</PDBx:cell_measurement_refln>
<PDBx:cell_measurement_refln index_h="3" index_k="0" index_l="2">
<PDBx:theta>9.46</PDBx:theta>
</PDBx:cell_measurement_refln>
<PDBx:cell_measurement_refln index_h="-3" index_k="4" index_l="1">
<PDBx:theta>8.93</PDBx:theta>
</PDBx:cell_measurement_refln>
<PDBx:cell_measurement_refln index_h="-2" index_k="1" index_l="-2">
<PDBx:theta>7.53</PDBx:theta>
</PDBx:cell_measurement_refln>
<PDBx:cell_measurement_refln index_h="10" index_k="0" index_l="0">
<PDBx:theta>23.77</PDBx:theta>
</PDBx:cell_measurement_refln>
<PDBx:cell_measurement_refln index_h="0" index_k="10" index_l="0">
<PDBx:theta>23.78</PDBx:theta>
</PDBx:cell_measurement_refln>
<PDBx:cell_measurement_refln index_h="-5" index_k="4" index_l="1">
<PDBx:theta>11.14</PDBx:theta>
</PDBx:cell_measurement_refln>
</PDBx:cell_measurement_reflnCategory>
0
1
1
1
1
cell_measurement_reflnCategory
This property indicates that datablock
has a category holder cell_measurement_reflnCategory.
cell_measurement_reflnCategory
This property indicates that cell_measurement_reflnCategory.
has a category cell_measurement_refln.
cell_measurement_reflnItem
Abstract datatype property for cell_measurement_refln items.
reference_to_cell_measurement_refln
cross-reference to cell_measurement_refln.
referenced_by_cell_measurement_refln
cross-reference from cell_measurement_refln.
cell_measurement_refln.theta
Theta angle for a reflection used for measurement of
the unit cell in degrees.
cell_measurement_refln.index_h
Miller index h of a reflection used for measurement of the unit
cell.
cell_measurement_refln.index_k
Miller index k of a reflection used for measurement of the unit
cell.
cell_measurement_refln.index_l
Miller index l of a reflection used for measurement of the unit
cell.
0
chem_comp
Data items in the CHEM_COMP category give details about each
of the chemical components from which the relevant chemical
structures can be constructed, such as name, mass or charge.
The related categories CHEM_COMP_ATOM, CHEM_COMP_BOND,
CHEM_COMP_ANGLE etc. describe the detailed geometry of these
chemical components.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:chem_compCategory>
<PDBx:chem_comp id="phe">
<PDBx:model_source>1987 Protin/Prolsq Ideals file</PDBx:model_source>
<PDBx:name>phenylalanine</PDBx:name>
</PDBx:chem_comp>
<PDBx:chem_comp id="val">
<PDBx:model_source>1987 Protin/Prolsq Ideals file</PDBx:model_source>
<PDBx:name>alanine</PDBx:name>
</PDBx:chem_comp>
</PDBx:chem_compCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
1
1
chem_compCategory
This property indicates that datablock
has a category holder chem_compCategory.
chem_compCategory
This property indicates that chem_compCategory.
has a category chem_comp.
chem_compItem
Abstract datatype property for chem_comp items.
reference_to_chem_comp
cross-reference to chem_comp.
referenced_by_chem_comp
cross-reference from chem_comp.
chem_comp.formula
The formula for the chemical component. Formulae are written
according to the following rules:
(1) Only recognized element symbols may be used.
(2) Each element symbol is followed by a 'count' number. A count
of '1' may be omitted.
(3) A space or parenthesis must separate each cluster of
(element symbol + count), but in general parentheses are
not used.
(4) The order of elements depends on whether carbon is
present or not. If carbon is present, the order should be:
C, then H, then the other elements in alphabetical order
of their symbol. If carbon is not present, the elements
are listed purely in alphabetic order of their symbol. This
is the 'Hill' system used by Chemical Abstracts.
C18 H19 N7 O8 S
chem_comp.formula_weight
Formula mass in daltons of the chemical component.
chem_comp.model_details
A description of special aspects of the generation of the
coordinates for the model of the component.
geometry idealized but not minimized
chem_comp.model_erf
A pointer to an external reference file from which the atomic
description of the component is taken.
chem_comp.model_source
The source of the coordinates for the model of the component.
CSD entry ABCDEF
built using Quanta/Charmm
chem_comp.mon_nstd_class
A description of the class of a nonstandard monomer if the
nonstandard monomer represents a modification of a
standard monomer.
iodinated base
phosphorylated amino acid
brominated base
modified amino acid
glycosylated amino acid
chem_comp.mon_nstd_details
A description of special details of a nonstandard monomer.
no
n
yes
y
'yes' indicates that this is a 'standard' monomer, 'no'
indicates that it is 'nonstandard'. Nonstandard monomers
should be described in more detail using the
_chem_comp.mon_nstd_parent, _chem_comp.mon_nstd_class and
attribute mon_nstd_details in category chem_comp data items.
chem_comp.mon_nstd_parent
The name of the parent monomer of the nonstandard monomer,
if the nonstandard monomer represents a modification of a
standard monomer.
tyrosine
cytosine
chem_comp.mon_nstd_parent_comp_id
The identifier for the parent component of the nonstandard
component. May be be a comma separated list if this component
is derived from multiple components.
Items in this indirectly point to attribute id in category chem_comp in
the CHEM_COMP category.
chem_comp.name
The full name of the component.
alanine
valine
adenine
cytosine
chem_comp.number_atoms_all
The total number of atoms in the component.
chem_comp.number_atoms_nh
The number of non-hydrogen atoms in the component.
chem_comp.one_letter_code
For standard polymer components, the one-letter code for
the component. For non-standard polymer components, the
one-letter code for parent component if this exists;
otherwise, the one-letter code should be given as 'X'.
Components that derived from multiple parents components
are described by a sequence of one-letter-codes.
alanine or adenine
A
ambiguous asparagine/aspartic acid
B
arginine
R
asparagine
N
aspartic acid
D
cysteine or cystine or cytosine
C
glutamine
Q
glutamic acid
E
ambiguous glutamine/glutamic acid
Z
glycine or guanine
G
histidine
H
isoleucine
I
leucine
L
lysine
K
methionine
M
phenylalanine
F
proline
P
serine
S
threonine or thymine
T
tryptophan
W
tyrosine
Y
valine
V
uracil
U
water
O
other
X
chem_comp.pdbx_ambiguous_flag
A preliminary classification used by PDB to indicate
that the chemistry of this component while described
as clearly as possible is still ambiguous. Software
tools may not be able to process this component
definition.
chem_comp.pdbx_casnum
Chemical Abstract Service identifier.
chem_comp.pdbx_class_1
Internal classifier used to organize ligand
dictionary (broad chemical class).
HETEROCYCLIC AROMATIC COMPOUNDS
chem_comp.pdbx_class_2
Internal classifier used to organize ligand
dictionary (notable chemical features).
COMPOUNDS WITH THIAZOLIDINE
solvent
organic ligand
inorganic ligand
organometalic ligand
metal cation
A type classification of this chemical component.
chem_comp.pdbx_component_no
A serial number used by PDB in the FORMUL record.
3
chem_comp.pdbx_formal_charge
The net integer charge assigned to this component. This is the
formal charge assignment normally found in chemical diagrams.
chem_comp.pdbx_ideal_coordinates_details
This data item identifies the source of the ideal coordinates in the
component definition.
Y
N
This data item identifies if ideal coordinates are missing in this definition.
chem_comp.pdbx_initial_date
Date component was added to database.
chem_comp.pdbx_model_coordinates_db_code
This data item identifies the PDB database code from which the heavy
atom model coordinates were obtained.
chem_comp.pdbx_model_coordinates_details
This data item provides additional details about the model coordinates
in the component definition.
Y
N
This data item identifies if model coordinates are missing in this definition.
chem_comp.pdbx_modification_details
For nonstandard components a text description
of modification of the parent component.
ATP
chem_comp.pdbx_modified_date
Date component was last modified.
chem_comp.pdbx_nscnum
NSC identifier for component.
chem_comp.pdbx_number_subcomponents
The number of subcomponents represented in this component.
Y
N
A flag to indicate if the CCD can be used to represent a protein modification.
Y
PDBE
EBI
PDBJ
PDBC
RCSB
This data item identifies the deposition site that processed
this chemical component defintion.
REL
HOLD
HPUB
OBS
DEL
REF_ONLY
This data item holds the current release status for the component.
chem_comp.pdbx_replaced_by
Identifies the attribute id in category chem_comp of the component that
has replaced this component.
q11
tvx
chem_comp.pdbx_replaces
Identifies the attribute id's in category chem_comp of the components
which have been replaced by this component.
Multiple id codes should be separated by commas.
q11
tvx,atv
chem_comp.pdbx_reserved_name
Previous chemical name used for this component if
a name correction has been made.
chem_comp.pdbx_smiles
SMILES code for component.
chem_comp.pdbx_status
Release status of component
chem_comp.pdbx_subcomponent_list
The list of subcomponents contained in this component.
TSM DPH HIS CHF EMR
chem_comp.pdbx_synonyms
Synonym list for the component.
ATP
chem_comp.pdbx_type
A preliminary classification used by PDB.
chem_comp.pdbx_type_modified
Modification flag.
chem_comp.three_letter_code
For standard polymer components, the common three-letter code for
the component. Non-standard polymer components and non-polymer
components are also assigned three-letter-codes.
For ambiguous polymer components three-letter code should
be given as 'UNK'. Ambiguous ions are assigned the code 'UNX'.
Ambiguous non-polymer components are assigned the code 'UNL'.
alanine
ALA
arginine
ARG
asparagine
ASN
aspartic acid
ASP
ambiguous asparagine/aspartic acid
ASX
cysteine
CYS
glutamine
GLN
glutamic acid
GLU
glycine
GLY
ambiguous glutamine/glutamic acid
GLX
histidine
HIS
isoleucine
ILE
leucine
LEU
lysine
LYS
methionine
MET
phenylalanine
PHE
proline
PRO
serine
SER
threonine
THR
tryptophan
TRP
tyrosine
TYR
valine
VAL
1-methyladenosine
1MA
5-methylcytosine
5MC
2(prime)-O-methylcytodine
OMC
1-methylguanosine
1MG
N(2)-methylguanosine
2MG
N(2)-dimethylguanosine
M2G
7-methylguanosine
7MG
2(prime)-O-methylguanosine
0MG
dihydrouridine
H2U
ribosylthymidine
5MU
pseudouridine
PSU
acetic acid
ACE
formic acid
FOR
water
HOH
other
UNK
D-peptide linking
L-peptide linking
D-peptide NH3 amino terminus
L-peptide NH3 amino terminus
D-peptide COOH carboxy terminus
L-peptide COOH carboxy terminus
DNA linking
RNA linking
L-RNA linking
L-DNA linking
DNA OH 5 prime terminus
RNA OH 5 prime terminus
DNA OH 3 prime terminus
RNA OH 3 prime terminus
D-saccharide, beta linking
D-saccharide, alpha linking
L-saccharide, beta linking
L-saccharide, alpha linking
L-saccharide
D-saccharide
saccharide
non-polymer
peptide linking
peptide-like
L-gamma-peptide, C-delta linking
D-gamma-peptide, C-delta linking
L-beta-peptide, C-gamma linking
D-beta-peptide, C-gamma linking
other
For standard polymer components, the type of the monomer.
Note that monomers that will form polymers are of three types:
linking monomers, monomers with some type of N-terminal (or 5')
cap and monomers with some type of C-terminal (or 3') cap.
chem_comp.id
The value of attribute id in category chem_comp must uniquely identify each item in
the CHEM_COMP list.
For protein polymer entities, this is the three-letter code for
the amino acid.
For nucleic acid polymer entities, this is the one-letter code
for the base.
ALA
VAL
DG
C
0
chem_comp_angle
Data items in the CHEM_COMP_ANGLE category record details about
angles in a chemical component. Angles are designated by three
atoms, with the second atom forming the vertex of the angle.
Target values may be specified as angles in degrees, as a
distance between the first and third atoms, or both.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:chem_comp_angleCategory>
<PDBx:chem_comp_angle atom_id_1="N" atom_id_2="CA" atom_id_3="C" comp_id="PHE">
<PDBx:value_angle>110.8</PDBx:value_angle>
</PDBx:chem_comp_angle>
<PDBx:chem_comp_angle atom_id_1="N" atom_id_2="CA" atom_id_3="CB" comp_id="PHE">
<PDBx:value_angle>110.1</PDBx:value_angle>
</PDBx:chem_comp_angle>
<PDBx:chem_comp_angle atom_id_1="C" atom_id_2="CA" atom_id_3="CB" comp_id="PHE">
<PDBx:value_angle>110.3</PDBx:value_angle>
</PDBx:chem_comp_angle>
<PDBx:chem_comp_angle atom_id_1="C" atom_id_2="CA" atom_id_3="HA" comp_id="PHE">
<PDBx:value_angle>108.3</PDBx:value_angle>
</PDBx:chem_comp_angle>
<PDBx:chem_comp_angle atom_id_1="CA" atom_id_2="C" atom_id_3="O" comp_id="PHE">
<PDBx:value_angle>118.4</PDBx:value_angle>
</PDBx:chem_comp_angle>
<PDBx:chem_comp_angle atom_id_1="CA" atom_id_2="C" atom_id_3="OXT" comp_id="PHE">
<PDBx:value_angle>117.8</PDBx:value_angle>
</PDBx:chem_comp_angle>
<PDBx:chem_comp_angle atom_id_1="CA" atom_id_2="CB" atom_id_3="CG" comp_id="PHE">
<PDBx:value_angle>114.0</PDBx:value_angle>
</PDBx:chem_comp_angle>
<PDBx:chem_comp_angle atom_id_1="O" atom_id_2="C" atom_id_3="OXT" comp_id="PHE">
<PDBx:value_angle>123.8</PDBx:value_angle>
</PDBx:chem_comp_angle>
<PDBx:chem_comp_angle atom_id_1="CB" atom_id_2="CG" atom_id_3="CD1" comp_id="PHE">
<PDBx:value_angle>120.8</PDBx:value_angle>
</PDBx:chem_comp_angle>
<PDBx:chem_comp_angle atom_id_1="CB" atom_id_2="CG" atom_id_3="CD2" comp_id="PHE">
<PDBx:value_angle>120.5</PDBx:value_angle>
</PDBx:chem_comp_angle>
</PDBx:chem_comp_angleCategory>
0
1
0
1
0
1
0
1
1
1
1
1
chem_comp_angleCategory
This property indicates that datablock
has a category holder chem_comp_angleCategory.
chem_comp_angleCategory
This property indicates that chem_comp_angleCategory.
has a category chem_comp_angle.
chem_comp_angleItem
Abstract datatype property for chem_comp_angle items.
reference_to_chem_comp_angle
cross-reference to chem_comp_angle.
referenced_by_chem_comp_angle
cross-reference from chem_comp_angle.
chem_comp_angle.value_angle
The value that should be taken as the target value for the angle
associated with the specified atoms, expressed in degrees.
chem_comp_angle.value_angle_esd
The standard uncertainty (estimated standard deviation)
of attribute value_angle in category chem_comp_angle.
chem_comp_angle.value_dist
The value that should be taken as the target value for the angle
associated with the specified atoms, expressed as the distance
between the atoms specified by attribute atom_id_1 in category chem_comp_angle and
attribute atom_id_3 in category chem_comp_angle.
chem_comp_angle.value_dist_esd
The standard uncertainty (estimated standard deviation)
of attribute value_dist in category chem_comp_angle.
chem_comp_angle.atom_id_1
The ID of the first of the three atoms that define the angle.
This data item is a pointer to attribute atom_id in category chem_comp_atom in the
CHEM_COMP_ATOM category.
chem_comp_angle.atom_id_2
The ID of the second of the three atoms that define the angle.
The second atom is taken to be the apex of the angle.
This data item is a pointer to attribute atom_id in category chem_comp_atom in the
CHEM_COMP_ATOM category.
chem_comp_angle.atom_id_3
The ID of the third of the three atoms that define the angle.
This data item is a pointer to attribute atom_id in category chem_comp_atom in the
CHEM_COMP_ATOM category.
chem_comp_angle.comp_id
This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP
category.
0
chem_comp_atom
Data items in the CHEM_COMP_ATOM category record details about
the atoms in a chemical component. Specifying the atomic
coordinates for the components in this category is an
alternative to specifying the structure of the component
via bonds, angles, planes etc. in the appropriate
CHEM_COMP subcategories.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:chem_comp_atomCategory>
<PDBx:chem_comp_atom atom_id="N" comp_id="phe">
<PDBx:model_Cartn_x>1.20134</PDBx:model_Cartn_x>
<PDBx:model_Cartn_y>0.84658</PDBx:model_Cartn_y>
<PDBx:model_Cartn_z>0.00000</PDBx:model_Cartn_z>
<PDBx:substruct_code>main</PDBx:substruct_code>
<PDBx:type_symbol>N</PDBx:type_symbol>
</PDBx:chem_comp_atom>
<PDBx:chem_comp_atom atom_id="CA" comp_id="phe">
<PDBx:model_Cartn_x>0.00000</PDBx:model_Cartn_x>
<PDBx:model_Cartn_y>0.00000</PDBx:model_Cartn_y>
<PDBx:model_Cartn_z>0.00000</PDBx:model_Cartn_z>
<PDBx:substruct_code>main</PDBx:substruct_code>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:chem_comp_atom>
<PDBx:chem_comp_atom atom_id="C" comp_id="phe">
<PDBx:model_Cartn_x>-1.25029</PDBx:model_Cartn_x>
<PDBx:model_Cartn_y>0.88107</PDBx:model_Cartn_y>
<PDBx:model_Cartn_z>0.00000</PDBx:model_Cartn_z>
<PDBx:substruct_code>main</PDBx:substruct_code>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:chem_comp_atom>
<PDBx:chem_comp_atom atom_id="O" comp_id="phe">
<PDBx:model_Cartn_x>-2.18525</PDBx:model_Cartn_x>
<PDBx:model_Cartn_y>0.66029</PDBx:model_Cartn_y>
<PDBx:model_Cartn_z>-0.78409</PDBx:model_Cartn_z>
<PDBx:substruct_code>main</PDBx:substruct_code>
<PDBx:type_symbol>O</PDBx:type_symbol>
</PDBx:chem_comp_atom>
<PDBx:chem_comp_atom atom_id="CB" comp_id="phe">
<PDBx:model_Cartn_x>0.00662</PDBx:model_Cartn_x>
<PDBx:model_Cartn_y>-1.03603</PDBx:model_Cartn_y>
<PDBx:model_Cartn_z>1.11081</PDBx:model_Cartn_z>
<PDBx:substruct_code>side</PDBx:substruct_code>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:chem_comp_atom>
<PDBx:chem_comp_atom atom_id="CG" comp_id="phe">
<PDBx:model_Cartn_x>0.03254</PDBx:model_Cartn_x>
<PDBx:model_Cartn_y>-0.49711</PDBx:model_Cartn_y>
<PDBx:model_Cartn_z>2.50951</PDBx:model_Cartn_z>
<PDBx:substruct_code>side</PDBx:substruct_code>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:chem_comp_atom>
<PDBx:chem_comp_atom atom_id="CD1" comp_id="phe">
<PDBx:model_Cartn_x>-1.15813</PDBx:model_Cartn_x>
<PDBx:model_Cartn_y>-0.12084</PDBx:model_Cartn_y>
<PDBx:model_Cartn_z>3.13467</PDBx:model_Cartn_z>
<PDBx:substruct_code>side</PDBx:substruct_code>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:chem_comp_atom>
<PDBx:chem_comp_atom atom_id="CE1" comp_id="phe">
<PDBx:model_Cartn_x>-1.15720</PDBx:model_Cartn_x>
<PDBx:model_Cartn_y>0.38038</PDBx:model_Cartn_y>
<PDBx:model_Cartn_z>4.42732</PDBx:model_Cartn_z>
<PDBx:substruct_code>side</PDBx:substruct_code>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:chem_comp_atom>
<PDBx:chem_comp_atom atom_id="CZ" comp_id="phe">
<PDBx:model_Cartn_x>0.05385</PDBx:model_Cartn_x>
<PDBx:model_Cartn_y>0.51332</PDBx:model_Cartn_y>
<PDBx:model_Cartn_z>5.11032</PDBx:model_Cartn_z>
<PDBx:substruct_code>side</PDBx:substruct_code>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:chem_comp_atom>
<PDBx:chem_comp_atom atom_id="CE2" comp_id="phe">
<PDBx:model_Cartn_x>1.26137</PDBx:model_Cartn_x>
<PDBx:model_Cartn_y>0.11613</PDBx:model_Cartn_y>
<PDBx:model_Cartn_z>4.50975</PDBx:model_Cartn_z>
<PDBx:substruct_code>side</PDBx:substruct_code>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:chem_comp_atom>
<PDBx:chem_comp_atom atom_id="CD2" comp_id="phe">
<PDBx:model_Cartn_x>1.23668</PDBx:model_Cartn_x>
<PDBx:model_Cartn_y>-0.38351</PDBx:model_Cartn_y>
<PDBx:model_Cartn_z>3.20288</PDBx:model_Cartn_z>
<PDBx:substruct_code>side</PDBx:substruct_code>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:chem_comp_atom>
<PDBx:chem_comp_atom atom_id="N" comp_id="val">
<PDBx:model_Cartn_x>1.20134</PDBx:model_Cartn_x>
<PDBx:model_Cartn_y>0.84658</PDBx:model_Cartn_y>
<PDBx:model_Cartn_z>0.00000</PDBx:model_Cartn_z>
<PDBx:substruct_code>main</PDBx:substruct_code>
<PDBx:type_symbol>N</PDBx:type_symbol>
</PDBx:chem_comp_atom>
<PDBx:chem_comp_atom atom_id="CA" comp_id="val">
<PDBx:model_Cartn_x>0.00000</PDBx:model_Cartn_x>
<PDBx:model_Cartn_y>0.00000</PDBx:model_Cartn_y>
<PDBx:model_Cartn_z>0.00000</PDBx:model_Cartn_z>
<PDBx:substruct_code>main</PDBx:substruct_code>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:chem_comp_atom>
<PDBx:chem_comp_atom atom_id="C" comp_id="val">
<PDBx:model_Cartn_x>-1.25029</PDBx:model_Cartn_x>
<PDBx:model_Cartn_y>0.88107</PDBx:model_Cartn_y>
<PDBx:model_Cartn_z>0.00000</PDBx:model_Cartn_z>
<PDBx:substruct_code>main</PDBx:substruct_code>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:chem_comp_atom>
<PDBx:chem_comp_atom atom_id="O" comp_id="val">
<PDBx:model_Cartn_x>-2.18525</PDBx:model_Cartn_x>
<PDBx:model_Cartn_y>0.66029</PDBx:model_Cartn_y>
<PDBx:model_Cartn_z>-0.78409</PDBx:model_Cartn_z>
<PDBx:substruct_code>main</PDBx:substruct_code>
<PDBx:type_symbol>O</PDBx:type_symbol>
</PDBx:chem_comp_atom>
<PDBx:chem_comp_atom atom_id="CB" comp_id="val">
<PDBx:model_Cartn_x>0.05260</PDBx:model_Cartn_x>
<PDBx:model_Cartn_y>-0.99339</PDBx:model_Cartn_y>
<PDBx:model_Cartn_z>1.17429</PDBx:model_Cartn_z>
<PDBx:substruct_code>side</PDBx:substruct_code>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:chem_comp_atom>
<PDBx:chem_comp_atom atom_id="CG1" comp_id="val">
<PDBx:model_Cartn_x>-0.13288</PDBx:model_Cartn_x>
<PDBx:model_Cartn_y>-0.31545</PDBx:model_Cartn_y>
<PDBx:model_Cartn_z>2.52668</PDBx:model_Cartn_z>
<PDBx:substruct_code>side</PDBx:substruct_code>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:chem_comp_atom>
<PDBx:chem_comp_atom atom_id="CG2" comp_id="val">
<PDBx:model_Cartn_x>-0.94265</PDBx:model_Cartn_x>
<PDBx:model_Cartn_y>-2.12930</PDBx:model_Cartn_y>
<PDBx:model_Cartn_z>0.99811</PDBx:model_Cartn_z>
<PDBx:substruct_code>side</PDBx:substruct_code>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:chem_comp_atom>
</PDBx:chem_comp_atomCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
1
1
1
chem_comp_atomCategory
This property indicates that datablock
has a category holder chem_comp_atomCategory.
chem_comp_atomCategory
This property indicates that chem_comp_atomCategory.
has a category chem_comp_atom.
chem_comp_atomItem
Abstract datatype property for chem_comp_atom items.
reference_to_chem_comp_atom
cross-reference to chem_comp_atom.
referenced_by_chem_comp_atom
cross-reference from chem_comp_atom.
chem_comp_atom.alt_atom_id
An alternative identifier for the atom. This data item would be
used in cases where alternative nomenclatures exist for labelling
atoms in a group.
chem_comp_atom.charge
The net integer charge assigned to this atom. This is the
formal charge assignment normally found in chemical diagrams.
for an ammonium nitrogen
1
for a chloride ion
-1
chem_comp_atom.model_Cartn_x
The x component of the coordinates for this atom in this
component specified as orthogonal angstroms. The choice of
reference axis frame for the coordinates is arbitrary.
The set of coordinates input for the entity here is intended to
correspond to the atomic model used to generate restraints for
structure refinement, not to atom sites in the ATOM_SITE
list.
chem_comp_atom.model_Cartn_x_esd
The standard uncertainty (estimated standard deviation)
of attribute model_Cartn_x in category chem_comp_atom.
chem_comp_atom.model_Cartn_y
The y component of the coordinates for this atom in this
component specified as orthogonal angstroms. The choice of
reference axis frame for the coordinates is arbitrary.
The set of coordinates input for the entity here is intended to
correspond to the atomic model used to generate restraints for
structure refinement, not to atom sites in the ATOM_SITE
list.
chem_comp_atom.model_Cartn_y_esd
The standard uncertainty (estimated standard deviation)
of attribute model_Cartn_y in category chem_comp_atom.
chem_comp_atom.model_Cartn_z
The z component of the coordinates for this atom in this
component specified as orthogonal angstroms. The choice of
reference axis frame for the coordinates is arbitrary.
The set of coordinates input for the entity here is intended to
correspond to the atomic model used to generate restraints for
structure refinement, not to atom sites in the ATOM_SITE
list.
chem_comp_atom.model_Cartn_z_esd
The standard uncertainty (estimated standard deviation)
of attribute model_Cartn_z in category chem_comp_atom.
chem_comp_atom.partial_charge
The partial charge assigned to this atom.
chem_comp_atom.pdbx_align
Atom name alignment offset in PDB atom field.
chem_comp_atom.pdbx_alt_atom_id
An alternative identifier for the atom. This data item would be
used in cases where alternative nomenclatures exist for labelling
atoms in a group.
chem_comp_atom.pdbx_alt_comp_id
An alternative identifier for the atom. This data item would be
used in cases where alternative nomenclatures exist for labelling
atoms in a group.
Y
N
A flag indicating an aromatic atom.
Y
N
A flag indicating the backbone atoms in polypeptide units.
Y
N
A flag indicating the C-terminal group atoms in polypeptide units.
chem_comp_atom.pdbx_component_atom_id
The atom identifier in the subcomponent where a
larger component has been divided subcomponents.
CB
CA
CG
chem_comp_atom.pdbx_component_comp_id
The component identifier for the subcomponent where a
larger component has been divided subcomponents.
HIS
PRO
chem_comp_atom.pdbx_component_entity_id
A reference to entity identifier in data category
pdbx_chem_comp_subcomponent_entity_list.
chem_comp_atom.pdbx_component_id
A reference to attribute component_id in category pdbx_reference_entity_list
Y
N
A flag indicating a leaving atom.
chem_comp_atom.pdbx_model_Cartn_x_ideal
An alternative x component of the coordinates for this atom in this
component specified as orthogonal angstroms.
chem_comp_atom.pdbx_model_Cartn_y_ideal
An alternative y component of the coordinates for this atom in this
component specified as orthogonal angstroms.
chem_comp_atom.pdbx_model_Cartn_z_ideal
An alternative z component of the coordinates for this atom in this
component specified as orthogonal angstroms.
Y
N
A flag indicating the N-terminal group atoms in polypeptide units.
chem_comp_atom.pdbx_ordinal
Ordinal index for the component atom list.
polymer
non-polymer
Is the atom in a polymer or non-polymer subcomponent in the BIRD definition.
chem_comp_atom.pdbx_ref_id
A reference to attribute ref_entity_id in category pdbx_reference_entity_list
chem_comp_atom.pdbx_residue_numbering
Preferred residue numbering in the BIRD definition.
R
S
N
The chiral configuration of the atom that is a chiral center.
chem_comp_atom.pdbx_stnd_atom_id
A standard identifier for the atom. This data item is used when
IUPAC/IUBMB nomenclature exists for labeling atoms.
main
side
base
phos
sugar
none
This data item assigns the atom to a substructure of the
component, if appropriate.
chem_comp_atom.type_symbol
The code used to identify the atom species representing
this atom type. Normally this code is the element
symbol.
C
N
O
chem_comp_atom.atom_id
The value of attribute atom_id in category chem_comp_atom must uniquely identify
each atom in each monomer in the CHEM_COMP_ATOM list.
The atom identifiers need not be unique over all atoms in the
data block; they need only be unique for each atom in a
component.
Note that this item need not be a number; it can be any unique
identifier.
chem_comp_atom.comp_id
This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP
category.
0
chem_comp_bond
Data items in the CHEM_COMP_BOND category record details about
the bonds between atoms in a chemical component. Target values
may be specified as bond orders, as a distance between the two
atoms, or both.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:chem_comp_bondCategory>
<PDBx:chem_comp_bond atom_id_1="N" atom_id_2="CA" comp_id="phe">
<PDBx:value_order>sing</PDBx:value_order>
</PDBx:chem_comp_bond>
<PDBx:chem_comp_bond atom_id_1="CA" atom_id_2="C" comp_id="phe">
<PDBx:value_order>sing</PDBx:value_order>
</PDBx:chem_comp_bond>
<PDBx:chem_comp_bond atom_id_1="C" atom_id_2="O" comp_id="phe">
<PDBx:value_order>doub</PDBx:value_order>
</PDBx:chem_comp_bond>
<PDBx:chem_comp_bond atom_id_1="CB" atom_id_2="CA" comp_id="phe">
<PDBx:value_order>sing</PDBx:value_order>
</PDBx:chem_comp_bond>
<PDBx:chem_comp_bond atom_id_1="CB" atom_id_2="CG" comp_id="phe">
<PDBx:value_order>sing</PDBx:value_order>
</PDBx:chem_comp_bond>
<PDBx:chem_comp_bond atom_id_1="CG" atom_id_2="CD1" comp_id="phe">
<PDBx:value_order>arom</PDBx:value_order>
</PDBx:chem_comp_bond>
<PDBx:chem_comp_bond atom_id_1="CD1" atom_id_2="CE1" comp_id="phe">
<PDBx:value_order>arom</PDBx:value_order>
</PDBx:chem_comp_bond>
<PDBx:chem_comp_bond atom_id_1="CE1" atom_id_2="CZ" comp_id="phe">
<PDBx:value_order>arom</PDBx:value_order>
</PDBx:chem_comp_bond>
<PDBx:chem_comp_bond atom_id_1="CZ" atom_id_2="CE2" comp_id="phe">
<PDBx:value_order>arom</PDBx:value_order>
</PDBx:chem_comp_bond>
<PDBx:chem_comp_bond atom_id_1="CE2" atom_id_2="CD2" comp_id="phe">
<PDBx:value_order>arom</PDBx:value_order>
</PDBx:chem_comp_bond>
<PDBx:chem_comp_bond atom_id_1="CD2" atom_id_2="CG" comp_id="phe">
<PDBx:value_order>arom</PDBx:value_order>
</PDBx:chem_comp_bond>
<PDBx:chem_comp_bond atom_id_1="N" atom_id_2="CA" comp_id="val">
<PDBx:value_order>sing</PDBx:value_order>
</PDBx:chem_comp_bond>
<PDBx:chem_comp_bond atom_id_1="CA" atom_id_2="C" comp_id="val">
<PDBx:value_order>sing</PDBx:value_order>
</PDBx:chem_comp_bond>
<PDBx:chem_comp_bond atom_id_1="C" atom_id_2="O" comp_id="val">
<PDBx:value_order>doub</PDBx:value_order>
</PDBx:chem_comp_bond>
<PDBx:chem_comp_bond atom_id_1="CB" atom_id_2="CA" comp_id="val">
<PDBx:value_order>sing</PDBx:value_order>
</PDBx:chem_comp_bond>
<PDBx:chem_comp_bond atom_id_1="CB" atom_id_2="CG1" comp_id="val">
<PDBx:value_order>sing</PDBx:value_order>
</PDBx:chem_comp_bond>
<PDBx:chem_comp_bond atom_id_1="CB" atom_id_2="CG2" comp_id="val">
<PDBx:value_order>sing</PDBx:value_order>
</PDBx:chem_comp_bond>
</PDBx:chem_comp_bondCategory>
0
1
0
1
0
1
0
1
0
1
0
1
1
1
1
chem_comp_bondCategory
This property indicates that datablock
has a category holder chem_comp_bondCategory.
chem_comp_bondCategory
This property indicates that chem_comp_bondCategory.
has a category chem_comp_bond.
chem_comp_bondItem
Abstract datatype property for chem_comp_bond items.
reference_to_chem_comp_bond
cross-reference to chem_comp_bond.
referenced_by_chem_comp_bond
cross-reference from chem_comp_bond.
Y
N
A flag indicating an aromatic bond.
chem_comp_bond.pdbx_ordinal
Ordinal index for the component bond list.
E
Z
N
Stereochemical configuration across a double bond.
chem_comp_bond.value_dist
The value that should be taken as the target for the chemical
bond associated with the specified atoms, expressed as a
distance.
chem_comp_bond.value_dist_esd
The standard uncertainty (estimated standard deviation)
of attribute value_dist in category chem_comp_bond.
sing
doub
trip
quad
arom
poly
delo
pi
The value that should be taken as the target for the chemical
bond associated with the specified atoms, expressed as a bond
order.
chem_comp_bond.atom_id_1
The ID of the first of the two atoms that define the bond.
This data item is a pointer to attribute atom_id in category chem_comp_atom in the
CHEM_COMP_ATOM category.
chem_comp_bond.atom_id_2
The ID of the second of the two atoms that define the bond.
This data item is a pointer to attribute atom_id in category chem_comp_atom in the
CHEM_COMP_ATOM category.
chem_comp_bond.comp_id
This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP
category.
0
chem_comp_chir
Data items in the CHEM_COMP_CHIR category provide details about
the chiral centres in a chemical component. The atoms bonded
to the chiral atom are specified in the CHEM_COMP_CHIR_ATOM
category.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:chem_comp_chirCategory>
<PDBx:chem_comp_chir comp_id="phe" id="phe1">
<PDBx:atom_id>CA</PDBx:atom_id>
</PDBx:chem_comp_chir>
<PDBx:chem_comp_chir comp_id="val" id="val1">
<PDBx:atom_id>CA</PDBx:atom_id>
</PDBx:chem_comp_chir>
</PDBx:chem_comp_chirCategory>
0
1
1
1
0
1
0
1
0
1
0
1
0
1
1
1
chem_comp_chirCategory
This property indicates that datablock
has a category holder chem_comp_chirCategory.
chem_comp_chirCategory
This property indicates that chem_comp_chirCategory.
has a category chem_comp_chir.
chem_comp_chirItem
Abstract datatype property for chem_comp_chir items.
reference_to_chem_comp_chir
cross-reference to chem_comp_chir.
referenced_by_chem_comp_chir
cross-reference from chem_comp_chir.
R
S
The chiral configuration of the atom that is a chiral centre.
chem_comp_chir.atom_id
The ID of the atom that is a chiral centre.
This data item is a pointer to attribute atom_id in category chem_comp_atom in the
CHEM_COMP_ATOM category.
chem_comp_chir.number_atoms_all
The total number of atoms bonded to the atom specified by
attribute atom_id in category chem_comp_chir.
chem_comp_chir.number_atoms_nh
The number of non-hydrogen atoms bonded to the atom specified by
attribute atom_id in category chem_comp_chir.
sign
nosign
A flag to indicate whether a chiral volume should match the
standard value in both magnitude and sign, or in magnitude only.
chem_comp_chir.volume_three
The chiral volume, V~c~, for chiral centres that involve a chiral
atom bonded to three non-hydrogen atoms and one hydrogen atom.
V~c~ = V1 * (V2 X V3)
V1 = the vector distance from the atom specified by
attribute atom_id in category chem_comp_chir to the first atom in the
CHEM_COMP_CHIR_ATOM list
V2 = the vector distance from the atom specified by
attribute atom_id in category chem_comp_chir to the second atom in the
CHEM_COMP_CHIR_ATOM list
V3 = the vector distance from the atom specified by
attribute atom_id in category chem_comp_chir to the third atom in the
CHEM_COMP_CHIR_ATOM list
* = the vector dot product
X = the vector cross product
chem_comp_chir.volume_three_esd
The standard uncertainty (estimated standard deviation)
of attribute volume_three in category chem_comp_chir.
chem_comp_chir.comp_id
This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP
category.
chem_comp_chir.id
The value of attribute id in category chem_comp_chir must uniquely identify a record
in the CHEM_COMP_CHIR list.
0
chem_comp_chir_atom
Data items in the CHEM_COMP_CHIR_ATOM category enumerate the
atoms bonded to a chiral atom within a chemical component.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:chem_comp_chir_atomCategory>
<PDBx:chem_comp_chir_atom atom_id="N" chir_id="1" comp_id="phe"></PDBx:chem_comp_chir_atom>
<PDBx:chem_comp_chir_atom atom_id="C" chir_id="1" comp_id="phe"></PDBx:chem_comp_chir_atom>
<PDBx:chem_comp_chir_atom atom_id="CB" chir_id="1" comp_id="phe"></PDBx:chem_comp_chir_atom>
<PDBx:chem_comp_chir_atom atom_id="N" chir_id="1" comp_id="val"></PDBx:chem_comp_chir_atom>
<PDBx:chem_comp_chir_atom atom_id="C" chir_id="1" comp_id="val"></PDBx:chem_comp_chir_atom>
<PDBx:chem_comp_chir_atom atom_id="CB" chir_id="1" comp_id="val"></PDBx:chem_comp_chir_atom>
</PDBx:chem_comp_chir_atomCategory>
0
1
1
1
1
chem_comp_chir_atomCategory
This property indicates that datablock
has a category holder chem_comp_chir_atomCategory.
chem_comp_chir_atomCategory
This property indicates that chem_comp_chir_atomCategory.
has a category chem_comp_chir_atom.
chem_comp_chir_atomItem
Abstract datatype property for chem_comp_chir_atom items.
reference_to_chem_comp_chir_atom
cross-reference to chem_comp_chir_atom.
referenced_by_chem_comp_chir_atom
cross-reference from chem_comp_chir_atom.
chem_comp_chir_atom.dev
The standard uncertainty (estimated standard deviation)
of the position of this atom from the plane defined by
all of the atoms in the plane.
chem_comp_chir_atom.atom_id
The ID of an atom bonded to the chiral atom.
This data item is a pointer to attribute atom_id in category chem_comp_atom in the
CHEM_COMP_ATOM category.
chem_comp_chir_atom.chir_id
This data item is a pointer to attribute id in category chem_comp_chir in the
CHEM_COMP_CHIR category.
chem_comp_chir_atom.comp_id
This data item is a pointer to attribute id in category chem_comp in the
CHEM_COMP category.
0
chem_comp_link
Data items in the CHEM_COMP_LINK category give details about
the links between chemical components.
0
1
1
1
1
1
1
chem_comp_linkCategory
This property indicates that datablock
has a category holder chem_comp_linkCategory.
chem_comp_linkCategory
This property indicates that chem_comp_linkCategory.
has a category chem_comp_link.
chem_comp_linkItem
Abstract datatype property for chem_comp_link items.
reference_to_chem_comp_link
cross-reference to chem_comp_link.
referenced_by_chem_comp_link
cross-reference from chem_comp_link.
chem_comp_link.details
A description of special aspects of a link between
chemical components in the structure.
chem_comp_link.type_comp_1
The type of the first of the two components joined by the
link.
This data item is a pointer to attribute type in category chem_comp in the CHEM_COMP
category.
chem_comp_link.type_comp_2
The type of the second of the two components joined by the
link.
This data item is a pointer to attribute type in category chem_comp in the CHEM_COMP
category.
chem_comp_link.link_id
This data item is a pointer to attribute id in category chem_link in the
CHEM_LINK category.
0
chem_comp_plane
Data items in the CHEM_COMP_PLANE category provide identifiers
for the planes in a chemical component. The atoms in the plane
are specified in the CHEM_COMP_PLANE_ATOM category.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:chem_comp_planeCategory>
<PDBx:chem_comp_plane comp_id="phe" id="phe1"></PDBx:chem_comp_plane>
</PDBx:chem_comp_planeCategory>
0
1
0
1
1
1
chem_comp_planeCategory
This property indicates that datablock
has a category holder chem_comp_planeCategory.
chem_comp_planeCategory
This property indicates that chem_comp_planeCategory.
has a category chem_comp_plane.
chem_comp_planeItem
Abstract datatype property for chem_comp_plane items.
reference_to_chem_comp_plane
cross-reference to chem_comp_plane.
referenced_by_chem_comp_plane
cross-reference from chem_comp_plane.
chem_comp_plane.number_atoms_all
The total number of atoms in the plane.
chem_comp_plane.number_atoms_nh
The number of non-hydrogen atoms in the plane.
chem_comp_plane.comp_id
This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP
category.
chem_comp_plane.id
The value of attribute id in category chem_comp_plane must uniquely identify a record
in the CHEM_COMP_PLANE list.
0
chem_comp_plane_atom
Data items in the CHEM_COMP_PLANE_ATOM category enumerate the
atoms in a plane within a chemical component.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:chem_comp_plane_atomCategory>
<PDBx:chem_comp_plane_atom atom_id="CB" comp_id="phe" plane_id="phe1"></PDBx:chem_comp_plane_atom>
<PDBx:chem_comp_plane_atom atom_id="CG" comp_id="phe" plane_id="phe1"></PDBx:chem_comp_plane_atom>
<PDBx:chem_comp_plane_atom atom_id="CD1" comp_id="phe" plane_id="phe1"></PDBx:chem_comp_plane_atom>
<PDBx:chem_comp_plane_atom atom_id="CE1" comp_id="phe" plane_id="phe1"></PDBx:chem_comp_plane_atom>
<PDBx:chem_comp_plane_atom atom_id="CZ" comp_id="phe" plane_id="phe1"></PDBx:chem_comp_plane_atom>
<PDBx:chem_comp_plane_atom atom_id="CE2" comp_id="phe" plane_id="phe1"></PDBx:chem_comp_plane_atom>
<PDBx:chem_comp_plane_atom atom_id="CD2" comp_id="phe" plane_id="phe1"></PDBx:chem_comp_plane_atom>
</PDBx:chem_comp_plane_atomCategory>
0
1
1
1
1
chem_comp_plane_atomCategory
This property indicates that datablock
has a category holder chem_comp_plane_atomCategory.
chem_comp_plane_atomCategory
This property indicates that chem_comp_plane_atomCategory.
has a category chem_comp_plane_atom.
chem_comp_plane_atomItem
Abstract datatype property for chem_comp_plane_atom items.
reference_to_chem_comp_plane_atom
cross-reference to chem_comp_plane_atom.
referenced_by_chem_comp_plane_atom
cross-reference from chem_comp_plane_atom.
chem_comp_plane_atom.dist_esd
This data item is the standard deviation of the
out-of-plane distance for this atom.
chem_comp_plane_atom.atom_id
The ID of an atom involved in the plane.
This data item is a pointer to attribute atom_id in category chem_comp_atom in the
CHEM_COMP_ATOM category.
chem_comp_plane_atom.comp_id
This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP
category.
chem_comp_plane_atom.plane_id
This data item is a pointer to attribute id in category chem_comp_plane in the
CHEM_COMP_PLANE category.
0
chem_comp_tor
Data items in the CHEM_COMP_TOR category record details about
the torsion angles in a chemical component. As torsion angles
can have more than one target value, the target values are
specified in the CHEM_COMP_TOR_VALUE category.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:chem_comp_torCategory>
<PDBx:chem_comp_tor comp_id="phe" id="phe_chi1">
<PDBx:atom_id_1>N</PDBx:atom_id_1>
<PDBx:atom_id_2>CA</PDBx:atom_id_2>
<PDBx:atom_id_3>CB</PDBx:atom_id_3>
<PDBx:atom_id_4>CG</PDBx:atom_id_4>
</PDBx:chem_comp_tor>
<PDBx:chem_comp_tor comp_id="phe" id="phe_chi2">
<PDBx:atom_id_1>CA</PDBx:atom_id_1>
<PDBx:atom_id_2>CB</PDBx:atom_id_2>
<PDBx:atom_id_3>CG</PDBx:atom_id_3>
<PDBx:atom_id_4>CD1</PDBx:atom_id_4>
</PDBx:chem_comp_tor>
<PDBx:chem_comp_tor comp_id="phe" id="phe_ring1">
<PDBx:atom_id_1>CB</PDBx:atom_id_1>
<PDBx:atom_id_2>CG</PDBx:atom_id_2>
<PDBx:atom_id_3>CD1</PDBx:atom_id_3>
<PDBx:atom_id_4>CE1</PDBx:atom_id_4>
</PDBx:chem_comp_tor>
<PDBx:chem_comp_tor comp_id="phe" id="phe_ring2">
<PDBx:atom_id_1>CB</PDBx:atom_id_1>
<PDBx:atom_id_2>CG</PDBx:atom_id_2>
<PDBx:atom_id_3>CD2</PDBx:atom_id_3>
<PDBx:atom_id_4>CE2</PDBx:atom_id_4>
</PDBx:chem_comp_tor>
<PDBx:chem_comp_tor comp_id="phe" id="phe_ring3">
<PDBx:atom_id_1>CG</PDBx:atom_id_1>
<PDBx:atom_id_2>CD1</PDBx:atom_id_2>
<PDBx:atom_id_3>CE1</PDBx:atom_id_3>
<PDBx:atom_id_4>CZ</PDBx:atom_id_4>
</PDBx:chem_comp_tor>
<PDBx:chem_comp_tor comp_id="phe" id="phe_ring4">
<PDBx:atom_id_1>CD1</PDBx:atom_id_1>
<PDBx:atom_id_2>CE1</PDBx:atom_id_2>
<PDBx:atom_id_3>CZ</PDBx:atom_id_3>
<PDBx:atom_id_4>CE2</PDBx:atom_id_4>
</PDBx:chem_comp_tor>
<PDBx:chem_comp_tor comp_id="phe" id="phe_ring5">
<PDBx:atom_id_1>CE1</PDBx:atom_id_1>
<PDBx:atom_id_2>CZ</PDBx:atom_id_2>
<PDBx:atom_id_3>CE2</PDBx:atom_id_3>
<PDBx:atom_id_4>CD2</PDBx:atom_id_4>
</PDBx:chem_comp_tor>
</PDBx:chem_comp_torCategory>
1
1
1
1
1
1
1
1
1
1
chem_comp_torCategory
This property indicates that datablock
has a category holder chem_comp_torCategory.
chem_comp_torCategory
This property indicates that chem_comp_torCategory.
has a category chem_comp_tor.
chem_comp_torItem
Abstract datatype property for chem_comp_tor items.
reference_to_chem_comp_tor
cross-reference to chem_comp_tor.
referenced_by_chem_comp_tor
cross-reference from chem_comp_tor.
chem_comp_tor.atom_id_1
The ID of the first of the four atoms that define the torsion
angle.
This data item is a pointer to attribute atom_id in category chem_comp_atom in the
CHEM_COMP_ATOM category.
chem_comp_tor.atom_id_2
The ID of the second of the four atoms that define the torsion
angle.
This data item is a pointer to attribute atom_id in category chem_comp_atom in the
CHEM_COMP_ATOM category.
chem_comp_tor.atom_id_3
The ID of the third of the four atoms that define the torsion
angle.
This data item is a pointer to attribute atom_id in category chem_comp_atom in the
CHEM_COMP_ATOM category.
chem_comp_tor.atom_id_4
The ID of the fourth of the four atoms that define the torsion
angle.
This data item is a pointer to attribute atom_id in category chem_comp_atom in the
CHEM_COMP_ATOM category.
chem_comp_tor.comp_id
This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP
category.
chem_comp_tor.id
The value of attribute id in category chem_comp_tor must uniquely identify a
record in the CHEM_COMP_TOR list.
0
chem_comp_tor_value
Data items in the CHEM_COMP_TOR_VALUE category record details
about the target values for the torsion angles enumerated in the
CHEM_COMP_TOR list. Target values may be specified as angles
in degrees, as a distance between the first and fourth atoms, or
both.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:chem_comp_tor_valueCategory>
<PDBx:chem_comp_tor_value comp_id="phe" tor_id="phe_chi1">
<PDBx:angle>-60.0</PDBx:angle>
<PDBx:dist>2.88</PDBx:dist>
</PDBx:chem_comp_tor_value>
<PDBx:chem_comp_tor_value comp_id="phe" tor_id="phe_chi1">
<PDBx:angle>180.0</PDBx:angle>
<PDBx:dist>3.72</PDBx:dist>
</PDBx:chem_comp_tor_value>
<PDBx:chem_comp_tor_value comp_id="phe" tor_id="phe_chi1">
<PDBx:angle>60.0</PDBx:angle>
<PDBx:dist>2.88</PDBx:dist>
</PDBx:chem_comp_tor_value>
<PDBx:chem_comp_tor_value comp_id="phe" tor_id="phe_chi2">
<PDBx:angle>90.0</PDBx:angle>
<PDBx:dist>3.34</PDBx:dist>
</PDBx:chem_comp_tor_value>
<PDBx:chem_comp_tor_value comp_id="phe" tor_id="phe_chi2">
<PDBx:angle>-90.0</PDBx:angle>
<PDBx:dist>3.34</PDBx:dist>
</PDBx:chem_comp_tor_value>
<PDBx:chem_comp_tor_value comp_id="phe" tor_id="phe_ring1">
<PDBx:angle>180.0</PDBx:angle>
<PDBx:dist>3.75</PDBx:dist>
</PDBx:chem_comp_tor_value>
<PDBx:chem_comp_tor_value comp_id="phe" tor_id="phe_ring2">
<PDBx:angle>180.0</PDBx:angle>
<PDBx:dist>3.75</PDBx:dist>
</PDBx:chem_comp_tor_value>
<PDBx:chem_comp_tor_value comp_id="phe" tor_id="phe_ring3">
<PDBx:angle>0.0</PDBx:angle>
<PDBx:dist>2.80</PDBx:dist>
</PDBx:chem_comp_tor_value>
<PDBx:chem_comp_tor_value comp_id="phe" tor_id="phe_ring4">
<PDBx:angle>0.0</PDBx:angle>
<PDBx:dist>2.80</PDBx:dist>
</PDBx:chem_comp_tor_value>
<PDBx:chem_comp_tor_value comp_id="phe" tor_id="phe_ring5">
<PDBx:angle>0.0</PDBx:angle>
<PDBx:dist>2.80</PDBx:dist>
</PDBx:chem_comp_tor_value>
</PDBx:chem_comp_tor_valueCategory>
1
1
1
1
0
1
0
1
1
1
chem_comp_tor_valueCategory
This property indicates that datablock
has a category holder chem_comp_tor_valueCategory.
chem_comp_tor_valueCategory
This property indicates that chem_comp_tor_valueCategory.
has a category chem_comp_tor_value.
chem_comp_tor_valueItem
Abstract datatype property for chem_comp_tor_value items.
reference_to_chem_comp_tor_value
cross-reference to chem_comp_tor_value.
referenced_by_chem_comp_tor_value
cross-reference from chem_comp_tor_value.
chem_comp_tor_value.angle
A value that should be taken as a potential target value for the
torsion angle associated with the specified atoms, expressed in
degrees.
chem_comp_tor_value.angle_esd
The standard uncertainty (estimated standard deviation)
of attribute angle in category chem_comp_tor_value.
chem_comp_tor_value.dist
A value that should be taken as a potential target value for the
torsion angle associated with the specified atoms, expressed as
the distance between the atoms specified by
_chem_comp_tor.atom_id_1 and _chem_comp_tor.atom_id_4 in the
referenced record in the CHEM_COMP_TOR list. Note that the
torsion angle cannot be fully specified by a distance (for
instance, a torsion angle of -60 degree will yield the same
distance as a 60 degree angle). However, the distance
specification can be useful for refinement in situations
in which the angle is already close to the desired value.
chem_comp_tor_value.dist_esd
The standard uncertainty (estimated standard deviation)
of attribute dist in category chem_comp_tor_value.
chem_comp_tor_value.comp_id
This data item is a pointer to attribute comp_id in category chem_comp_atom in the
CHEM_COMP_ATOM category.
chem_comp_tor_value.tor_id
This data item is a pointer to attribute id in category chem_comp_tor in the
CHEM_COMP_TOR category.
0
chem_link
Data items in the CHEM_LINK category give details about
the links between chemical components.
0
1
1
chem_linkCategory
This property indicates that datablock
has a category holder chem_linkCategory.
chem_linkCategory
This property indicates that chem_linkCategory.
has a category chem_link.
chem_linkItem
Abstract datatype property for chem_link items.
reference_to_chem_link
cross-reference to chem_link.
referenced_by_chem_link
cross-reference from chem_link.
chem_link.details
A description of special aspects of a link between
chemical components in the structure.
chem_link.id
The value of attribute id in category chem_link must uniquely identify each
item in the CHEM_LINK list.
peptide
oligosaccharide 1,4
DNA
0
chem_link_angle
Data items in the CHEM_LINK_ANGLE category record details
about angles in a link between chemical components.
Example 1 - Engh & Huber parameters [Acta Cryst. (1991), A47,
392-400] as interpreted by J. P. Priestle (1995). Consistent
Stereochemical Dictionaries for Refinement and Model
Building. CCP4 Daresbury Study Weekend,
DL-CONF-95-001, ISSN 1358-6254. Warrington: Daresbury
Laboratory.
<PDBx:chem_link_angleCategory>
<PDBx:chem_link_angle atom_id_1="N" atom_id_2="CA" atom_id_3="C" link_id="PEPTIDE">
<PDBx:atom_1_comp_id>1</PDBx:atom_1_comp_id>
<PDBx:atom_2_comp_id>1</PDBx:atom_2_comp_id>
<PDBx:atom_3_comp_id>1</PDBx:atom_3_comp_id>
<PDBx:value_angle>111.2</PDBx:value_angle>
<PDBx:value_angle_esd>2.8</PDBx:value_angle_esd>
</PDBx:chem_link_angle>
<PDBx:chem_link_angle atom_id_1="CA" atom_id_2="C" atom_id_3="O" link_id="PEPTIDE">
<PDBx:atom_1_comp_id>1</PDBx:atom_1_comp_id>
<PDBx:atom_2_comp_id>1</PDBx:atom_2_comp_id>
<PDBx:atom_3_comp_id>1</PDBx:atom_3_comp_id>
<PDBx:value_angle>120.8</PDBx:value_angle>
<PDBx:value_angle_esd>1.7</PDBx:value_angle_esd>
</PDBx:chem_link_angle>
<PDBx:chem_link_angle atom_id_1="CA" atom_id_2="C" atom_id_3="N" link_id="PEPTIDE">
<PDBx:atom_1_comp_id>1</PDBx:atom_1_comp_id>
<PDBx:atom_2_comp_id>1</PDBx:atom_2_comp_id>
<PDBx:atom_3_comp_id>2</PDBx:atom_3_comp_id>
<PDBx:value_angle>116.2</PDBx:value_angle>
<PDBx:value_angle_esd>2.0</PDBx:value_angle_esd>
</PDBx:chem_link_angle>
<PDBx:chem_link_angle atom_id_1="O" atom_id_2="C" atom_id_3="N" link_id="PEPTIDE">
<PDBx:atom_1_comp_id>1</PDBx:atom_1_comp_id>
<PDBx:atom_2_comp_id>1</PDBx:atom_2_comp_id>
<PDBx:atom_3_comp_id>2</PDBx:atom_3_comp_id>
<PDBx:value_angle>123.0</PDBx:value_angle>
<PDBx:value_angle_esd>1.6</PDBx:value_angle_esd>
</PDBx:chem_link_angle>
<PDBx:chem_link_angle atom_id_1="C" atom_id_2="N" atom_id_3="CA" link_id="PEPTIDE">
<PDBx:atom_1_comp_id>1</PDBx:atom_1_comp_id>
<PDBx:atom_2_comp_id>2</PDBx:atom_2_comp_id>
<PDBx:atom_3_comp_id>2</PDBx:atom_3_comp_id>
<PDBx:value_angle>121.7</PDBx:value_angle>
<PDBx:value_angle_esd>1.8</PDBx:value_angle_esd>
</PDBx:chem_link_angle>
</PDBx:chem_link_angleCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
1
1
1
chem_link_angleCategory
This property indicates that datablock
has a category holder chem_link_angleCategory.
chem_link_angleCategory
This property indicates that chem_link_angleCategory.
has a category chem_link_angle.
chem_link_angleItem
Abstract datatype property for chem_link_angle items.
reference_to_chem_link_angle
cross-reference to chem_link_angle.
referenced_by_chem_link_angle
cross-reference from chem_link_angle.
1
2
This data item indicates whether atom 1 is found in the first
or the second of the two components connected by the link.
1
2
This data item indicates whether atom 2 is found in the first
or the second of the two components connected by the link.
1
2
This data item indicates whether atom 3 is found in the first
or the second of the two components connected by the link.
chem_link_angle.value_angle
The value that should be taken as the target value for the angle
associated with the specified atoms, expressed in degrees.
chem_link_angle.value_angle_esd
The standard uncertainty (estimated standard deviation)
of attribute value_angle in category chem_link_angle.
chem_link_angle.value_dist
The value that should be taken as the target value for the angle
associated with the specified atoms, expressed as the distance
between the atoms specified by attribute atom_id_1 in category chem_comp_angle and
attribute atom_id_3 in category chem_comp_angle.
chem_link_angle.value_dist_esd
The standard uncertainty (estimated standard deviation)
of attribute value_dist in category chem_comp_angle.
chem_link_angle.atom_id_1
The ID of the first of the three atoms that define the angle.
An atom with this ID must exist in the component of the type
specified by attribute type_comp_1 in category chem_comp_link (or
attribute type_comp_2 in category chem_comp_link, where the appropriate data item
is indicated by the value of attribute atom_1_comp_id) in category chem_comp_angle.
chem_link_angle.atom_id_2
The ID of the second of the three atoms that define the angle.
The second atom is taken to be the apex of the angle.
An atom with this ID must exist in the component of the type
specified by attribute type_comp_1 in category chem_comp_link (or
attribute type_comp_2 in category chem_comp_link, where the appropriate data item
is indicated by the value of attribute atom_2_comp_id) in category chem_comp_angle.
chem_link_angle.atom_id_3
The ID of the third of the three atoms that define the angle.
An atom with this ID must exist in the component of the type
specified by attribute type_comp_1 in category chem_comp_link (or
attribute type_comp_2 in category chem_comp_link, where the appropriate data item
is indicated by the value of attribute atom_3_comp_id) in category chem_comp_angle.
chem_link_angle.link_id
This data item is a pointer to attribute id in category chem_link in the CHEM_LINK
category.
0
chem_link_bond
Data items in the CHEM_LINK_BOND category record details about
bonds in a link between components in the chemical structure.
Example 1 - Engh & Huber parameters [Acta Cryst. (1991), A47,
392-400] as interpreted by J. P. Priestle (1995). Consistent
Stereochemical Dictionaries for Refinement and Model
Building. CCP4 Daresbury Study Weekend,
DL-CONF-95-001, ISSN 1358-6254. Warrington: Daresbury
Laboratory.
<PDBx:chem_link_bondCategory>
<PDBx:chem_link_bond atom_id_1="N" atom_id_2="CA" link_id="PEPTIDE">
<PDBx:atom_1_comp_id>1</PDBx:atom_1_comp_id>
<PDBx:atom_2_comp_id>1</PDBx:atom_2_comp_id>
<PDBx:value_dist>1.458</PDBx:value_dist>
<PDBx:value_dist_esd>0.019</PDBx:value_dist_esd>
</PDBx:chem_link_bond>
<PDBx:chem_link_bond atom_id_1="CA" atom_id_2="C" link_id="PEPTIDE">
<PDBx:atom_1_comp_id>1</PDBx:atom_1_comp_id>
<PDBx:atom_2_comp_id>1</PDBx:atom_2_comp_id>
<PDBx:value_dist>1.525</PDBx:value_dist>
<PDBx:value_dist_esd>0.021</PDBx:value_dist_esd>
</PDBx:chem_link_bond>
<PDBx:chem_link_bond atom_id_1="C" atom_id_2="N" link_id="PEPTIDE">
<PDBx:atom_1_comp_id>1</PDBx:atom_1_comp_id>
<PDBx:atom_2_comp_id>2</PDBx:atom_2_comp_id>
<PDBx:value_dist>1.329</PDBx:value_dist>
<PDBx:value_dist_esd>0.014</PDBx:value_dist_esd>
</PDBx:chem_link_bond>
<PDBx:chem_link_bond atom_id_1="C" atom_id_2="O" link_id="PEPTIDE">
<PDBx:atom_1_comp_id>1</PDBx:atom_1_comp_id>
<PDBx:atom_2_comp_id>1</PDBx:atom_2_comp_id>
<PDBx:value_dist>1.231</PDBx:value_dist>
<PDBx:value_dist_esd>0.020</PDBx:value_dist_esd>
</PDBx:chem_link_bond>
</PDBx:chem_link_bondCategory>
0
1
0
1
0
1
0
1
0
1
1
1
1
chem_link_bondCategory
This property indicates that datablock
has a category holder chem_link_bondCategory.
chem_link_bondCategory
This property indicates that chem_link_bondCategory.
has a category chem_link_bond.
chem_link_bondItem
Abstract datatype property for chem_link_bond items.
reference_to_chem_link_bond
cross-reference to chem_link_bond.
referenced_by_chem_link_bond
cross-reference from chem_link_bond.
1
2
This data item indicates whether atom 1 is found in the first
or the second of the two components connected by the link.
1
2
This data item indicates whether atom 2 is found in the first
or the second of the two chemical components connected by
the link.
chem_link_bond.value_dist
The value that should be taken as the target for the chemical
bond associated with the specified atoms, expressed as a
distance.
chem_link_bond.value_dist_esd
The standard uncertainty (estimated standard deviation)
of attribute value_dist in category chem_link_bond.
sing
doub
trip
quad
arom
poly
delo
pi
The value that should be taken as the target for the chemical
bond associated with the specified atoms, expressed as a bond
order.
chem_link_bond.atom_id_1
The ID of the first of the two atoms that define the bond.
As this data item does not point to a specific atom in a
specific chemical component, it is not a child in the
linkage sense.
chem_link_bond.atom_id_2
The ID of the second of the two atoms that define the bond.
As this data item does not point to a specific atom in a
specific component, it is not a child in the linkage sense.
chem_link_bond.link_id
This data item is a pointer to attribute id in category chem_link in the CHEM_LINK
category.
0
chem_link_chir
Data items in the CHEM_LINK_CHIR category provide details about
the chiral centres in a link between two chemical components.
The atoms bonded to the chiral atom are specified in the
CHEM_LINK_CHIR_ATOM category.
0
1
0
1
1
1
0
1
0
1
0
1
0
1
0
1
1
1
chem_link_chirCategory
This property indicates that datablock
has a category holder chem_link_chirCategory.
chem_link_chirCategory
This property indicates that chem_link_chirCategory.
has a category chem_link_chir.
chem_link_chirItem
Abstract datatype property for chem_link_chir items.
reference_to_chem_link_chir
cross-reference to chem_link_chir.
referenced_by_chem_link_chir
cross-reference from chem_link_chir.
1
2
This data item indicates whether the chiral atom is found in the
first or the second of the two components connected by the
link.
R
S
The chiral configuration of the atom that is a chiral centre.
chem_link_chir.atom_id
The ID of the atom that is a chiral centre.
As this data item does not point to a specific atom in a
specific chemical component, it is not a child in the linkage
sense.
chem_link_chir.number_atoms_all
The total number of atoms bonded to the atom specified by
attribute atom_id in category chem_link_chir.
chem_link_chir.number_atoms_nh
The number of non-hydrogen atoms bonded to the atom specified by
attribute atom_id in category chem_link_chir.
sign
nosign
A flag to indicate whether a chiral volume should match the
standard value in both magnitude and sign, or in magnitude only.
chem_link_chir.volume_three
The chiral volume, V(c), for chiral centres that involve a chiral
atom bonded to three non-hydrogen atoms and one hydrogen atom.
V~c~ = V1 * (V2 X V3)
V1 = the vector distance from the atom specified by
attribute atom_id in category chem_link_chir to the first atom in the
CHEM_LINK_CHIR_ATOM list
V2 = the vector distance from the atom specified by
attribute atom_id in category chem_link_chir to the second atom in the
CHEM_LINK_CHIR_ATOM list
V3 = the vector distance from the atom specified by
attribute atom_id in category chem_link_chir to the third atom in the
CHEM_LINK_CHIR_ATOM list
* = the vector dot product
X = the vector cross product
chem_link_chir.volume_three_esd
The standard uncertainty (estimated standard deviation)
of attribute volume_three in category chem_link_chir.
chem_link_chir.id
The value of attribute id in category chem_link_chir must uniquely identify a record
in the CHEM_LINK_CHIR list.
chem_link_chir.link_id
This data item is a pointer to attribute id in category chem_link in the CHEM_LINK
category.
0
chem_link_chir_atom
Data items in the CHEM_LINK_CHIR_ATOM category enumerate the
atoms bonded to a chiral atom in a link between two
chemical components.
0
1
0
1
1
1
chem_link_chir_atomCategory
This property indicates that datablock
has a category holder chem_link_chir_atomCategory.
chem_link_chir_atomCategory
This property indicates that chem_link_chir_atomCategory.
has a category chem_link_chir_atom.
chem_link_chir_atomItem
Abstract datatype property for chem_link_chir_atom items.
reference_to_chem_link_chir_atom
cross-reference to chem_link_chir_atom.
referenced_by_chem_link_chir_atom
cross-reference from chem_link_chir_atom.
1
2
This data item indicates whether the atom bonded to a chiral
atom is found in the first or the second of the two components
connected by the link.
chem_link_chir_atom.dev
The standard uncertainty (estimated standard deviation)
of the position of this atom from the plane defined by
all of the atoms in the plane.
chem_link_chir_atom.atom_id
The ID of an atom bonded to the chiral atom.
As this data item does not point to a specific atom in a
specific chemical component, it is not a child in the linkage
sense.
chem_link_chir_atom.chir_id
This data item is a pointer to attribute id in category chem_link_chir in the
CHEM_LINK_CHIR category.
0
chem_link_plane
Data items in the CHEM_LINK_PLANE category provide identifiers
for the planes in a link between two chemical components.
The atoms in the plane are specified in the CHEM_LINK_PLANE_ATOM
category.
0
1
0
1
1
1
chem_link_planeCategory
This property indicates that datablock
has a category holder chem_link_planeCategory.
chem_link_planeCategory
This property indicates that chem_link_planeCategory.
has a category chem_link_plane.
chem_link_planeItem
Abstract datatype property for chem_link_plane items.
reference_to_chem_link_plane
cross-reference to chem_link_plane.
referenced_by_chem_link_plane
cross-reference from chem_link_plane.
chem_link_plane.number_atoms_all
The total number of atoms in the plane.
chem_link_plane.number_atoms_nh
The number of non-hydrogen atoms in the plane.
chem_link_plane.id
The value of attribute id in category chem_link_plane must uniquely identify a record
in the CHEM_LINK_PLANE list.
chem_link_plane.link_id
This data item is a pointer to attribute id in category chem_link in the CHEM_LINK
category.
0
chem_link_plane_atom
Data items in the CHEM_LINK_PLANE_ATOM category enumerate the
atoms in a plane in a link between two chemical components.
0
1
1
1
chem_link_plane_atomCategory
This property indicates that datablock
has a category holder chem_link_plane_atomCategory.
chem_link_plane_atomCategory
This property indicates that chem_link_plane_atomCategory.
has a category chem_link_plane_atom.
chem_link_plane_atomItem
Abstract datatype property for chem_link_plane_atom items.
reference_to_chem_link_plane_atom
cross-reference to chem_link_plane_atom.
referenced_by_chem_link_plane_atom
cross-reference from chem_link_plane_atom.
1
2
This data item indicates whether the atom in a plane is found in
the first or the second of the two components connected by the
link.
chem_link_plane_atom.atom_id
The ID of an atom involved in the plane.
As this data item does not point to a specific atom in a
specific chemical component, it is not a child in the linkage
sense.
chem_link_plane_atom.plane_id
This data item is a pointer to attribute id in category chem_link_plane in the
CHEM_LINK_PLANE category.
0
chem_link_tor
Data items in the CHEM_LINK_TOR category record details about
the torsion angles in a link between two chemical components.
As torsion angles can have more than one target value, the
target values are specified in the CHEM_LINK_TOR_VALUE category.
0
1
0
1
0
1
0
1
1
1
1
1
1
1
1
1
1
1
chem_link_torCategory
This property indicates that datablock
has a category holder chem_link_torCategory.
chem_link_torCategory
This property indicates that chem_link_torCategory.
has a category chem_link_tor.
chem_link_torItem
Abstract datatype property for chem_link_tor items.
reference_to_chem_link_tor
cross-reference to chem_link_tor.
referenced_by_chem_link_tor
cross-reference from chem_link_tor.
1
2
This data item indicates whether atom 1 is found in the first
or the second of the two components connected by the link.
1
2
This data item indicates whether atom 2 is found in the first
or the second of the two components connected by the link.
1
2
This data item indicates whether atom 3 is found in the first
or the second of the two components connected by the link.
1
2
This data item indicates whether atom 4 is found in the first
or the second of the two components connected by the link.
chem_link_tor.atom_id_1
The ID of the first of the four atoms that define the torsion
angle.
As this data item does not point to a specific atom in a
specific chemical component, it is not a child in the linkage
sense.
chem_link_tor.atom_id_2
The ID of the second of the four atoms that define the torsion
angle.
As this data item does not point to a specific atom in a
specific chemical component, it is not a child in the linkage
sense.
chem_link_tor.atom_id_3
The ID of the third of the four atoms that define the torsion
angle.
As this data item does not point to a specific atom in a
specific chemical component, it is not a child in the linkage
sense.
chem_link_tor.atom_id_4
The ID of the fourth of the four atoms that define the torsion
angle.
As this data item does not point to a specific atom in a
specific chemical component, it is not a child in the linkage
sense.
chem_link_tor.id
The value of attribute id in category chem_link_tor must uniquely identify a
record in the CHEM_LINK_TOR list.
chem_link_tor.link_id
This data item is a pointer to attribute id in category chem_link in the CHEM_LINK
category.
0
chem_link_tor_value
Data items in the CHEM_LINK_TOR_VALUE category record details
about the target values for the torsion angles enumerated in the
CHEM_LINK_TOR list. Target values may be specified as angles
in degrees, as a distance between the first and fourth atoms, or
both.
1
1
1
1
0
1
0
1
1
chem_link_tor_valueCategory
This property indicates that datablock
has a category holder chem_link_tor_valueCategory.
chem_link_tor_valueCategory
This property indicates that chem_link_tor_valueCategory.
has a category chem_link_tor_value.
chem_link_tor_valueItem
Abstract datatype property for chem_link_tor_value items.
reference_to_chem_link_tor_value
cross-reference to chem_link_tor_value.
referenced_by_chem_link_tor_value
cross-reference from chem_link_tor_value.
chem_link_tor_value.angle
A value that should be taken as a potential target value for the
torsion angle associated with the specified atoms, expressed in
degrees.
chem_link_tor_value.angle_esd
The standard uncertainty (estimated standard deviation)
of attribute angle in category chem_link_tor_value.
chem_link_tor_value.dist
A value that should be taken as a potential target value for the
torsion angle associated with the specified atoms, expressed as
the distance between the atoms specified by
_chem_link_tor.atom_id_1 and _chem_link_tor.atom_id_4 in the
referenced record in the CHEM_LINK_TOR list. Note that the
torsion angle cannot be fully specified by a distance (for
instance, a torsion angle of -60 degree will yield the same
distance as a 60 degree angle). However, the distance
specification can be useful for refinement in situations in
which the angle is already close to the desired value.
chem_link_tor_value.dist_esd
The standard uncertainty (estimated standard deviation)
of attribute dist in category chem_link_tor_value.
chem_link_tor_value.tor_id
This data item is a pointer to attribute id in category chem_link_tor in the
CHEM_LINK_TOR category.
0
chemical
Data items in the CHEMICAL category would not in general be
used in a macromolecular CIF. See instead the ENTITY data
items.
Data items in the CHEMICAL category record details about the
composition and chemical properties of the compounds. The
formula data items must agree with those that specify the
density, unit-cell and Z values.
Example 1 - based on data set 9597gaus of Alyea, Ferguson & Kannan
[Acta Cryst. (1996), C52, 765-767].
<PDBx:chemicalCategory>
<PDBx:chemical entry_id="9597gaus">
<PDBx:name_systematic>trans-bis(tricyclohexylphosphine)tetracarbonylmolybdenum(0)</PDBx:name_systematic>
</PDBx:chemical>
</PDBx:chemicalCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
chemicalCategory
This property indicates that datablock
has a category holder chemicalCategory.
chemicalCategory
This property indicates that chemicalCategory.
has a category chemical.
chemicalItem
Abstract datatype property for chemical items.
reference_to_chemical
cross-reference to chemical.
referenced_by_chemical
cross-reference from chemical.
rm
ad
rmad
syn
unk
Necessary conditions for the assignment of
attribute absolute_configuration in category chemical are given by H. D. Flack and
G. Bernardinelli (1999, 2000).
Ref: Flack, H. D. & Bernardinelli, G. (1999). Acta Cryst. A55,
908-915. (http://www.iucr.org/paper?sh0129)
Flack, H. D. & Bernardinelli, G. (2000). J. Appl. Cryst.
33, 1143-1148. (http://www.iucr.org/paper?ks0021)
chemical.compound_source
Description of the source of the compound under study, or of the
parent molecule if a simple derivative is studied. This includes
the place of discovery for minerals or the actual source of a
natural product.
From Norilsk (USSR)
Extracted from the bark of Cinchona Naturalis
chemical.melting_point
The temperature in kelvins at which the crystalline solid changes
to a liquid.
chemical.melting_point_gt
A temperature in kelvins above
which the melting point (the temperature at which the
crystalline solid changes to a liquid) lies.
_chemical.melting_point_gt and _chemical.melting_point_lt
allow a range of temperatures to be given.
attribute melting_point in category chemical should always be used in preference
to these two items whenever possible.
chemical.melting_point_lt
A temperature in kelvins below which the melting point (the
temperature at which the crystalline solid changes to a liquid)
lies. _chemical.melting_point_gt and _chemical.melting_point_lt
allow a range of temperatures to be given.
attribute melting_point in category chemical should always be used in preference
to these two items whenever possible.
chemical.name_common
Trivial name by which the compound is commonly known.
1-bromoestradiol
chemical.name_mineral
Mineral name accepted by the International Mineralogical
Association. Use only for natural minerals. See also
attribute compound_source in category chemical.
chalcopyrite
chemical.name_structure_type
Commonly used structure-type name. Usually only applied to
minerals or inorganic compounds.
perovskite
sphalerite
A15
chemical.name_systematic
IUPAC or Chemical Abstracts full name of the compound.
1-bromoestra-1,3,5(10)-triene-3,17\b-diol
chemical.optical_rotation
The optical rotation in solution of the compound is
specified in the following format:
'[\a]^TEMP^~WAVE~ = SORT (c = CONC, SOLV)'
where:
TEMP is the temperature of the measurement in degrees
Celsius,
WAVE is an indication of the wavelength of the light
used for the measurement,
CONC is the concentration of the solution given as the
mass of the substance in g in 100 ml of solution,
SORT is the signed value (preceded by a + or a - sign)
of 100.\a/(l.c), where \a is the signed optical
rotation in degrees measured in a cell of length l in
dm and c is the value of CONC as defined above, and
SOLV is the chemical formula of the solvent.
[\a]^25^~D~ = +108 (c = 3.42, CHCl~3~)
chemical.properties_biological
A free-text description of the biological properties of the
material.
diverse biological activities including use as a
laxative and strong antibacterial activity against
S. aureus and weak activity against
cyclooxygenase-1 (COX-1)
antibiotic activity against Bacillus subtilis
(ATCC 6051) but no significant activity against
Candida albicans (ATCC 14053), Aspergillus flavus
(NRRL 6541) and Fusarium verticillioides (NRRL
25457)
weakly potent lipoxygenase nonredox inhibitor
no influenza A virus sialidase inhibitory and
plaque reduction activities
low toxicity against Drosophila melanogaster
chemical.properties_physical
A free-text description of the physical properties of the material.
air-sensitive
moisture-sensitive
hygroscopic
deliquescent
oxygen-sensitive
photo-sensitive
pyrophoric
semiconductor
ferromagnetic at low temperature
paramagnetic and thermochromic
chemical.temperature_decomposition
The temperature in kelvins at which the solid decomposes.
350
chemical.temperature_decomposition_esd
The estimated standard deviation of
attribute temperature_decomposition in category chemical.
chemical.temperature_decomposition_gt
A temperature in kelvins above which the solid is known to
decompose. attribute temperature_decomposition_gt in category chemical and
attribute temperature_decomposition_lt in category chemical allow
a range of temperatures to be given.
attribute temperature_decomposition in category chemical should always be used in
preference to these two items whenever possible.
350
chemical.temperature_decomposition_lt
A temperature in kelvins below which the solid is known to
decompose. attribute temperature_decomposition_gt in category chemical and
attribute temperature_decomposition_lt in category chemical allow
a range of temperatures to be given.
attribute temperature_decomposition in category chemical should always be used in
preference to these two items whenever possible.
350
chemical.temperature_sublimation
The temperature in kelvins at which the solid sublimes.
350
chemical.temperature_sublimation_esd
The estimated standard deviation of
attribute temperature_sublimation in category chemical.
chemical.temperature_sublimation_gt
A temperature in kelvins above which the solid is known to
sublime. attribute temperature_sublimation_gt in category chemical and
attribute temperature_sublimation_lt in category chemical allow a
range of temperatures to be given.
attribute temperature_sublimation in category chemical should always be used in
preference to these two items whenever possible.
350
chemical.temperature_sublimation_lt
A temperature in kelvins below which the solid is known to
sublime. attribute temperature_sublimation_gt in category chemical and
attribute temperature_sublimation_lt in category chemical allow a
range of temperatures to be given.
attribute temperature_sublimation in category chemical should always be used in
preference to these two items whenever possible.
350
chemical.entry_id
This data item is a pointer to attribute id in category entry in the ENTRY category.
0
chemical_conn_atom
Data items in the CHEMICAL_CONN_ATOM category would not, in
general, be used in a macromolecular CIF. See instead the
ENTITY data items.
Data items in the CHEMICAL_CONN_ATOM and CHEMICAL_CONN_BOND
categories record details about the two-dimensional (2D)
chemical structure of the molecular species. They allow
a 2D chemical diagram to be reconstructed for use in a
publication or in a database search for structural and
substructural relationships.
The CHEMICAL_CONN_ATOM data items provide information about the
chemical properties of the atoms in the structure. In cases
where crystallographic and molecular symmetry elements coincide,
they must also contain symmetry-generated atoms, so that the
CHEMICAL_CONN_ATOM and CHEMICAL_CONN_BOND data items will always
describe a complete chemical entity.
Example 1 - based on data set DPTD of Yamin, Suwandi, Fun, Sivakumar &
bin Shawkataly [Acta Cryst. (1996), C52, 951-953].
<PDBx:chemical_conn_atomCategory>
<PDBx:chemical_conn_atom number="1">
<PDBx:NCA>1</PDBx:NCA>
<PDBx:NH>0</PDBx:NH>
<PDBx:display_x>.39</PDBx:display_x>
<PDBx:display_y>.81</PDBx:display_y>
<PDBx:type_symbol>S</PDBx:type_symbol>
</PDBx:chemical_conn_atom>
<PDBx:chemical_conn_atom number="2">
<PDBx:NCA>2</PDBx:NCA>
<PDBx:NH>0</PDBx:NH>
<PDBx:display_x>.39</PDBx:display_x>
<PDBx:display_y>.96</PDBx:display_y>
<PDBx:type_symbol>S</PDBx:type_symbol>
</PDBx:chemical_conn_atom>
<PDBx:chemical_conn_atom number="3">
<PDBx:NCA>3</PDBx:NCA>
<PDBx:NH>0</PDBx:NH>
<PDBx:display_x>.14</PDBx:display_x>
<PDBx:display_y>.88</PDBx:display_y>
<PDBx:type_symbol>N</PDBx:type_symbol>
</PDBx:chemical_conn_atom>
<PDBx:chemical_conn_atom number="4">
<PDBx:NCA>3</PDBx:NCA>
<PDBx:NH>0</PDBx:NH>
<PDBx:display_x>.33</PDBx:display_x>
<PDBx:display_y>.88</PDBx:display_y>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:chemical_conn_atom>
<PDBx:chemical_conn_atom number="5">
<PDBx:NCA>2</PDBx:NCA>
<PDBx:NH>2</PDBx:NH>
<PDBx:display_x>.11</PDBx:display_x>
<PDBx:display_y>.96</PDBx:display_y>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:chemical_conn_atom>
<PDBx:chemical_conn_atom number="6">
<PDBx:NCA>2</PDBx:NCA>
<PDBx:NH>2</PDBx:NH>
<PDBx:display_x>.03</PDBx:display_x>
<PDBx:display_y>.96</PDBx:display_y>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:chemical_conn_atom>
<PDBx:chemical_conn_atom number="7">
<PDBx:NCA>2</PDBx:NCA>
<PDBx:NH>2</PDBx:NH>
<PDBx:display_x>.03</PDBx:display_x>
<PDBx:display_y>.80</PDBx:display_y>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:chemical_conn_atom>
<PDBx:chemical_conn_atom number="8">
<PDBx:NCA>2</PDBx:NCA>
<PDBx:NH>2</PDBx:NH>
<PDBx:display_x>.11</PDBx:display_x>
<PDBx:display_y>.80</PDBx:display_y>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:chemical_conn_atom>
<PDBx:chemical_conn_atom number="9">
<PDBx:NCA>1</PDBx:NCA>
<PDBx:NH>0</PDBx:NH>
<PDBx:display_x>.54</PDBx:display_x>
<PDBx:display_y>.81</PDBx:display_y>
<PDBx:type_symbol>S</PDBx:type_symbol>
</PDBx:chemical_conn_atom>
<PDBx:chemical_conn_atom number="10">
<PDBx:NCA>2</PDBx:NCA>
<PDBx:NH>0</PDBx:NH>
<PDBx:display_x>.54</PDBx:display_x>
<PDBx:display_y>.96</PDBx:display_y>
<PDBx:type_symbol>S</PDBx:type_symbol>
</PDBx:chemical_conn_atom>
<PDBx:chemical_conn_atom number="11">
<PDBx:NCA>3</PDBx:NCA>
<PDBx:NH>0</PDBx:NH>
<PDBx:display_x>.80</PDBx:display_x>
<PDBx:display_y>.88</PDBx:display_y>
<PDBx:type_symbol>N</PDBx:type_symbol>
</PDBx:chemical_conn_atom>
<PDBx:chemical_conn_atom number="12">
<PDBx:NCA>3</PDBx:NCA>
<PDBx:NH>0</PDBx:NH>
<PDBx:display_x>.60</PDBx:display_x>
<PDBx:display_y>.88</PDBx:display_y>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:chemical_conn_atom>
<PDBx:chemical_conn_atom number="13">
<PDBx:NCA>2</PDBx:NCA>
<PDBx:NH>2</PDBx:NH>
<PDBx:display_x>.84</PDBx:display_x>
<PDBx:display_y>.96</PDBx:display_y>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:chemical_conn_atom>
<PDBx:chemical_conn_atom number="14">
<PDBx:NCA>2</PDBx:NCA>
<PDBx:NH>2</PDBx:NH>
<PDBx:display_x>.91</PDBx:display_x>
<PDBx:display_y>.96</PDBx:display_y>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:chemical_conn_atom>
<PDBx:chemical_conn_atom number="15">
<PDBx:NCA>2</PDBx:NCA>
<PDBx:NH>2</PDBx:NH>
<PDBx:display_x>.91</PDBx:display_x>
<PDBx:display_y>.80</PDBx:display_y>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:chemical_conn_atom>
<PDBx:chemical_conn_atom number="16">
<PDBx:NCA>2</PDBx:NCA>
<PDBx:NH>2</PDBx:NH>
<PDBx:display_x>.84</PDBx:display_x>
<PDBx:display_y>.80</PDBx:display_y>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:chemical_conn_atom>
</PDBx:chemical_conn_atomCategory>
0
1
0
1
0
1
0
1
0
1
1
1
1
chemical_conn_atomCategory
This property indicates that datablock
has a category holder chemical_conn_atomCategory.
chemical_conn_atomCategory
This property indicates that chemical_conn_atomCategory.
has a category chemical_conn_atom.
chemical_conn_atomItem
Abstract datatype property for chemical_conn_atom items.
reference_to_chemical_conn_atom
cross-reference to chemical_conn_atom.
referenced_by_chemical_conn_atom
cross-reference from chemical_conn_atom.
chemical_conn_atom.NCA
The number of connected atoms excluding terminal hydrogen atoms.
chemical_conn_atom.NH
The total number of hydrogen atoms attached to this atom,
regardless of whether they are included in the refinement or
the ATOM_SITE list. This number is the same as
attribute attached_hydrogens in category atom_site only if none of the hydrogen
atoms appear in the ATOM_SITE list.
chemical_conn_atom.charge
The net integer charge assigned to this atom. This is the
formal charge assignment normally found in chemical diagrams.
for an ammonium nitrogen
1
for a chloride ion
-1
chemical_conn_atom.display_x
The 2D Cartesian x coordinate of the position of this atom in a
recognizable chemical diagram. The coordinate origin is at the
lower left corner, the x axis is horizontal and the y axis
is vertical. The coordinates must lie in the range 0.0 to 1.0.
These coordinates can be obtained from projections of a suitable
uncluttered view of the molecular structure.
chemical_conn_atom.display_y
The 2D Cartesian y coordinate of the position of this atom in a
recognizable chemical diagram. The coordinate origin is at the
lower left corner, the x axis is horizontal and the y axis
is vertical. The coordinates must lie in the range 0.0 to 1.0.
These coordinates can be obtained from projections of a suitable
uncluttered view of the molecular structure.
chemical_conn_atom.type_symbol
This data item is a pointer to attribute symbol in category atom_type in the
ATOM_TYPE category.
chemical_conn_atom.number
The chemical sequence number to be associated with this atom.
Within an ATOM_SITE list, this number must match one of
the attribute chemical_conn_number in category atom_site values.
0
chemical_conn_bond
Data items in the CHEMICAL_CONN_BOND category would not, in
general, be used in a macromolecular CIF. See instead the
ENTITY data items.
Data items in the CHEMICAL_CONN_ATOM and CHEMICAL_CONN_BOND
categories record details about the two-dimensional (2D)
chemical structure of the molecular species. They allow a
2D chemical diagram to be reconstructed for use in a
publication or in a database search for structural and
substructural relationships.
The CHEMICAL_CONN_BOND data items specify the connections
between the atoms in the CHEMICAL_CONN_ATOM list and the nature
of the chemical bond between these atoms.
Example 1 - based on data set DPTD of Yamin, Suwandi, Fun, Sivakumar &
bin Shawkataly [Acta Cryst. (1996), C52, 951-953].
<PDBx:chemical_conn_bondCategory>
<PDBx:chemical_conn_bond atom_1="4" atom_2="1">
<PDBx:type>doub</PDBx:type>
</PDBx:chemical_conn_bond>
<PDBx:chemical_conn_bond atom_1="4" atom_2="3">
<PDBx:type>sing</PDBx:type>
</PDBx:chemical_conn_bond>
<PDBx:chemical_conn_bond atom_1="4" atom_2="2">
<PDBx:type>sing</PDBx:type>
</PDBx:chemical_conn_bond>
<PDBx:chemical_conn_bond atom_1="5" atom_2="3">
<PDBx:type>sing</PDBx:type>
</PDBx:chemical_conn_bond>
<PDBx:chemical_conn_bond atom_1="6" atom_2="5">
<PDBx:type>sing</PDBx:type>
</PDBx:chemical_conn_bond>
<PDBx:chemical_conn_bond atom_1="7" atom_2="6">
<PDBx:type>sing</PDBx:type>
</PDBx:chemical_conn_bond>
<PDBx:chemical_conn_bond atom_1="8" atom_2="7">
<PDBx:type>sing</PDBx:type>
</PDBx:chemical_conn_bond>
<PDBx:chemical_conn_bond atom_1="8" atom_2="3">
<PDBx:type>sing</PDBx:type>
</PDBx:chemical_conn_bond>
<PDBx:chemical_conn_bond atom_1="10" atom_2="2">
<PDBx:type>sing</PDBx:type>
</PDBx:chemical_conn_bond>
<PDBx:chemical_conn_bond atom_1="12" atom_2="9">
<PDBx:type>doub</PDBx:type>
</PDBx:chemical_conn_bond>
<PDBx:chemical_conn_bond atom_1="12" atom_2="11">
<PDBx:type>sing</PDBx:type>
</PDBx:chemical_conn_bond>
<PDBx:chemical_conn_bond atom_1="12" atom_2="10">
<PDBx:type>sing</PDBx:type>
</PDBx:chemical_conn_bond>
<PDBx:chemical_conn_bond atom_1="13" atom_2="11">
<PDBx:type>sing</PDBx:type>
</PDBx:chemical_conn_bond>
<PDBx:chemical_conn_bond atom_1="14" atom_2="13">
<PDBx:type>sing</PDBx:type>
</PDBx:chemical_conn_bond>
<PDBx:chemical_conn_bond atom_1="15" atom_2="14">
<PDBx:type>sing</PDBx:type>
</PDBx:chemical_conn_bond>
<PDBx:chemical_conn_bond atom_1="16" atom_2="15">
<PDBx:type>sing</PDBx:type>
</PDBx:chemical_conn_bond>
<PDBx:chemical_conn_bond atom_1="16" atom_2="11">
<PDBx:type>sing</PDBx:type>
</PDBx:chemical_conn_bond>
<PDBx:chemical_conn_bond atom_1="17" atom_2="5">
<PDBx:type>sing</PDBx:type>
</PDBx:chemical_conn_bond>
<PDBx:chemical_conn_bond atom_1="18" atom_2="5">
<PDBx:type>sing</PDBx:type>
</PDBx:chemical_conn_bond>
<PDBx:chemical_conn_bond atom_1="19" atom_2="6">
<PDBx:type>sing</PDBx:type>
</PDBx:chemical_conn_bond>
<PDBx:chemical_conn_bond atom_1="20" atom_2="6">
<PDBx:type>sing</PDBx:type>
</PDBx:chemical_conn_bond>
<PDBx:chemical_conn_bond atom_1="21" atom_2="7">
<PDBx:type>sing</PDBx:type>
</PDBx:chemical_conn_bond>
<PDBx:chemical_conn_bond atom_1="22" atom_2="7">
<PDBx:type>sing</PDBx:type>
</PDBx:chemical_conn_bond>
<PDBx:chemical_conn_bond atom_1="23" atom_2="8">
<PDBx:type>sing</PDBx:type>
</PDBx:chemical_conn_bond>
<PDBx:chemical_conn_bond atom_1="24" atom_2="8">
<PDBx:type>sing</PDBx:type>
</PDBx:chemical_conn_bond>
<PDBx:chemical_conn_bond atom_1="25" atom_2="13">
<PDBx:type>sing</PDBx:type>
</PDBx:chemical_conn_bond>
<PDBx:chemical_conn_bond atom_1="26" atom_2="13">
<PDBx:type>sing</PDBx:type>
</PDBx:chemical_conn_bond>
<PDBx:chemical_conn_bond atom_1="27" atom_2="14">
<PDBx:type>sing</PDBx:type>
</PDBx:chemical_conn_bond>
<PDBx:chemical_conn_bond atom_1="28" atom_2="14">
<PDBx:type>sing</PDBx:type>
</PDBx:chemical_conn_bond>
<PDBx:chemical_conn_bond atom_1="29" atom_2="15">
<PDBx:type>sing</PDBx:type>
</PDBx:chemical_conn_bond>
<PDBx:chemical_conn_bond atom_1="30" atom_2="15">
<PDBx:type>sing</PDBx:type>
</PDBx:chemical_conn_bond>
<PDBx:chemical_conn_bond atom_1="31" atom_2="16">
<PDBx:type>sing</PDBx:type>
</PDBx:chemical_conn_bond>
<PDBx:chemical_conn_bond atom_1="32" atom_2="16">
<PDBx:type>sing</PDBx:type>
</PDBx:chemical_conn_bond>
</PDBx:chemical_conn_bondCategory>
0
1
1
1
chemical_conn_bondCategory
This property indicates that datablock
has a category holder chemical_conn_bondCategory.
chemical_conn_bondCategory
This property indicates that chemical_conn_bondCategory.
has a category chemical_conn_bond.
chemical_conn_bondItem
Abstract datatype property for chemical_conn_bond items.
reference_to_chemical_conn_bond
cross-reference to chemical_conn_bond.
referenced_by_chemical_conn_bond
cross-reference from chemical_conn_bond.
sing
doub
trip
quad
arom
poly
delo
pi
The chemical bond type associated with the connection between
the two sites attribute atom_1 in category chemical_conn_bond and
attribute atom_2 in category chemical_conn_bond.
chemical_conn_bond.atom_1
This data item is a pointer to attribute number in category chemical_conn_atom in the
CHEMICAL_CONN_ATOM category.
chemical_conn_bond.atom_2
This data item is a pointer to attribute number in category chemical_conn_atom in the
CHEMICAL_CONN_ATOM category.
0
chemical_formula
Data items in the CHEMICAL_FORMULA category would not, in
general, be used in a macromolecular CIF. See instead the
ENTITY data items.
Data items in the CHEMICAL_FORMULA category specify the
composition and chemical properties of the compound. The formula
data items must agree with those that specify the density,
unit-cell and Z values.
The following rules apply to the construction of the data items
_chemical_formula.analytical, _chemical_formula.structural and
attribute sum in category chemical_formula. For the data item
attribute moiety in category chemical_formula, the formula construction is broken up
into residues or moieties, i.e. groups of atoms that form a
molecular unit or molecular ion. The rules given below apply
within each moiety but different requirements apply to the way
that moieties are connected (see attribute moiety).
in category chemical_formula
(1) Only recognized element symbols may be used.
(2) Each element symbol is followed by a 'count' number. A count
of '1' may be omitted.
(3) A space or parenthesis must separate each cluster of (element
symbol + count).
(4) Where a group of elements is enclosed in parentheses, the
multiplier for the group must follow the closing parenthesis.
That is, all element and group multipliers are assumed to be
printed as subscripted numbers. (An exception to this rule
exists for attribute moiety in category chemical_formula formulae where pre- and
post-multipliers are permitted for molecular units.)
(5) Unless the elements are ordered in a manner that corresponds
to their chemical structure, as in
attribute structural in category chemical_formula, the order of the elements within
any group or moiety should be: C, then H, then the other
elements in alphabetical order of their symbol. This is the
'Hill' system used by Chemical Abstracts. This ordering is
used in _chemical_formula.moiety and _chemical_formula.sum.
Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991).
Acta Cryst. C47, 2276-2277].
<PDBx:chemical_formulaCategory>
<PDBx:chemical_formula entry_id="TOZ">
<PDBx:moiety>C18 H25 N O3</PDBx:moiety>
<PDBx:sum>C18 H25 N O3</PDBx:sum>
<PDBx:weight>303.40</PDBx:weight>
</PDBx:chemical_formula>
</PDBx:chemical_formulaCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
chemical_formulaCategory
This property indicates that datablock
has a category holder chemical_formulaCategory.
chemical_formulaCategory
This property indicates that chemical_formulaCategory.
has a category chemical_formula.
chemical_formulaItem
Abstract datatype property for chemical_formula items.
reference_to_chemical_formula
cross-reference to chemical_formula.
referenced_by_chemical_formula
cross-reference from chemical_formula.
chemical_formula.analytical
Formula determined by standard chemical analysis including trace
elements. See the CHEMICAL_FORMULA category description for
rules for writing chemical formulae. Parentheses are used only
for standard uncertainties (estimated standard deviations).
Fe2.45(2) Ni1.60(3) S4
chemical_formula.iupac
Formula expressed in conformance with IUPAC rules for inorganic
and metal-organic compounds where these conflict with the rules
for any other CHEMICAL_FORMULA entries. Typically used for
formatting a formula in accordance with journal rules. This
should appear in the data block in addition to the most
appropriate of the other CHEMICAL_FORMULA data names.
Ref: IUPAC (1990). Nomenclature of Inorganic Chemistry.
Oxford: Blackwell Scientific Publications.
[Co Re (C12 H22 P)2 (C O)6].0.5C H3 O H
chemical_formula.moiety
Formula with each discrete bonded residue or ion shown as a
separate moiety. See the CHEMICAL_FORMULA category description
for rules for writing chemical formulae. In addition to the
general formulae requirements, the following rules apply:
(1) Moieties are separated by commas ','.
(2) The order of elements within a moiety follows general rule
(5) in the CHEMICAL_FORMULA category description.
(3) Parentheses are not used within moieties but may surround
a moiety. Parentheses may not be nested.
(4) Charges should be placed at the end of the moiety. The
charge '+' or '-' may be preceded by a numerical multiplier
and should be separated from the last (element symbol +
count) by a space. Pre- or post-multipliers may be used for
individual moieties.
C7 H4 Cl Hg N O3 S
C12 H17 N4 O S 1+, C6 H2 N3 O7 1-
C12 H16 N2 O6, 5(H2 O1)
(Cd 2+)3, (C6 N6 Cr 3-)2, 2(H2 O)
chemical_formula.structural
See the CHEMICAL_FORMULA category description for the rules for
writing chemical formulae for inorganics, organometallics, metal
complexes etc., in which bonded groups are preserved as
discrete entities within parentheses, with post-multipliers as
required. The order of the elements should give as much
information as possible about the chemical structure.
Parentheses may be used and nested as required. This formula
should correspond to the structure as actually reported, i.e.
trace elements not included in atom-type and atom-site data
should not be included in this formula (see also
attribute analytical) in category chemical_formula.
Ca ((Cl O3)2 O)2 (H2 O)6
(Pt (N H3)2 (C5 H7 N3 O)2) (Cl O4)2
chemical_formula.sum
See the CHEMICAL_FORMULA category description for the rules
for writing chemical formulae in which all discrete bonded
residues and ions are summed over the constituent elements,
following the ordering given in general rule (5) in the
CHEMICAL_FORMULA category description. Parentheses are not
normally used.
C18 H19 N7 O8 S
chemical_formula.weight
Formula mass in daltons. This mass should correspond to the
formulae given under attribute structural,
in category chemical_formula _chemical_formula.moiety or _chemical_formula.sum and,
together with the Z value and cell parameters, should
yield the density given as attribute density_diffrn in category exptl_crystal.
chemical_formula.weight_meas
Formula mass in daltons measured by a non-diffraction experiment.
chemical_formula.entry_id
This data item is a pointer to attribute id in category entry in the ENTRY category.
0
citation
Data items in the CITATION category record details about the
literature cited as being relevant to the contents of the data
block.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:citationCategory>
<PDBx:citation id="primary">
<PDBx:book_id_ISBN xsi:nil="true" />
<PDBx:book_publisher xsi:nil="true" />
<PDBx:book_title xsi:nil="true" />
<PDBx:coordinate_linkage>yes</PDBx:coordinate_linkage>
<PDBx:country>US</PDBx:country>
<PDBx:details> The publication that directly relates to this coordinate
set.</PDBx:details>
<PDBx:journal_abbrev>J. Biol. Chem.</PDBx:journal_abbrev>
<PDBx:journal_id_ASTM>HBCHA3</PDBx:journal_id_ASTM>
<PDBx:journal_id_CSD>071</PDBx:journal_id_CSD>
<PDBx:journal_id_ISSN>0021-9258</PDBx:journal_id_ISSN>
<PDBx:journal_issue xsi:nil="true" />
<PDBx:journal_volume>265</PDBx:journal_volume>
<PDBx:page_first>14209</PDBx:page_first>
<PDBx:page_last>14219</PDBx:page_last>
<PDBx:title> Crystallographic analysis of a complex between human
immunodeficiency virus type 1 protease and acetyl-pepstatin
at 2.0-Angstroms resolution.</PDBx:title>
<PDBx:year>1990</PDBx:year>
</PDBx:citation>
<PDBx:citation id="2">
<PDBx:book_id_ISBN xsi:nil="true" />
<PDBx:book_publisher xsi:nil="true" />
<PDBx:book_title xsi:nil="true" />
<PDBx:coordinate_linkage>no</PDBx:coordinate_linkage>
<PDBx:country>UK</PDBx:country>
<PDBx:details> Determination of the structure of the unliganded enzyme.</PDBx:details>
<PDBx:journal_abbrev>Nature</PDBx:journal_abbrev>
<PDBx:journal_id_ASTM>NATUAS</PDBx:journal_id_ASTM>
<PDBx:journal_id_CSD>006</PDBx:journal_id_CSD>
<PDBx:journal_id_ISSN>0028-0836</PDBx:journal_id_ISSN>
<PDBx:journal_issue xsi:nil="true" />
<PDBx:journal_volume>337</PDBx:journal_volume>
<PDBx:page_first>615</PDBx:page_first>
<PDBx:page_last>619</PDBx:page_last>
<PDBx:title> Three-dimensional structure of aspartyl-protease from human
immunodeficiency virus HIV-1.</PDBx:title>
<PDBx:year>1989</PDBx:year>
</PDBx:citation>
<PDBx:citation id="3">
<PDBx:book_id_ISBN xsi:nil="true" />
<PDBx:book_publisher xsi:nil="true" />
<PDBx:book_title xsi:nil="true" />
<PDBx:coordinate_linkage>no</PDBx:coordinate_linkage>
<PDBx:country>US</PDBx:country>
<PDBx:details> Crystallization of the unliganded enzyme.</PDBx:details>
<PDBx:journal_abbrev>J. Biol. Chem.</PDBx:journal_abbrev>
<PDBx:journal_id_ASTM>HBCHA3</PDBx:journal_id_ASTM>
<PDBx:journal_id_CSD>071</PDBx:journal_id_CSD>
<PDBx:journal_id_ISSN>0021-9258</PDBx:journal_id_ISSN>
<PDBx:journal_issue xsi:nil="true" />
<PDBx:journal_volume>264</PDBx:journal_volume>
<PDBx:page_first>1919</PDBx:page_first>
<PDBx:page_last>1921</PDBx:page_last>
<PDBx:title> Crystallization of the aspartylprotease from human
immunodeficiency virus, HIV-1.</PDBx:title>
<PDBx:year>1989</PDBx:year>
</PDBx:citation>
<PDBx:citation id="4">
<PDBx:book_id_ISBN xsi:nil="true" />
<PDBx:book_publisher xsi:nil="true" />
<PDBx:book_title xsi:nil="true" />
<PDBx:coordinate_linkage>no</PDBx:coordinate_linkage>
<PDBx:country>US</PDBx:country>
<PDBx:details> Expression and purification of the enzyme.</PDBx:details>
<PDBx:journal_abbrev>J. Biol. Chem.</PDBx:journal_abbrev>
<PDBx:journal_id_ASTM>HBCHA3</PDBx:journal_id_ASTM>
<PDBx:journal_id_CSD>071</PDBx:journal_id_CSD>
<PDBx:journal_id_ISSN>0021-9258</PDBx:journal_id_ISSN>
<PDBx:journal_issue xsi:nil="true" />
<PDBx:journal_volume>264</PDBx:journal_volume>
<PDBx:page_first>2307</PDBx:page_first>
<PDBx:page_last>2312</PDBx:page_last>
<PDBx:title> Human immunodeficiency virus protease. Bacterial expression
and characterization of the purified aspartic protease.</PDBx:title>
<PDBx:year>1989</PDBx:year>
</PDBx:citation>
</PDBx:citationCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
citationCategory
This property indicates that datablock
has a category holder citationCategory.
citationCategory
This property indicates that citationCategory.
has a category citation.
citationItem
Abstract datatype property for citation items.
reference_to_citation
cross-reference to citation.
referenced_by_citation
cross-reference from citation.
citation.abstract
Abstract for the citation. This is used most when the
citation is extracted from a bibliographic database that
contains full text or abstract information.
citation.abstract_id_CAS
The Chemical Abstracts Service (CAS) abstract identifier;
relevant for journal articles.
citation.book_id_ISBN
The International Standard Book Number (ISBN) code assigned to
the book cited; relevant for books or book chapters.
citation.book_publisher
The name of the publisher of the citation; relevant
for books or book chapters.
John Wiley and Sons
citation.book_publisher_city
The location of the publisher of the citation; relevant
for books or book chapters.
London
citation.book_title
The title of the book in which the citation appeared; relevant
for books or book chapters.
no
n
yes
y
attribute coordinate_linkage in category citation states whether this citation
is concerned with precisely the set of coordinates given in the
data block. If, for instance, the publication described the same
structure, but the coordinates had undergone further refinement
prior to the creation of the data block, the value of this data
item would be 'no'.
citation.country
The country/region of publication; relevant for books
and book chapters.
citation.database_id_CSD
Identifier ('refcode') of the database record in the Cambridge
Structural Database that contains details of the cited structure.
LEKKUH
citation.database_id_Medline
Accession number used by Medline to categorize a specific
bibliographic entry.
89064067
citation.details
A description of special aspects of the relationship
of the contents of the data block to the literature item cited.
citation relates to this precise
coordinate set
citation relates to earlier low-resolution
structure
citation relates to further refinement of
structure reported in citation 2
citation.journal_abbrev
Abbreviated name of the cited journal as given in the
Chemical Abstracts Service Source Index.
J. Mol. Biol.
citation.journal_full
Full name of the cited journal; relevant for journal articles.
Journal of Molecular Biology
citation.journal_id_ASTM
The American Society for Testing and Materials (ASTM) code
assigned to the journal cited (also referred to as the CODEN
designator of the Chemical Abstracts Service); relevant for
journal articles.
citation.journal_id_CSD
The Cambridge Structural Database (CSD) code assigned to the
journal cited; relevant for journal articles. This is also the
system used at the Protein Data Bank (PDB).
0070
citation.journal_id_ISSN
The International Standard Serial Number (ISSN) code assigned to
the journal cited; relevant for journal articles.
citation.journal_issue
Issue number of the journal cited; relevant for journal
articles.
2
citation.journal_volume
Volume number of the journal cited; relevant for journal
articles.
174
citation.language
Language in which the cited article is written.
German
citation.page_first
The first page of the citation; relevant for journal
articles, books and book chapters.
citation.page_last
The last page of the citation; relevant for journal
articles, books and book chapters.
citation.pdbx_database_id_DOI
Document Object Identifier used by doi.org to uniquely
specify bibliographic entry.
10.2345/S1384107697000225
citation.pdbx_database_id_PubMed
Ascession number used by PubMed to categorize a specific
bibliographic entry.
12627512
citation.pdbx_database_id_patent
If citation is a patent, the accession issued by a
patent office.
citation.title
The title of the citation; relevant for journal articles, books
and book chapters.
Structure of diferric duck ovotransferrin
at 2.35 Angstroms resolution.
Y
N
Flag to indicate that this citation will not be published.
citation.year
The year of the citation; relevant for journal articles, books
and book chapters.
1984
citation.id
The value of attribute id in category citation must uniquely identify a record in the
CITATION list.
The attribute id in category citation 'primary' should be used to indicate the
citation that the author(s) consider to be the most pertinent to
the contents of the data block.
Note that this item need not be a number; it can be any unique
identifier.
primary
1
2
0
citation_author
Data items in the CITATION_AUTHOR category record details
about the authors associated with the citations in the
CITATION list.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:citation_authorCategory>
<PDBx:citation_author citation_id="primary" name="Fitzgerald, P.M.D." ordinal="1"></PDBx:citation_author>
<PDBx:citation_author citation_id="primary" name="McKeever, B.M." ordinal="2"></PDBx:citation_author>
<PDBx:citation_author citation_id="primary" name="Van Middlesworth, J.F." ordinal="3"></PDBx:citation_author>
<PDBx:citation_author citation_id="primary" name="Springer, J.P." ordinal="4"></PDBx:citation_author>
<PDBx:citation_author citation_id="primary" name="Heimbach, J.C." ordinal="5"></PDBx:citation_author>
<PDBx:citation_author citation_id="primary" name="Leu, C.-T." ordinal="6"></PDBx:citation_author>
<PDBx:citation_author citation_id="primary" name="Herber, W.K." ordinal="7"></PDBx:citation_author>
<PDBx:citation_author citation_id="primary" name="Dixon, R.A.F." ordinal="8"></PDBx:citation_author>
<PDBx:citation_author citation_id="primary" name="Darke, P.L." ordinal="9"></PDBx:citation_author>
<PDBx:citation_author citation_id="2" name="Navia, M.A." ordinal="1"></PDBx:citation_author>
<PDBx:citation_author citation_id="2" name="Fitzgerald, P.M.D." ordinal="2"></PDBx:citation_author>
<PDBx:citation_author citation_id="2" name="McKeever, B.M." ordinal="3"></PDBx:citation_author>
<PDBx:citation_author citation_id="2" name="Leu, C.-T." ordinal="4"></PDBx:citation_author>
<PDBx:citation_author citation_id="2" name="Heimbach, J.C." ordinal="5"></PDBx:citation_author>
<PDBx:citation_author citation_id="2" name="Herber, W.K." ordinal="6"></PDBx:citation_author>
<PDBx:citation_author citation_id="2" name="Sigal, I.S." ordinal="7"></PDBx:citation_author>
<PDBx:citation_author citation_id="2" name="Darke, P.L." ordinal="8"></PDBx:citation_author>
<PDBx:citation_author citation_id="2" name="Springer, J.P." ordinal="9"></PDBx:citation_author>
<PDBx:citation_author citation_id="3" name="McKeever, B.M." ordinal="1"></PDBx:citation_author>
<PDBx:citation_author citation_id="3" name="Navia, M.A." ordinal="2"></PDBx:citation_author>
<PDBx:citation_author citation_id="3" name="Fitzgerald, P.M.D." ordinal="3"></PDBx:citation_author>
<PDBx:citation_author citation_id="3" name="Springer, J.P." ordinal="4"></PDBx:citation_author>
<PDBx:citation_author citation_id="3" name="Leu, C.-T." ordinal="5"></PDBx:citation_author>
<PDBx:citation_author citation_id="3" name="Heimbach, J.C." ordinal="6"></PDBx:citation_author>
<PDBx:citation_author citation_id="3" name="Herber, W.K." ordinal="7"></PDBx:citation_author>
<PDBx:citation_author citation_id="3" name="Sigal, I.S." ordinal="8"></PDBx:citation_author>
<PDBx:citation_author citation_id="3" name="Darke, P.L." ordinal="9"></PDBx:citation_author>
<PDBx:citation_author citation_id="4" name="Darke, P.L." ordinal="1"></PDBx:citation_author>
<PDBx:citation_author citation_id="4" name="Leu, C.-T." ordinal="2"></PDBx:citation_author>
<PDBx:citation_author citation_id="4" name="Davis, L.J." ordinal="3"></PDBx:citation_author>
<PDBx:citation_author citation_id="4" name="Heimbach, J.C." ordinal="4"></PDBx:citation_author>
<PDBx:citation_author citation_id="4" name="Diehl, R.E." ordinal="5"></PDBx:citation_author>
<PDBx:citation_author citation_id="4" name="Hill, W.S." ordinal="6"></PDBx:citation_author>
<PDBx:citation_author citation_id="4" name="Dixon, R.A.F." ordinal="7"></PDBx:citation_author>
<PDBx:citation_author citation_id="4" name="Sigal, I.S." ordinal="8"></PDBx:citation_author>
</PDBx:citation_authorCategory>
0
1
1
1
1
citation_authorCategory
This property indicates that datablock
has a category holder citation_authorCategory.
citation_authorCategory
This property indicates that citation_authorCategory.
has a category citation_author.
citation_authorItem
Abstract datatype property for citation_author items.
reference_to_citation_author
cross-reference to citation_author.
referenced_by_citation_author
cross-reference from citation_author.
citation_author.identifier_ORCID
The Open Researcher and Contributor ID (ORCID).
0000-0002-6681-547X
citation_author.citation_id
This data item is a pointer to attribute id in category citation in the CITATION
category.
citation_author.name
Name of an author of the citation; relevant for journal
articles, books and book chapters.
The family name(s), followed by a comma and including any
dynastic components, precedes the first name(s) or initial(s).
Bleary, Percival R.
O'Neil, F.K.
Van den Bossche, G.
Yang, D.-L.
Simonov, Yu.A
citation_author.ordinal
This data item defines the order of the author's name in the
list of authors of a citation.
0
citation_editor
Data items in the CITATION_EDITOR category record details
about the editors associated with the books or book chapters
cited in the CITATION list.
Example 1 - hypothetical example.
<PDBx:citation_editorCategory>
<PDBx:citation_editor citation_id="5" name="McKeever, B.M."></PDBx:citation_editor>
<PDBx:citation_editor citation_id="5" name="Navia, M.A."></PDBx:citation_editor>
<PDBx:citation_editor citation_id="5" name="Fitzgerald, P.M.D."></PDBx:citation_editor>
<PDBx:citation_editor citation_id="5" name="Springer, J.P."></PDBx:citation_editor>
</PDBx:citation_editorCategory>
0
1
1
1
citation_editorCategory
This property indicates that datablock
has a category holder citation_editorCategory.
citation_editorCategory
This property indicates that citation_editorCategory.
has a category citation_editor.
citation_editorItem
Abstract datatype property for citation_editor items.
reference_to_citation_editor
cross-reference to citation_editor.
referenced_by_citation_editor
cross-reference from citation_editor.
citation_editor.ordinal
This data item defines the order of the editor's name in the
list of editors of a citation.
citation_editor.citation_id
This data item is a pointer to attribute id in category citation in the CITATION
category.
citation_editor.name
Names of an editor of the citation; relevant for books and
book chapters.
The family name(s), followed by a comma and including any
dynastic components, precedes the first name(s) or initial(s).
Bleary, Percival R.
O'Neil, F.K.
Van den Bossche, G.
Yang, D.-L.
Simonov, Yu.A
0
computing
Data items in the COMPUTING category record details about the
computer programs used in the crystal structure analysis.
Data items in this category would not, in general, be used in
a macromolecular CIF. The category SOFTWARE, which allows
a more detailed description of computer programs and
their attributes to be given, would be used instead.
Example 1 - Rodr\'iguez-Romera, Ruiz-P\'erez & Solans [Acta
Cryst. (1996), C52, 1415-1417].
<PDBx:computingCategory>
<PDBx:computing entry_id="1ABC">
<PDBx:cell_refinement>CAD-4 (Enraf-Nonius, 1989)</PDBx:cell_refinement>
<PDBx:data_collection>CAD-4 (Enraf-Nonius, 1989)</PDBx:data_collection>
<PDBx:data_reduction>CFEO (Solans, 1978)</PDBx:data_reduction>
<PDBx:molecular_graphics>ORTEPII (Johnson, 1976)</PDBx:molecular_graphics>
<PDBx:publication_material>PARST (Nardelli, 1983)</PDBx:publication_material>
<PDBx:structure_refinement>SHELXL93 (Sheldrick, 1993)</PDBx:structure_refinement>
<PDBx:structure_solution>SHELXS86 (Sheldrick, 1990)</PDBx:structure_solution>
</PDBx:computing>
</PDBx:computingCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
computingCategory
This property indicates that datablock
has a category holder computingCategory.
computingCategory
This property indicates that computingCategory.
has a category computing.
computingItem
Abstract datatype property for computing items.
reference_to_computing
cross-reference to computing.
referenced_by_computing
cross-reference from computing.
computing.cell_refinement
Software used for cell refinement.
Give the program or package name and a brief reference.
CAD4 (Enraf-Nonius, 1989)
computing.data_collection
Software used for data collection.
Give the program or package name and a brief reference.
CAD4 (Enraf-Nonius, 1989)
computing.data_reduction
Software used for data reduction.
Give the program or package name and a brief reference.
DIFDAT, SORTRF, ADDREF (Hall & Stewart, 1990)
computing.molecular_graphics
Software used for molecular graphics.
Give the program or package name and a brief reference.
FRODO (Jones, 1986), ORTEP (Johnson, 1965)
computing.pdbx_data_reduction_ds
Program/package name for data reduction/data scaling
computing.pdbx_data_reduction_ii
Program/package name for data reduction/intensity integration software
computing.pdbx_structure_refinement_method
Program/package name for structure refinement method.
computing.publication_material
Software used for generating material for publication.
Give the program or package name and a brief reference.
computing.structure_refinement
Software used for refinement of the structure.
Give the program or package name and a brief reference.
SHELX85 (Sheldrick, 1985)
X-PLOR (Brunger, 1992)
computing.structure_solution
Software used for solution of the structure.
Give the program or package name and a brief reference.
SHELX85 (Sheldrick, 1985)
computing.entry_id
This data item is a pointer to attribute id in category entry in the ENTRY category.
0
database
Data items in the DATABASE category have been superseded by
data items in the DATABASE_2 category. They are included
here only for compliance with older CIFs.
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
databaseCategory
This property indicates that datablock
has a category holder databaseCategory.
databaseCategory
This property indicates that databaseCategory.
has a category database.
databaseItem
Abstract datatype property for database items.
reference_to_database
cross-reference to database.
referenced_by_database
cross-reference from database.
database.CSD_history
A history of changes made by the Cambridge Crystallographic Data
Centre and incorporated into the Cambridge Structural Database
(CSD).
database.code_CAS
The code assigned by Chemical Abstracts.
database.code_CSD
The code assigned by the Cambridge Structural Database.
database.code_ICSD
The code assigned by the Inorganic Crystal Structure
Database.
database.code_MDF
The code assigned by the Metals Data File.
database.code_NBS
The code assigned by the NBS (NIST) Crystal Data Database.
database.code_PDB
The code assigned by the Protein Data Bank.
database.code_PDF
The code assigned by the Powder Diffraction File (JCPDS/ICDD).
database.code_depnum_ccdc_archive
Deposition numbers assigned by the Cambridge Crystallographic
Data Centre (CCDC) to files containing structural information
archived by the CCDC.
database.code_depnum_ccdc_fiz
Deposition numbers assigned by the Fachinformationszentrum
Karlsruhe (FIZ) to files containing structural information
archived by the Cambridge Crystallographic Data Centre (CCDC).
database.code_depnum_ccdc_journal
Deposition numbers assigned by various journals to files
containing structural information archived by the Cambridge
Crystallographic Data Centre (CCDC).
database.journal_ASTM
The ASTM CODEN designator for a journal as given in the Chemical
Source List maintained by the Chemical Abstracts Service.
database.journal_CSD
The journal code used in the Cambridge Structural Database.
database.pdbx_code_NDB
The code assigned by the NDB.
BDL001
database.pdbx_code_PDB
The code assigned by the PDB.
1BNA
database.pdbx_related_codes_PDB
The codes of related PDB entries.
1NK1,1NK2
database.entry_id
This data item is a pointer to attribute id in category entry in the ENTRY category.
0
database_2
Data items in the DATABASE_2 category record details about the
database identifiers of the data block.
These data items are assigned by database managers and should
only appear in a data block if they originate from that source.
The name of this category, DATABASE_2, arose because the
category name DATABASE was already in use in the core CIF
dictionary, but was used differently from the way it needed
to be used in the mmCIF dictionary. Since CIF data names
cannot be changed once they have been adopted, a new category
had to be created.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:database_2Category>
<PDBx:database_2 database_code="5HVP" database_id="PDB"></PDBx:database_2>
</PDBx:database_2Category>
0
1
0
1
1
1
database_2Category
This property indicates that datablock
has a category holder database_2Category.
database_2Category
This property indicates that database_2Category.
has a category database_2.
database_2Item
Abstract datatype property for database_2 items.
reference_to_database_2
cross-reference to database_2.
referenced_by_database_2
cross-reference from database_2.
database_2.pdbx_DOI
Document Object Identifier (DOI) for this entry registered
with http://crossref.org.
10.2210/pdb6lu7/pdb
database_2.pdbx_database_accession
Extended accession code issued for for attribute database_code in category database_2 assigned by the database identified in
attribute database_id in category database_2.
pdb_00006lu7
database_2.database_code
The code assigned by the database identified in
attribute database_id in category database_2.
1ABC
ABCDEF
AlphaFoldDB
CAS
CSD
EMDB
ICSD
ModelArchive
MDF
MODBASE
NDB
NBS
PDB
PDB-Dev
PDF
RCSB
SWISS-MODEL_REPOSITORY
EBI
PDBE
BMRB
WWPDB
PDB_ACC
An abbreviation that identifies the database.
0
database_PDB_caveat
Data items in the DATABASE_PDB_CAVEAT category record details
about features of the data block flagged as 'caveats' by the
Protein Data Bank (PDB).
These data items are included only for consistency with PDB
format files. They should appear in a data block only if that
data block was created by reformatting a PDB format file.
Example 1 - hypothetical example.
<PDBx:database_PDB_caveatCategory>
<PDBx:database_PDB_caveat id="1">
<PDBx:text> THE CRYSTAL TRANSFORMATION IS IN ERROR BUT IS</PDBx:text>
</PDBx:database_PDB_caveat>
<PDBx:database_PDB_caveat id="2">
<PDBx:text> UNCORRECTABLE AT THIS TIME</PDBx:text>
</PDBx:database_PDB_caveat>
</PDBx:database_PDB_caveatCategory>
0
1
1
database_PDB_caveatCategory
This property indicates that datablock
has a category holder database_PDB_caveatCategory.
database_PDB_caveatCategory
This property indicates that database_PDB_caveatCategory.
has a category database_PDB_caveat.
database_PDB_caveatItem
Abstract datatype property for database_PDB_caveat items.
reference_to_database_PDB_caveat
cross-reference to database_PDB_caveat.
referenced_by_database_PDB_caveat
cross-reference from database_PDB_caveat.
database_PDB_caveat.text
The full text of the PDB caveat record.
database_PDB_caveat.id
A unique identifier for the PDB caveat record.
0
database_PDB_matrix
The DATABASE_PDB_MATRIX category provides placeholders for
transformation matrices and vectors used by the Protein Data
Bank (PDB).
These data items are included only for consistency with older
PDB format files. They should appear in a data block only if
that data block was created by reformatting a PDB format file.
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
database_PDB_matrixCategory
This property indicates that datablock
has a category holder database_PDB_matrixCategory.
database_PDB_matrixCategory
This property indicates that database_PDB_matrixCategory.
has a category database_PDB_matrix.
database_PDB_matrixItem
Abstract datatype property for database_PDB_matrix items.
reference_to_database_PDB_matrix
cross-reference to database_PDB_matrix.
referenced_by_database_PDB_matrix
cross-reference from database_PDB_matrix.
database_PDB_matrix.origx11
The [1][1] element of the PDB ORIGX matrix.
database_PDB_matrix.origx12
The [1][2] element of the PDB ORIGX matrix.
database_PDB_matrix.origx13
The [1][3] element of the PDB ORIGX matrix.
database_PDB_matrix.origx21
The [2][1] element of the PDB ORIGX matrix.
database_PDB_matrix.origx22
The [2][2] element of the PDB ORIGX matrix.
database_PDB_matrix.origx23
The [2][3] element of the PDB ORIGX matrix.
database_PDB_matrix.origx31
The [3][1] element of the PDB ORIGX matrix.
database_PDB_matrix.origx32
The [3][2] element of the PDB ORIGX matrix.
database_PDB_matrix.origx33
The [3][3] element of the PDB ORIGX matrix.
database_PDB_matrix.origx_vector1
The [1] element of the PDB ORIGX vector.
database_PDB_matrix.origx_vector2
The [2] element of the PDB ORIGX vector.
database_PDB_matrix.origx_vector3
The [3] element of the PDB ORIGX vector.
database_PDB_matrix.scale11
The [1][1] element of the PDB SCALE matrix.
database_PDB_matrix.scale12
The [1][2] element of the PDB SCALE matrix.
database_PDB_matrix.scale13
The [1][3] element of the PDB SCALE matrix.
database_PDB_matrix.scale21
The [2][1] element of the PDB SCALE matrix.
database_PDB_matrix.scale22
The [2][2] element of the PDB SCALE matrix.
database_PDB_matrix.scale23
The [2][3] element of the PDB SCALE matrix.
database_PDB_matrix.scale31
The [3][1] element of the PDB SCALE matrix.
database_PDB_matrix.scale32
The [3][2] element of the PDB SCALE matrix.
database_PDB_matrix.scale33
The [3][3] element of the PDB SCALE matrix.
database_PDB_matrix.scale_vector1
The [1] element of the PDB SCALE vector.
database_PDB_matrix.scale_vector2
The [2] element of the PDB SCALE vector.
database_PDB_matrix.scale_vector3
The [3] element of the PDB SCALE vector.
database_PDB_matrix.entry_id
This data item is a pointer to attribute id in category entry in the ENTRY category.
0
database_PDB_remark
Data items in the DATABASE_PDB_REMARK category record details
about the data block as archived by the Protein Data Bank (PDB).
Some data appearing in PDB REMARK records can be
algorithmically extracted into the appropriate data items
in the data block.
These data items are included only for consistency with older
PDB format files. They should appear in a data block only if
that data block was created by reformatting a PDB format file.
NOTE: These remark records in this category are not uniformly
annotated by the PDB and may not be consistent with
nomenclature or labeling used in the entry.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:database_PDB_remarkCategory>
<PDBx:database_PDB_remark id="3">
<PDBx:text> REFINEMENT. BY THE RESTRAINED LEAST-SQUARES PROCEDURE OF J.
KONNERT AND W. HENDRICKSON (PROGRAM *PROLSQ*). THE R
VALUE IS 0.176 FOR 12901 REFLECTIONS IN THE RESOLUTION
RANGE 8.0 TO 2.0 ANGSTROMS WITH I .GT. SIGMA(I).
RMS DEVIATIONS FROM IDEAL VALUES (THE VALUES OF
SIGMA, IN PARENTHESES, ARE THE INPUT ESTIMATED
STANDARD DEVIATIONS THAT DETERMINE THE RELATIVE
WEIGHTS OF THE CORRESPONDING RESTRAINTS)
DISTANCE RESTRAINTS (ANGSTROMS)
BOND DISTANCE 0.018(0.020)
ANGLE DISTANCE 0.038(0.030)
PLANAR 1-4 DISTANCE 0.043(0.040)
PLANE RESTRAINT (ANGSTROMS) 0.015(0.020)
CHIRAL-CENTER RESTRAINT (ANGSTROMS**3) 0.177(0.150)
NON-BONDED CONTACT RESTRAINTS (ANGSTROMS)
SINGLE TORSION CONTACT 0.216(0.500)
MULTIPLE TORSION CONTACT 0.207(0.500)
POSSIBLE HYDROGEN BOND 0.245(0.500)
CONFORMATIONAL TORSION ANGLE RESTRAINT (DEGREES)
PLANAR (OMEGA) 2.6(3.0)
STAGGERED 17.4(15.0)
ORTHONORMAL 18.1(20.0)</PDBx:text>
</PDBx:database_PDB_remark>
<PDBx:database_PDB_remark id="4">
<PDBx:text> THE TWO CHAINS OF THE DIMERIC ENZYME HAS BEEN ASSIGNED
THE CHAIN INDICATORS *A* AND *B*.</PDBx:text>
</PDBx:database_PDB_remark>
</PDBx:database_PDB_remarkCategory>
0
1
1
database_PDB_remarkCategory
This property indicates that datablock
has a category holder database_PDB_remarkCategory.
database_PDB_remarkCategory
This property indicates that database_PDB_remarkCategory.
has a category database_PDB_remark.
database_PDB_remarkItem
Abstract datatype property for database_PDB_remark items.
reference_to_database_PDB_remark
cross-reference to database_PDB_remark.
referenced_by_database_PDB_remark
cross-reference from database_PDB_remark.
database_PDB_remark.text
The full text of the PDB remark record.
database_PDB_remark.id
A unique identifier for the PDB remark record.
0
database_PDB_rev
Data items in the DATABASE_PDB_REV category record details
about the history of the data block as archived by the Protein
Data Bank (PDB).
These data items are assigned by the PDB database managers and
should only appear in a data block if they originate from that
source.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:database_PDB_revCategory>
<PDBx:database_PDB_rev num="1">
<PDBx:author_name>Fitzgerald, Paula M.D</PDBx:author_name>
<PDBx:date>1991-10-15</PDBx:date>
<PDBx:date_original>1990-04-30</PDBx:date_original>
<PDBx:mod_type>0</PDBx:mod_type>
<PDBx:status>full release</PDBx:status>
</PDBx:database_PDB_rev>
</PDBx:database_PDB_revCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
database_PDB_revCategory
This property indicates that datablock
has a category holder database_PDB_revCategory.
database_PDB_revCategory
This property indicates that database_PDB_revCategory.
has a category database_PDB_rev.
database_PDB_revItem
Abstract datatype property for database_PDB_rev items.
reference_to_database_PDB_rev
cross-reference to database_PDB_rev.
referenced_by_database_PDB_rev
cross-reference from database_PDB_rev.
database_PDB_rev.author_name
The name of the person responsible for submitting this revision
to the PDB.
The family name(s) followed by a comma precedes the first
name(s) or initial(s).
Bleary, Percival R.
O'Neil, F.K.
Van den Bossche, G.
Yang, D.-L.
Simonov, Yu.A
database_PDB_rev.date
Date the PDB revision took place. Taken from the REVDAT record.
database_PDB_rev.date_original
Date the entry first entered the PDB database in the form
yyyy-mm-dd. Taken from the PDB HEADER record.
1980-08-21
0
1
2
3
4
5
A code taken from the REVDAT record classifying common types of entry
revisions.
database_PDB_rev.pdbx_record_revised_1
The first PDB record name that was revised.
OBSOLETE LOCAL ITEM -- Replaced by attribute type in category database_PDB_rev_record
TITLE
HEADER
COMPND
SOURCE
database_PDB_rev.pdbx_record_revised_2
The second PDB record name that was revised.
OBSOLETE LOCAL ITEM -- Replaced by attribute type in category database_PDB_rev_record
TITLE
HEADER
COMPND
SOURCE
database_PDB_rev.pdbx_record_revised_3
The third PDB record name that was revised.
OBSOLETE LOCAL ITEM -- Replaced by attribute type in category database_PDB_rev_record
TITLE
HEADER
COMPND
SOURCE
database_PDB_rev.pdbx_record_revised_4
The fourth PDB record name that was revised.
OBSOLETE LOCAL ITEM -- Replaced by attribute type in category database_PDB_rev_record
TITLE
HEADER
COMPND
SOURCE
database_PDB_rev.replaced_by
The PDB code for a subsequent PDB entry that replaced the
PDB file corresponding to this data block.
database_PDB_rev.replaces
The PDB code for a previous PDB entry that was replaced by
the PDB file corresponding to this data block.
in preparation
prerelease
full release
obsolete
The status of this revision.
database_PDB_rev.num
The value of attribute num in category database_PDB_rev must uniquely and
sequentially identify a record in the DATABASE_PDB_REV list.
Note that this item must be a number and that modification
numbers are assigned in increasing numerical order.
0
database_PDB_rev_record
Data items in the DATABASE_PDB_REV_RECORD category record
details about specific record types that were changed in a
given revision of a PDB entry.
These data items are assigned by the PDB database managers and
should only appear in a data block if they originate from that
source.
Example 1 - hypothetical example.
<PDBx:database_PDB_rev_recordCategory>
<PDBx:database_PDB_rev_record rev_num="1" type="CONECT">
<PDBx:details> Error fix - incorrect connection between
atoms 2312 and 2317</PDBx:details>
</PDBx:database_PDB_rev_record>
<PDBx:database_PDB_rev_record rev_num="2" type="MATRIX">
<PDBx:details>For consistency with 1995-08-04 style-guide</PDBx:details>
</PDBx:database_PDB_rev_record>
<PDBx:database_PDB_rev_record rev_num="3" type="ORIGX">
<PDBx:details>Based on new data from author</PDBx:details>
</PDBx:database_PDB_rev_record>
</PDBx:database_PDB_rev_recordCategory>
0
1
1
1
database_PDB_rev_recordCategory
This property indicates that datablock
has a category holder database_PDB_rev_recordCategory.
database_PDB_rev_recordCategory
This property indicates that database_PDB_rev_recordCategory.
has a category database_PDB_rev_record.
database_PDB_rev_recordItem
Abstract datatype property for database_PDB_rev_record items.
reference_to_database_PDB_rev_record
cross-reference to database_PDB_rev_record.
referenced_by_database_PDB_rev_record
cross-reference from database_PDB_rev_record.
database_PDB_rev_record.details
A description of special aspects of the revision of records in
this PDB entry.
Based on new data from author
For consistency with 1995-08-04 style-guide
For consistency with structural class
database_PDB_rev_record.rev_num
This data item is a pointer to attribute num in category database_PDB_rev in the
DATABASE_PDB_REV category.
database_PDB_rev_record.type
The types of records that were changed in this revision to a
PDB entry.
CRYST1
SCALE
MTRIX
ATOM
HETATM
0
database_PDB_tvect
The DATABASE_PDB_TVECT category provides placeholders for
the TVECT matrices and vectors used by the Protein Data
Bank (PDB).
These data items are included only for consistency with older
PDB format files. They should appear in a data block only if
the data block was created by reformatting a PDB format file.
0
1
0
1
0
1
0
1
1
database_PDB_tvectCategory
This property indicates that datablock
has a category holder database_PDB_tvectCategory.
database_PDB_tvectCategory
This property indicates that database_PDB_tvectCategory.
has a category database_PDB_tvect.
database_PDB_tvectItem
Abstract datatype property for database_PDB_tvect items.
reference_to_database_PDB_tvect
cross-reference to database_PDB_tvect.
referenced_by_database_PDB_tvect
cross-reference from database_PDB_tvect.
database_PDB_tvect.details
A description of special aspects of this TVECT.
database_PDB_tvect.vector1
The [1] element of the PDB TVECT vector.
database_PDB_tvect.vector2
The [2] element of the PDB TVECT vector.
database_PDB_tvect.vector3
The [3] element of the PDB TVECT vector.
database_PDB_tvect.id
The value of attribute id in category database_PDB_tvect must uniquely identify a
record in the DATABASE_PDB_TVECT list.
Note that this item need not be a number; it can be any unique
identifier.
0
diffrn
Data items in the DIFFRN category record details about the
diffraction data and their measurement.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:diffrnCategory>
<PDBx:diffrn id="Set1">
<PDBx:ambient_environment> Mother liquor from the reservoir of the vapor diffusion experiment, mounted in room air</PDBx:ambient_environment>
<PDBx:ambient_temp>293.0</PDBx:ambient_temp>
<PDBx:crystal_support> 0.7 mm glass capillary, sealed with dental wax</PDBx:crystal_support>
<PDBx:crystal_treatment> Equilibrated in rotating anode radiation enclosure for
18 hours prior to beginning of data collection</PDBx:crystal_treatment>
</PDBx:diffrn>
</PDBx:diffrnCategory>
Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991).
Acta Cryst. C47, 2276-2277].
<PDBx:diffrnCategory>
<PDBx:diffrn id="d1">
<PDBx:ambient_temp>293</PDBx:ambient_temp>
<PDBx:details> \q scan width (1.0 + 0.14tan\q)\%, \q scan rate 1.2\% per
min. Background counts for 5 sec on each side every scan.</PDBx:details>
</PDBx:diffrn>
</PDBx:diffrnCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
1
0
1
0
1
0
1
0
1
1
diffrnCategory
This property indicates that datablock
has a category holder diffrnCategory.
diffrnCategory
This property indicates that diffrnCategory.
has a category diffrn.
diffrnItem
Abstract datatype property for diffrn items.
reference_to_diffrn
cross-reference to diffrn.
referenced_by_diffrn
cross-reference from diffrn.
diffrn.ambient_environment
The gas or liquid surrounding the sample, if not air.
diffrn.ambient_pressure
The mean hydrostatic pressure in kilopascals at which the
intensities were measured.
diffrn.ambient_pressure_esd
The estimated standard deviation of attribute ambient_pressure in category diffrn.
diffrn.ambient_pressure_gt
The mean hydrostatic pressure in kilopascals above which
the intensities were measured. attribute ambient_pressure_gt in category diffrn and
attribute ambient_pressure_lt in category diffrn allow a pressure range to be given.
attribute ambient_pressure in category diffrn should always be used in
preference to these two items whenever possible.
diffrn.ambient_pressure_lt
The mean hydrostatic pressure in kilopascals below which
the intensities were measured. attribute ambient_pressure_gt in category diffrn and
attribute ambient_pressure_lt in category diffrn allow a pressure range to be given.
attribute ambient_pressure in category diffrn should always be used in
preference to these two items whenever possible.
diffrn.ambient_temp
The mean temperature in kelvins at which the intensities were
measured.
diffrn.ambient_temp_details
A description of special aspects of temperature control during
data collection.
diffrn.ambient_temp_esd
The standard uncertainty (estimated standard deviation)
of attribute ambient_temp in category diffrn.
diffrn.ambient_temp_gt
The mean temperature in kelvins above which the intensities were
measured. _diffrn.ambient_temp_gt and _diffrn.ambient_temp_lt
allow a range of temperatures to be given.
attribute ambient_temp in category diffrn should always be used in preference
to these two items whenever possible.
diffrn.ambient_temp_lt
The mean temperature in kelvins below which the intensities were
measured. _diffrn.ambient_temp_gt and _diffrn.ambient_temp_lt
allow a range of temperatures to be given.
attribute ambient_temp in category diffrn should always be used in preference
to these two items whenever possible.
diffrn.crystal_id
This data item is a pointer to attribute id in category exptl_crystal in the
EXPTL_CRYSTAL category.
diffrn.crystal_support
The physical device used to support the crystal during data
collection.
glass capillary
quartz capillary
fiber
metal loop
diffrn.crystal_treatment
Remarks about how the crystal was treated prior to intensity
measurement. Particularly relevant when intensities were
measured at low temperature.
equilibrated in hutch for 24 hours
flash frozen in liquid nitrogen
slow cooled with direct air stream
diffrn.details
Special details of the diffraction measurement process. Should
include information about source instability, crystal motion,
degradation and so on.
diffrn.pdbx_serial_crystal_experiment
Y/N if using serial crystallography experiment in which multiple crystals contribute to each diffraction frame in the experiment.
Y
N
diffrn.id
This data item uniquely identifies a set of diffraction
data.
0
diffrn_attenuator
Data items in the DIFFRN_ATTENUATOR category record details
about the diffraction attenuator scales employed.
Example 2 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
<PDBx:diffrn_attenuatorCategory>
<PDBx:diffrn_attenuator code="1">
<PDBx:scale>16.976</PDBx:scale>
</PDBx:diffrn_attenuator>
</PDBx:diffrn_attenuatorCategory>
0
1
0
1
1
diffrn_attenuatorCategory
This property indicates that datablock
has a category holder diffrn_attenuatorCategory.
diffrn_attenuatorCategory
This property indicates that diffrn_attenuatorCategory.
has a category diffrn_attenuator.
diffrn_attenuatorItem
Abstract datatype property for diffrn_attenuator items.
reference_to_diffrn_attenuator
cross-reference to diffrn_attenuator.
referenced_by_diffrn_attenuator
cross-reference from diffrn_attenuator.
diffrn_attenuator.material
Material from which the attenuator is made.
diffrn_attenuator.scale
The scale factor applied when an intensity measurement is
reduced by an attenuator identified by attribute code.
in category diffrn_attenuator The measured intensity must be multiplied by this scale to
convert it to the same scale as unattenuated intensities.
diffrn_attenuator.code
A code associated with a particular attenuator setting. This
code is referenced by the attribute attenuator_code in category diffrn_refln which is
stored with the diffraction data. See attribute scale in category diffrn_attenuator.
0
diffrn_data_frame
Data items in the DIFFRN_DATA_FRAME category record
the details about each frame of data.
The items in this category were previously in a
DIFFRN_FRAME_DATA category, which is now deprecated.
The items from the old category are provided
as aliases but should not be used for new work.
Example 1. a frame containing data from four frame elements.
Each frame element has a common array configuration
'array_1' described in ARRAY_STRUCTURE and related
categories. The data for each detector element are
stored in four groups of binary data in the
ARRAY_DATA category, linked by the array_id and
binary_id.
<PDBx:diffrn_data_frameCategory>
<PDBx:diffrn_data_frame detector_element_id="d1_ccd_1" id="frame_1">
<PDBx:array_id>array_1</PDBx:array_id>
<PDBx:binary_id>1</PDBx:binary_id>
</PDBx:diffrn_data_frame>
<PDBx:diffrn_data_frame detector_element_id="d1_ccd_2" id="frame_1">
<PDBx:array_id>array_1</PDBx:array_id>
<PDBx:binary_id>2</PDBx:binary_id>
</PDBx:diffrn_data_frame>
<PDBx:diffrn_data_frame detector_element_id="d1_ccd_3" id="frame_1">
<PDBx:array_id>array_1</PDBx:array_id>
<PDBx:binary_id>3</PDBx:binary_id>
</PDBx:diffrn_data_frame>
<PDBx:diffrn_data_frame detector_element_id="d1_ccd_4" id="frame_1">
<PDBx:array_id>array_1</PDBx:array_id>
<PDBx:binary_id>4</PDBx:binary_id>
</PDBx:diffrn_data_frame>
</PDBx:diffrn_data_frameCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
1
diffrn_data_frameCategory
This property indicates that datablock
has a category holder diffrn_data_frameCategory.
diffrn_data_frameCategory
This property indicates that diffrn_data_frameCategory.
has a category diffrn_data_frame.
diffrn_data_frameItem
Abstract datatype property for diffrn_data_frame items.
reference_to_diffrn_data_frame
cross-reference to diffrn_data_frame.
referenced_by_diffrn_data_frame
cross-reference from diffrn_data_frame.
diffrn_data_frame.array_id
This item is a pointer to attribute id in category array_structure in the
ARRAY_STRUCTURE category.
diffrn_data_frame.array_section_id
This item is a pointer to attribute id
in category array_structure_list_section in the ARRAY_STRUCTURE_LIST_SECTION category.
diffrn_data_frame.binary_id
This item is a pointer to attribute binary_id in category array_data in the
ARRAY_DATA category.
diffrn_data_frame.center_derived
The value of attribute center_derived
in category diffrn_data_frame is assumed to be 'yes', i.e. that values of
attribute center_fast in category diffrn_data_frame and
attribute center_slow
in category diffrn_data_frame are derived from the axis settings rather than measured.
diffrn_data_frame.center_fast
The value of attribute center_fast in category diffrn_data_frame is
the fast index axis beam centre position relative to the detector
element face in the units specified in the data item
attribute center_units in category diffrn_data_frame along the fast
axis of the detector from the centre of the first pixel to
the point at which the Z axis (which should be collinear with the
beam) intersects the face of the detector, if in fact it does.
At the time of the measurement the current settings of
the detector positioner for the given frame are used.
It is important to note that for measurements in mm,
the sense of the axis is used, rather than the sign of the
pixel-to-pixel increments.
diffrn_data_frame.center_slow
The value of attribute center_slow in category diffrn_data_frame is
the slow index axis beam centre position relative to the detector
element face in the units specified in the data item
attribute center_units in category diffrn_data_frame along the slow
axis of the detector from the centre of the first pixel to
the point at which the Z axis (which should be collinear with the
beam) intersects the face of the detector, if in fact it does.
At the time of the measurement the current settings of
the detector positioner for the given frame are used.
It is important to note that the sense of the axis is used,
rather than the sign of the pixel-to-pixel increments.
mm
pixels
bins
The value of attribute center_units
in category diffrn_data_frame specifies the units in which the values of
attribute center_fast in category diffrn_data_frame and
attribute center_slow
in category diffrn_data_frame are presented. The default is 'mm' for millimetres. The
alternatives are 'pixels' and 'bins'. In all cases the
centre distances are measured from the centre of the
first pixel, i.e. in a 2x2 binning, the measuring origin
is offset from the centres of the bins by one half pixel
towards the first pixel.
If 'bins' is specified, the data in
attribute pixel_fast_bin_size,
in category array_intensities attribute pixel_slow_bin_size in category array_intensities, and
attribute pixel_binning_method
in category array_intensities are used to define the binning scheme.
diffrn_data_frame.details
The value of attribute details in category diffrn_data_frame should give a
description of special aspects of each frame of data.
This is an appropriate location in which to record
information from vendor headers as presented in those
headers, but it should never be used as a substitute
for providing the fully parsed information within
the appropriate imgCIF/CBF categories.
Normally, when a conversion from a miniCBF has been done
the data from attribute header_convention
in category array_data should be transferred to this data item and
attribute header_convention
in category array_data should be removed.
Example of header information extracted from an ADSC Quantum
315 detector header by CBFlib_0.7.6. Image provided by Chris
Nielsen of ADSC from a data collection at SSRL beamline 1-5.
HEADER_BYTES = 512;
DIM = 2;
BYTE_ORDER = big_endian;
TYPE = unsigned_short;
SIZE1 = 3072;
SIZE2 = 3072;
PIXEL_SIZE = 0.102588;
BIN = 2x2;
DETECTOR_SN = 901;
TIME = 29.945155;
DISTANCE = 200.000000;
PHI = 85.000000;
OSC_START = 85.000000;
OSC_RANGE = 1.000000;
WAVELENGTH = 0.979381;
BEAM_CENTER_X = 157.500000;
BEAM_CENTER_Y = 157.500000;
PIXEL SIZE = 0.102588;
OSCILLATION RANGE = 1;
EXPOSURE TIME = 29.9452;
TWO THETA = 0;
BEAM CENTRE = 157.5 157.5;
diffrn_data_frame.detector_element_id
This item is a pointer to attribute id
in category diffrn_detector_element in the DIFFRN_DETECTOR_ELEMENT category.
diffrn_data_frame.id
The value of attribute id in category diffrn_data_frame must uniquely identify
each complete frame of data.
0
diffrn_detector
Data items in the DIFFRN_DETECTOR category describe the
detector used to measure the scattered radiation, including
any analyser and post-sample collimation.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:diffrn_detectorCategory>
<PDBx:diffrn_detector diffrn_id="d1">
<PDBx:detector>multiwire</PDBx:detector>
<PDBx:type>Siemens</PDBx:type>
</PDBx:diffrn_detector>
</PDBx:diffrn_detectorCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
diffrn_detectorCategory
This property indicates that datablock
has a category holder diffrn_detectorCategory.
diffrn_detectorCategory
This property indicates that diffrn_detectorCategory.
has a category diffrn_detector.
diffrn_detectorItem
Abstract datatype property for diffrn_detector items.
reference_to_diffrn_detector
cross-reference to diffrn_detector.
referenced_by_diffrn_detector
cross-reference from diffrn_detector.
diffrn_detector.area_resol_mean
The resolution of an area detector, in pixels/mm.
diffrn_detector.details
A description of special aspects of the radiation detector.
diffrn_detector.detector
The general class of the radiation detector.
photographic film
scintillation counter
CCD plate
BF~3~ counter
diffrn_detector.dtime
The deadtime in microseconds of the detector used to measure
the diffraction intensities.
diffrn_detector.id
The value of attribute id in category diffrn_detector must uniquely identify
each detector used to collect each diffraction data set.
If the value of attribute id in category diffrn_detector is not given, it is
implicitly equal to the value of
attribute diffrn_id in category diffrn_detector.
diffrn_detector.number_of_axes
The value of attribute number_of_axes in category diffrn_detector gives the
number of axes of the positioner for the detector identified
by attribute id.
in category diffrn_detector
The word 'positioner' is a general term used in
instrumentation design for devices that are used to change
the positions of portions of apparatus by linear
translation, rotation or combinations of such motions.
Axes which are used to provide a coordinate system for the
face of an area detector should not be counted for this
data item.
The description of each axis should be provided by entries
in DIFFRN_DETECTOR_AXIS.
diffrn_detector.pdbx_collection_date
The date of data collection.
1996-12-25
diffrn_detector.pdbx_collection_time_total
The total number of seconds required to measure this
data set.
120.0
diffrn_detector.pdbx_frames_total
The total number of data frames collected for this
data set.
20
100
diffrn_detector.pdbx_frequency
The operating frequency of the detector (Hz) used in data collection.
diffrn_detector.type
The make, model or name of the detector device used.
diffrn_detector.diffrn_id
This data item is a pointer to attribute id in category diffrn in the DIFFRN
category.
0
diffrn_detector_axis
Data items in the DIFFRN_DETECTOR_AXIS category associate
axes with detectors.
1
1
diffrn_detector_axisCategory
This property indicates that datablock
has a category holder diffrn_detector_axisCategory.
diffrn_detector_axisCategory
This property indicates that diffrn_detector_axisCategory.
has a category diffrn_detector_axis.
diffrn_detector_axisItem
Abstract datatype property for diffrn_detector_axis items.
reference_to_diffrn_detector_axis
cross-reference to diffrn_detector_axis.
referenced_by_diffrn_detector_axis
cross-reference from diffrn_detector_axis.
diffrn_detector_axis.axis_id
This data item is a pointer to attribute id in category axis in
the AXIS category.
diffrn_detector_axis.detector_id
This data item is a pointer to attribute id in category diffrn_detector in
the DIFFRN_DETECTOR category.
This item was previously named attribute id
in category diffrn_detector_axis which is now a deprecated name. The old name is
provided as an alias but should not be used for new work.
0
diffrn_detector_element
Data items in the DIFFRN_DETECTOR_ELEMENT category record
the details about spatial layout and other characteristics
of each element of a detector which may have multiple elements.
In most cases, giving more detailed information
in ARRAY_STRUCTURE_LIST and ARRAY_STRUCTURE_LIST_AXIS
is preferable to simply providing the centre of the
detector element.
Example 1. Detector d1 is composed of four CCD detector elements,
each 200 mm by 200 mm, arranged in a square, in the pattern
1 2
*
3 4
Note that the beam centre is slightly displaced from each of the
detector elements, just beyond the lower right corner of 1,
the lower left corner of 2, the upper right corner of 3 and
the upper left corner of 4. For each element, the detector
face coordinate system is assumed to have the fast axis
running from left to right and the slow axis running from
top to bottom with the origin at the top left corner.
<PDBx:diffrn_detector_elementCategory>
<PDBx:diffrn_detector_element detector_id="d1" id="d1_ccd_1">
<PDBx:reference_center_fast>201.5</PDBx:reference_center_fast>
<PDBx:reference_center_slow>201.5</PDBx:reference_center_slow>
<PDBx:reference_center_units>mm</PDBx:reference_center_units>
</PDBx:diffrn_detector_element>
<PDBx:diffrn_detector_element detector_id="d1" id="d1_ccd_2">
<PDBx:reference_center_fast>-1.8</PDBx:reference_center_fast>
<PDBx:reference_center_slow>201.5</PDBx:reference_center_slow>
<PDBx:reference_center_units>mm</PDBx:reference_center_units>
</PDBx:diffrn_detector_element>
<PDBx:diffrn_detector_element detector_id="d1" id="d1_ccd_3">
<PDBx:reference_center_fast>201.6</PDBx:reference_center_fast>
<PDBx:reference_center_slow>-1.4</PDBx:reference_center_slow>
<PDBx:reference_center_units>mm</PDBx:reference_center_units>
</PDBx:diffrn_detector_element>
<PDBx:diffrn_detector_element detector_id="d1" id="d1_ccd_4">
<PDBx:reference_center_fast>-1.7</PDBx:reference_center_fast>
<PDBx:reference_center_slow>-1.5</PDBx:reference_center_slow>
<PDBx:reference_center_units>mm</PDBx:reference_center_units>
</PDBx:diffrn_detector_element>
</PDBx:diffrn_detector_elementCategory>
0
1
0
1
0
1
1
1
diffrn_detector_elementCategory
This property indicates that datablock
has a category holder diffrn_detector_elementCategory.
diffrn_detector_elementCategory
This property indicates that diffrn_detector_elementCategory.
has a category diffrn_detector_element.
diffrn_detector_elementItem
Abstract datatype property for diffrn_detector_element items.
reference_to_diffrn_detector_element
cross-reference to diffrn_detector_element.
referenced_by_diffrn_detector_element
cross-reference from diffrn_detector_element.
diffrn_detector_element.reference_center_fast
The value of attribute reference_center_fast in category diffrn_detector_element is
the fast index axis beam centre position relative to the detector
element face in the units specified in the data item
attribute reference_center_units in category diffrn_detector_element along the fast
axis of the detector from the centre of the first pixel to
the point at which the Z-axis (which should be collinear with the
beam) intersects the face of the detector, if in fact it does.
At the time of the measurement all settings of the detector
positioner should be at their reference settings. If more than
one reference setting has been used the value given should be
representative of the beam centre as determined from the ensemble
of settings.
It is important to note that for measurements in mm,
the sense of the axis is used, rather than the sign of the
pixel-to-pixel increments.
diffrn_detector_element.reference_center_slow
The value of attribute reference_center_slow in category diffrn_detector_element is
the slow index axis beam centre position relative to the detector
element face in the units specified in the data item
attribute reference_center_units in category diffrn_detector_element along the slow
axis of the detector from the centre of the first pixel to
the point at which the Z-axis (which should be collinear with the
beam) intersects the face of the detector, if in fact it does.
At the time of the measurement all settings of the detector
positioner should be at their reference settings. If more than
one reference setting has been used the value given should be
representative of the beam centre as determined from the ensemble
of settings.
It is important to note that the sense of the axis is used,
rather than the sign of the pixel-to-pixel increments.
mm
pixels
bins
The value of attribute reference_center_units
in category diffrn_detector_element specifies the units in which the values of
attribute reference_center_fast in category diffrn_detector_element and
attribute reference_center_slow
in category diffrn_detector_element are presented. The default is 'mm' for millimetres. The
alternatives are 'pixels' and 'bins'. In all cases the
centre distances are measured from the centre of the
first pixel, i.e. in a 2x2 binning, the measuring origin
is offset from the centres of the bins by one half pixel
towards the first pixel.
If 'bins' is specified, the data in
attribute pixel_fast_bin_size,
in category array_intensities attribute pixel_slow_bin_size in category array_intensities, and
attribute pixel_binning_method
in category array_intensities are used to define the binning scheme.
diffrn_detector_element.detector_id
This item is a pointer to attribute id
in category diffrn_detector in the DIFFRN_DETECTOR category.
diffrn_detector_element.id
The value of attribute id in category diffrn_detector_element must uniquely
identify each element of a detector.
0
diffrn_measurement
Data items in the DIFFRN_MEASUREMENT category record details
about the device used to orient and/or position the crystal
during data measurement and the manner in which the diffraction
data were measured.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:diffrn_measurementCategory>
<PDBx:diffrn_measurement diffrn_id="d1">
<PDBx:details> 440 frames, 0.20 degrees, 150 sec, detector distance 12 cm,
detector angle 22.5 degrees</PDBx:details>
<PDBx:device>3-circle camera</PDBx:device>
<PDBx:device_details>none</PDBx:device_details>
<PDBx:device_type>Supper model x</PDBx:device_type>
<PDBx:method>omega scan</PDBx:method>
</PDBx:diffrn_measurement>
</PDBx:diffrn_measurementCategory>
Example 2 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
<PDBx:diffrn_measurementCategory>
<PDBx:diffrn_measurement diffrn_id="s1">
<PDBx:device_type>Philips PW1100/20 diffractometer</PDBx:device_type>
<PDBx:method>\q/2\q</PDBx:method>
</PDBx:diffrn_measurement>
</PDBx:diffrn_measurementCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
diffrn_measurementCategory
This property indicates that datablock
has a category holder diffrn_measurementCategory.
diffrn_measurementCategory
This property indicates that diffrn_measurementCategory.
has a category diffrn_measurement.
diffrn_measurementItem
Abstract datatype property for diffrn_measurement items.
reference_to_diffrn_measurement
cross-reference to diffrn_measurement.
referenced_by_diffrn_measurement
cross-reference from diffrn_measurement.
diffrn_measurement.details
A description of special aspects of the intensity measurement.
440 frames, 0.20 degrees, 150 sec, detector
distance 12 cm, detector angle 22.5 degrees
diffrn_measurement.device
The general class of goniometer or device used to support and
orient the specimen.
3-circle camera
4-circle camera
kappa-geometry camera
oscillation camera
precession camera
diffrn_measurement.device_details
A description of special aspects of the device used to measure
the diffraction intensities.
commercial goniometer modified locally to
allow for 90\% \t arc
diffrn_measurement.device_type
The make, model or name of the measurement device
(goniometer) used.
Supper model q
Huber model r
Enraf-Nonius model s
homemade
diffrn_measurement.method
Method used to measure intensities.
profile data from theta/2theta scans
diffrn_measurement.pdbx_date
The date of data measurement
yyyy-mm-dd
diffrn_measurement.specimen_support
The physical device used to support the crystal during data
collection.
glass capillary
quartz capillary
fiber
metal loop
diffrn_measurement.diffrn_id
This data item is a pointer to attribute id in category diffrn in the DIFFRN
category.
0
diffrn_orient_matrix
Data items in the DIFFRN_ORIENT_MATRIX category record details
about the orientation matrix used in the measurement of the
diffraction data.
Example 1 - based on CAD-4 diffractometer data obtained for
Yb(S-C5H4N)2(THF)4.
<PDBx:diffrn_orient_matrixCategory>
<PDBx:diffrn_orient_matrix diffrn_id="set1">
<PDBx:UB11>-0.071479</PDBx:UB11>
<PDBx:UB12>0.020208</PDBx:UB12>
<PDBx:UB13>0.039076</PDBx:UB13>
<PDBx:UB21>0.035372</PDBx:UB21>
<PDBx:UB22>0.056209</PDBx:UB22>
<PDBx:UB23>0.078324</PDBx:UB23>
<PDBx:UB31>-0.007470</PDBx:UB31>
<PDBx:UB32>0.067854</PDBx:UB32>
<PDBx:UB33>-0.017832</PDBx:UB33>
<PDBx:type> reciprocal axis matrix, multiplies hkl vector to generate
diffractometer xyz vector and diffractometer angles</PDBx:type>
</PDBx:diffrn_orient_matrix>
</PDBx:diffrn_orient_matrixCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
diffrn_orient_matrixCategory
This property indicates that datablock
has a category holder diffrn_orient_matrixCategory.
diffrn_orient_matrixCategory
This property indicates that diffrn_orient_matrixCategory.
has a category diffrn_orient_matrix.
diffrn_orient_matrixItem
Abstract datatype property for diffrn_orient_matrix items.
reference_to_diffrn_orient_matrix
cross-reference to diffrn_orient_matrix.
referenced_by_diffrn_orient_matrix
cross-reference from diffrn_orient_matrix.
diffrn_orient_matrix.UB11
The [1][1] element of the 3x3 matrix that defines the dimensions
of the reciprocal cell and its orientation with respect to the
local diffractometer axes. See also attribute type in category diffrn_orient_matrix.
diffrn_orient_matrix.UB12
The [1][2] element of the 3x3 matrix that defines the dimensions
of the reciprocal cell and its orientation with respect to the
local diffractometer axes. See also attribute type in category diffrn_orient_matrix.
diffrn_orient_matrix.UB13
The [1][3] element of the 3x3 matrix that defines the dimensions
of the reciprocal cell and its orientation with respect to the
local diffractometer axes. See also attribute type in category diffrn_orient_matrix.
diffrn_orient_matrix.UB21
The [2][1] element of the 3x3 matrix that defines the dimensions
of the reciprocal cell and its orientation with respect to the
local diffractometer axes. See also attribute type in category diffrn_orient_matrix.
diffrn_orient_matrix.UB22
The [2][2] element of the 3x3 matrix that defines the dimensions
of the reciprocal cell and its orientation with respect to the
local diffractometer axes. See also attribute type in category diffrn_orient_matrix.
diffrn_orient_matrix.UB23
The [2][3] element of the 3x3 matrix that defines the dimensions
of the reciprocal cell and its orientation with respect to the
local diffractometer axes. See also attribute type in category diffrn_orient_matrix.
diffrn_orient_matrix.UB31
The [3][1] element of the 3x3 matrix that defines the dimensions
of the reciprocal cell and its orientation with respect to the
local diffractometer axes. See also attribute type in category diffrn_orient_matrix.
diffrn_orient_matrix.UB32
The [3][2] element of the 3x3 matrix that defines the dimensions
of the reciprocal cell and its orientation with respect to the
local diffractometer axes. See also attribute type in category diffrn_orient_matrix.
diffrn_orient_matrix.UB33
The [3][3] element of the 3x3 matrix that defines the dimensions
of the reciprocal cell and its orientation with respect to the
local diffractometer axes. See also attribute type in category diffrn_orient_matrix.
diffrn_orient_matrix.type
A description of the orientation matrix type and how it should
be applied to define the orientation of the crystal precisely
with respect to the diffractometer axes.
diffrn_orient_matrix.diffrn_id
This data item is a pointer to attribute id in category diffrn in the DIFFRN
category.
0
diffrn_orient_refln
Data items in the DIFFRN_ORIENT_REFLN category record details
about the reflections that define the orientation matrix used in
the measurement of the diffraction intensities.
Example 1 - based on CAD-4 diffractometer data obtained for
Yb(S-C5H4N)2(THF)4.
<PDBx:diffrn_orient_reflnCategory>
<PDBx:diffrn_orient_refln diffrn_id="myset1" index_h="2" index_k="0" index_l="2">
<PDBx:angle_chi>-28.45</PDBx:angle_chi>
<PDBx:angle_kappa>-11.32</PDBx:angle_kappa>
<PDBx:angle_omega>5.33</PDBx:angle_omega>
<PDBx:angle_phi>101.78</PDBx:angle_phi>
<PDBx:angle_psi>0.00</PDBx:angle_psi>
<PDBx:angle_theta>10.66</PDBx:angle_theta>
</PDBx:diffrn_orient_refln>
</PDBx:diffrn_orient_reflnCategory>
0
1
0
1
0
1
0
1
0
1
0
1
1
1
1
1
diffrn_orient_reflnCategory
This property indicates that datablock
has a category holder diffrn_orient_reflnCategory.
diffrn_orient_reflnCategory
This property indicates that diffrn_orient_reflnCategory.
has a category diffrn_orient_refln.
diffrn_orient_reflnItem
Abstract datatype property for diffrn_orient_refln items.
reference_to_diffrn_orient_refln
cross-reference to diffrn_orient_refln.
referenced_by_diffrn_orient_refln
cross-reference from diffrn_orient_refln.
diffrn_orient_refln.angle_chi
Diffractometer angle chi of a reflection used to
define the orientation matrix in degrees. See
attribute UB[][] in category diffrn_orient_matrix and the Miller indices
in the DIFFRN_ORIENT_REFLN category.
diffrn_orient_refln.angle_kappa
Diffractometer angle kappa of a reflection used to
define the orientation matrix in degrees. See
attribute UB[][] in category diffrn_orient_matrix and the Miller indices
in the DIFFRN_ORIENT_REFLN category.
diffrn_orient_refln.angle_omega
Diffractometer angle omega of a reflection used to
define the orientation matrix in degrees. See
attribute UB[][] in category diffrn_orient_matrix and the Miller indices in
the DIFFRN_ORIENT_REFLN category.
diffrn_orient_refln.angle_phi
Diffractometer angle phi of a reflection used to
define the orientation matrix in degrees. See
attribute UB[][] in category diffrn_orient_matrix and the Miller indices
in the DIFFRN_ORIENT_REFLN category.
diffrn_orient_refln.angle_psi
Diffractometer angle psi of a reflection used to
define the orientation matrix in degrees. See
attribute UB[][] in category diffrn_orient_matrix and the Miller indices
in the DIFFRN_ORIENT_REFLN category.
diffrn_orient_refln.angle_theta
Diffractometer angle theta of a reflection used to
define the orientation matrix in degrees. See
attribute UB[][] in category diffrn_orient_matrix and the Miller indices
in the DIFFRN_ORIENT_REFLN category.
diffrn_orient_refln.diffrn_id
This data item is a pointer to attribute id in category diffrn in the DIFFRN
category.
diffrn_orient_refln.index_h
Miller index h of a reflection used to define the orientation
matrix.
diffrn_orient_refln.index_k
Miller index k of a reflection used to define the orientation
matrix.
diffrn_orient_refln.index_l
Miller index l of a reflection used to define the orientation
matrix.
0
diffrn_radiation
Data items in the DIFFRN_RADIATION category describe
the radiation used in measuring the diffraction intensities,
its collimation and monochromatization before the sample.
Post-sample treatment of the beam is described by data
items in the DIFFRN_DETECTOR category.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:diffrn_radiationCategory>
<PDBx:diffrn_radiation diffrn_id="set1">
<PDBx:collimation>0.3 mm double pinhole</PDBx:collimation>
<PDBx:monochromator>graphite</PDBx:monochromator>
<PDBx:type>Cu K\a</PDBx:type>
<PDBx:wavelength_id>1</PDBx:wavelength_id>
</PDBx:diffrn_radiation>
</PDBx:diffrn_radiationCategory>
Example 2 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
<PDBx:diffrn_radiationCategory>
<PDBx:diffrn_radiation diffrn_id="set1">
<PDBx:monochromator>graphite</PDBx:monochromator>
<PDBx:type>Cu K\a</PDBx:type>
<PDBx:wavelength_id>1</PDBx:wavelength_id>
</PDBx:diffrn_radiation>
</PDBx:diffrn_radiationCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
diffrn_radiationCategory
This property indicates that datablock
has a category holder diffrn_radiationCategory.
diffrn_radiationCategory
This property indicates that diffrn_radiationCategory.
has a category diffrn_radiation.
diffrn_radiationItem
Abstract datatype property for diffrn_radiation items.
reference_to_diffrn_radiation
cross-reference to diffrn_radiation.
referenced_by_diffrn_radiation
cross-reference from diffrn_radiation.
diffrn_radiation.collimation
The collimation or focusing applied to the radiation.
0.3 mm double-pinhole
0.5 mm
focusing mirrors
diffrn_radiation.filter_edge
Absorption edge in angstroms of the radiation filter used.
diffrn_radiation.inhomogeneity
Half-width in millimetres of the incident beam in the
direction perpendicular to the diffraction plane.
diffrn_radiation.monochromator
The method used to obtain monochromatic radiation. If a mono-
chromator crystal is used, the material and the indices of the
Bragg reflection are specified.
Zr filter
Ge 220
none
equatorial mounted graphite
diffrn_radiation.pdbx_analyzer
Indicates the method used to obtain monochromatic radiation.
attribute monochromator in category diffrn_radiation describes the primary beam
monochromator (pre-specimen monochromation).
attribute pdbx_analyzer in category diffrn_radiation specifies the
post-diffraction analyser (post-specimen) monochromation.
Note that monochromators may have either 'parallel' or
'antiparallel' orientation. It is assumed that the
geometry is parallel unless specified otherwise.
In a parallel geometry, the position of the monochromator
allows the incident beam and the final post-specimen
and post-monochromator beam to be as close to parallel
as possible. In a parallel geometry, the diffracting
planes in the specimen and monochromator will be parallel
when 2*theta(monochromator) is equal to 2*theta (specimen).
For further discussion see R. Jenkins and R. Snyder,
Introduction to X-ray Powder Diffraction, Wiley (1996),
pp. 164-5.
GE(111)
Zr filter
Ge 220
none
equatorial mounted graphite (0001)
Si (111), antiparallel
diffrn_radiation.pdbx_diffrn_protocol
SINGLE WAVELENGTH, LAUE, or MAD.
SINGLE WAVELENGTH
MONOCHROMATIC
LAUE
MAD
OTHER
M
L
Monochromatic or Laue.
M
L
x-ray
neutron
electron
The radiation scattering type for this diffraction data set.
diffrn_radiation.pdbx_wavelength
Wavelength of radiation.
diffrn_radiation.pdbx_wavelength_list
Comma separated list of wavelengths or wavelength range.
diffrn_radiation.polarisn_norm
The angle in degrees, as viewed from the specimen, between the
perpendicular component of the polarization and the diffraction
plane. See attribute polarisn_ratio in category diffrn_radiation.
diffrn_radiation.polarisn_ratio
Polarization ratio of the diffraction beam incident on the
crystal. This is the ratio of the perpendicularly polarized
to the parallel-polarized component of the radiation. The
perpendicular component forms an angle of
attribute polarisn_norm in category diffrn_radiation to the normal to the
diffraction plane of the sample (i.e. the plane containing
the incident and reflected beams).
x-ray
neutron
electron
gamma
The nature of the radiation used (i.e. the name of the
subatomic particle or the region of the electromagnetic
spectrum). It is strongly recommended that this information
is given, so that the probe radiation can be simply determined.
diffrn_radiation.type
The nature of the radiation. This is typically a description
of the X-ray wavelength in Siegbahn notation.
CuK\a
Cu K\a~1~
Cu K-L~2,3~
white-beam
diffrn_radiation.wavelength_id
This data item is a pointer to attribute id
in category diffrn_radiation_wavelength in the DIFFRN_RADIATION_WAVELENGTH category.
K-L~3~
K-L~2~
K-M~3~
K-L~2,3~
The IUPAC symbol for the X-ray wavelength for the probe
radiation.
diffrn_radiation.diffrn_id
This data item is a pointer to attribute id in category diffrn in the DIFFRN
category.
0
diffrn_radiation_wavelength
Data items in the DIFFRN_RADIATION_WAVELENGTH category
describe the wavelength of the radiation used to measure the
diffraction intensities. Items may be looped to identify
and assign weights to distinct components of a
polychromatic beam.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:diffrn_radiation_wavelengthCategory>
<PDBx:diffrn_radiation_wavelength id="1">
<PDBx:wavelength>1.54</PDBx:wavelength>
<PDBx:wt>1.0</PDBx:wt>
</PDBx:diffrn_radiation_wavelength>
</PDBx:diffrn_radiation_wavelengthCategory>
1
1
0
1
1
diffrn_radiation_wavelengthCategory
This property indicates that datablock
has a category holder diffrn_radiation_wavelengthCategory.
diffrn_radiation_wavelengthCategory
This property indicates that diffrn_radiation_wavelengthCategory.
has a category diffrn_radiation_wavelength.
diffrn_radiation_wavelengthItem
Abstract datatype property for diffrn_radiation_wavelength items.
reference_to_diffrn_radiation_wavelength
cross-reference to diffrn_radiation_wavelength.
referenced_by_diffrn_radiation_wavelength
cross-reference from diffrn_radiation_wavelength.
diffrn_radiation_wavelength.wavelength
The radiation wavelength in angstroms.
diffrn_radiation_wavelength.wt
The relative weight of a wavelength identified by the code
attribute id in category diffrn_radiation_wavelength in the list of wavelengths.
diffrn_radiation_wavelength.id
The code identifying each value of
attribute wavelength.
in category diffrn_radiation_wavelength Items in the DIFFRN_RADIATION_WAVELENGTH category are looped
when multiple wavelengths are used.
This code is used to link with the DIFFRN_REFLN category.
The attribute wavelength_id in category diffrn_refln codes must match one of
the codes defined in this category.
x1
x2
neut
0
diffrn_refln
Data items in the DIFFRN_REFLN category record details about
the intensities in the diffraction data set
identified by attribute diffrn_id.
in category diffrn_refln
The DIFFRN_REFLN data items refer to individual intensity
measurements and must be included in looped lists.
The DIFFRN_REFLNS data items specify the parameters that apply
to all intensity measurements in the particular diffraction
data set identified by attribute diffrn_id in category diffrn_reflns.
Example 1 - based on CAD-4 diffractometer data obtained for
Yb(S-C5H4N)2(THF)4 for data set 'set1' reflection 1102.
<PDBx:diffrn_reflnCategory>
<PDBx:diffrn_refln diffrn_id="set1" id="1102">
<PDBx:angle_chi>32.21</PDBx:angle_chi>
<PDBx:angle_kappa>20.12</PDBx:angle_kappa>
<PDBx:angle_omega>11.54</PDBx:angle_omega>
<PDBx:angle_phi>176.02</PDBx:angle_phi>
<PDBx:angle_psi>0.00</PDBx:angle_psi>
<PDBx:angle_theta>23.08</PDBx:angle_theta>
<PDBx:attenuator_code>Ni.005</PDBx:attenuator_code>
<PDBx:counts_bg_1>22</PDBx:counts_bg_1>
<PDBx:counts_bg_2>25</PDBx:counts_bg_2>
<PDBx:counts_net>3450</PDBx:counts_net>
<PDBx:counts_peak>321</PDBx:counts_peak>
<PDBx:counts_total>3499</PDBx:counts_total>
<PDBx:detect_slit_horiz>0.04</PDBx:detect_slit_horiz>
<PDBx:detect_slit_vert>0.02</PDBx:detect_slit_vert>
<PDBx:elapsed_time>1.00</PDBx:elapsed_time>
<PDBx:index_h>4</PDBx:index_h>
<PDBx:index_k>0</PDBx:index_k>
<PDBx:index_l>2</PDBx:index_l>
<PDBx:intensity_net>202.56</PDBx:intensity_net>
<PDBx:intensity_sigma>2.18</PDBx:intensity_sigma>
<PDBx:scale_group_code>A24</PDBx:scale_group_code>
<PDBx:scan_mode>om</PDBx:scan_mode>
<PDBx:scan_mode_backgd>mo</PDBx:scan_mode_backgd>
<PDBx:scan_rate>1.2</PDBx:scan_rate>
<PDBx:scan_time_backgd>900.00</PDBx:scan_time_backgd>
<PDBx:scan_width>1.0</PDBx:scan_width>
<PDBx:sint_over_lambda>0.25426</PDBx:sint_over_lambda>
<PDBx:standard_code>1</PDBx:standard_code>
<PDBx:wavelength>1.54184</PDBx:wavelength>
<PDBx:wavelength_id>Cu1fixed</PDBx:wavelength_id>
</PDBx:diffrn_refln>
</PDBx:diffrn_reflnCategory>
0
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0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
1
1
1
1
1
0
1
0
1
0
1
0
1
0
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0
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0
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0
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0
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1
1
diffrn_reflnCategory
This property indicates that datablock
has a category holder diffrn_reflnCategory.
diffrn_reflnCategory
This property indicates that diffrn_reflnCategory.
has a category diffrn_refln.
diffrn_reflnItem
Abstract datatype property for diffrn_refln items.
reference_to_diffrn_refln
cross-reference to diffrn_refln.
referenced_by_diffrn_refln
cross-reference from diffrn_refln.
diffrn_refln.angle_chi
The diffractometer angle chi of a reflection in degrees. This
angle corresponds to the specified orientation matrix
and the original measured cell before any subsequent cell
transformations.
diffrn_refln.angle_kappa
The diffractometer angle kappa of a reflection in degrees. This
angle corresponds to the specified orientation matrix
and the original measured cell before any subsequent cell
transformations.
diffrn_refln.angle_omega
The diffractometer angle omega of a reflection in degrees. This
angle corresponds to the specified orientation matrix
and the original measured cell before any subsequent cell
transformations.
diffrn_refln.angle_phi
The diffractometer angle phi of a reflection in degrees. This
angle corresponds to the specified orientation matrix
and the original measured cell before any subsequent cell
transformations.
diffrn_refln.angle_psi
The diffractometer angle psi of a reflection in degrees. This
angle corresponds to the specified orientation matrix
and the original measured cell before any subsequent cell
transformations.
diffrn_refln.angle_theta
The diffractometer angle theta of a reflection in degrees. This
angle corresponds to the specified orientation matrix
and the original measured cell before any subsequent cell
transformations.
diffrn_refln.attenuator_code
The code identifying the attenuator setting for this reflection.
This code must match one of the attribute code in category diffrn_attenuator values.
diffrn_refln.class_code
The code identifying the class to which this reflection has
been assigned. This code must match a value of
attribute code in category diffrn_reflns_class. Reflections may be grouped into
classes for a variety of purposes. For example, for modulated
structures each reflection class may be defined by the
number m=sum|m~i~|, where the m~i~ are the integer coefficients
that, in addition to h,k,l, index the corresponding diffraction
vector in the basis defined for the reciprocal lattice.
diffrn_refln.counts_bg_1
The diffractometer counts for the measurement of the background
before the peak.
diffrn_refln.counts_bg_2
The diffractometer counts for the measurement of the background
after the peak.
diffrn_refln.counts_net
The diffractometer counts for the measurement of net counts after
background removal.
diffrn_refln.counts_peak
The diffractometer counts for the measurement of counts for the
peak scan or position.
diffrn_refln.counts_total
The diffractometer counts for the measurement of total counts
(background plus peak).
diffrn_refln.detect_slit_horiz
Total slit aperture in degrees in the diffraction plane.
diffrn_refln.detect_slit_vert
Total slit aperture in degrees perpendicular to the
diffraction plane.
diffrn_refln.elapsed_time
Elapsed time in minutes from the start of the diffraction
experiment to the measurement of this intensity.
diffrn_refln.frame_id
Pointer to attribute frame_id in category diffrn_scan_frame in the DIFFRN_SCAN_FRAME
category.
diffrn_refln.index_h
Miller index h of a reflection. The values of
the Miller indices in the DIFFRN_REFLN category need not match
the values of the Miller indices in the REFLN category if a
transformation of the original measured cell has taken place.
Details of the cell transformation are given in
attribute reduction_process in category diffrn_reflns. See also
attribute transf_matrix[][] in category diffrn_reflns.
diffrn_refln.index_k
Miller index k of a reflection. The values of
the Miller indices in the DIFFRN_REFLN category need not match
the values of the Miller indices in the REFLN category if a
transformation of the original measured cell has taken place.
Details of the cell transformation are given in
attribute reduction_process in category diffrn_reflns. See also
attribute transf_matrix[][] in category diffrn_reflns.
diffrn_refln.index_l
Miller index l of a reflection. The values of
the Miller indices in the DIFFRN_REFLN category need not match
the values of the Miller indices in the REFLN category if a
transformation of the original measured cell has taken place.
Details of the cell transformation are given in
attribute reduction_process in category diffrn_reflns. See also
attribute transf_matrix[][] in category diffrn_reflns.
diffrn_refln.intensity_net
Net intensity calculated from the diffraction counts after the
attenuator and standard scales have been applied.
diffrn_refln.intensity_sigma
Standard uncertainty (estimated standard deviation) of the
intensity calculated from the diffraction counts after the
attenuator and standard scales have been applied.
diffrn_refln.intensity_u
Standard uncertainty of the net intensity calculated from
the diffraction counts after the attenuator and standard
scales have been applied.
diffrn_refln.pdbx_batch_id
Pointer to attribute id in category pdbx_diffrn_batch in the PDBX_DIFFRN_BATCH category.
diffrn_refln.pdbx_detector_calc_fast
Detector coordinate (in pixels) along the direction of
the fast changing array index (of the 2D diffraction
data) for this reflection. This is often the position
where the calculated reflection is predicted to occur.
The fast changing array index of the 2D diffraction
array is often also defined as the detector
X-coordinate, while the slow changing array index is
defined as the Y-coordinate. This can vary depending on
the convention of the detector and the facility,
especially for multi-panel detectors.
diffrn_refln.pdbx_detector_calc_slow
Detector coordinate (in pixels) along the direction of
the slow changing array index (of the 2D diffraction
data) for this reflection. This is often the position
where the calculated reflection is predicted to occur.
The slow changing array index of the 2D diffraction
array is often also defined as the detector
Y-coordinate, while the fast changing array index is
defined as the X-coordinate. This can vary depending on
the convention of the detector and the facility,
especially for multi-panel detectors.
diffrn_refln.pdbx_detector_obs_fast
Detector coordinate (in pixels) along the direction of
the fast changing array index (of the 2D diffraction
data) as observed for this reflection. This is often
the position where the reflection centroid is observed.
The fast changing array index of the 2D diffraction
array is often also defined as the detector
X-coordinate, while the slow changing array index is
defined as the Y-coordinate. This can vary depending on
the convention of the detector and the facility,
especially for multi-panel detectors.
diffrn_refln.pdbx_detector_obs_slow
Detector coordinate (in pixels) along the direction of
the slow changing array index (of the 2D diffraction
data) as observed for this reflection. This is often
the position where the reflection centroid is observed.
The slow changing array index of the 2D diffraction
array is often also defined as the detector
Y-coordinate, while the fast changing array index is
defined as the X-coordinate. This can vary depending on
the convention of the detector and the facility,
especially for multi-panel detectors.
diffrn_refln.pdbx_detector_x
Detector coordinate (in pixels) along the X-direction
for this reflection. This is often the position where
the calculated reflection centroid is predicted to occur.
The detector X-direction is most often along the fast
changing array index of the 2D diffraction array, while
the Y-coordinate is along the slow changing array
index.
diffrn_refln.pdbx_detector_y
Detector coordinate (in pixels) along the Y-direction
for this reflection. This is often the position where
the calculated reflection centroid is predicted to occur.
The detector X-direction is most often along the fast
changing array index of the 2D diffraction array, while
the Y-coordinate is along the slow changing array
index.
diffrn_refln.pdbx_image_id
The identifier of the diffraction image this reflection
is associated with. This is often the image where the
calculated reflection centroid is predicted to occur.
diffrn_refln.pdbx_panel_mapping_id
Pointer to attribute id in category pdbx_diffrn_detector_panel_mapping in the
PDBX_DIFFRN_DETECTOR_PANEL_MAPPING category
diffrn_refln.pdbx_rotation_angle
The value of the angle around the scan axis for this
reflection. This is often the scan angle at which the
calculated reflection centroid is predicted to occur.
diffrn_refln.pdbx_scale_value
The scale factor applied to an individual reflection
intensity at the last scaling step before merging
all measurements belonging to symmetry-unique
reflections into a merged intensity.
diffrn_refln.pdbx_scan_angle
The value of the angle around the scan axis for this
reflection. This is often the scan angle at which the
calculated reflection centroid is predicted to occur.
diffrn_refln.scale_group_code
The code identifying the scale applying to this reflection.
This data item is a pointer to attribute code in category diffrn_scale_group in the
DIFFRN_SCALE_GROUP category.
om
ot
q
The code identifying the mode of scanning for measurements
using a diffractometer.
See _diffrn_refln.scan_width and _diffrn_refln.scan_mode_backgd.
st
mo
The code identifying the mode of scanning a reflection to
measure the background intensity.
diffrn_refln.scan_rate
The rate of scanning a reflection in degrees per minute
to measure the intensity.
diffrn_refln.scan_time_backgd
The time spent measuring each background in seconds.
diffrn_refln.scan_width
The scan width in degrees of the scan mode defined by the code
attribute scan_mode in category diffrn_refln.
diffrn_refln.sint_over_lambda
The (sin theta)/lambda value in reciprocal angstroms for this
reflection.
diffrn_refln.standard_code
The code identifying that this reflection was measured as a
standard intensity.
This data item is a pointer to attribute code in category diffrn_standard_refln in the
DIFFRN_STANDARD_REFLN category.
diffrn_refln.wavelength
The mean wavelength in angstroms of the radiation used to measure
the intensity of this reflection. This is an important parameter
for data collected using energy-dispersive detectors or the
Laue method.
diffrn_refln.wavelength_id
This data item is a pointer to attribute wavelength_id in category diffrn_radiation in
the DIFFRN_RADIATION category.
diffrn_refln.diffrn_id
This data item is a pointer to attribute id in category diffrn in the DIFFRN
category.
diffrn_refln.id
The value of attribute id in category diffrn_refln must uniquely identify the
reflection in the data set identified by the item
attribute diffrn_id.
in category diffrn_refln
Note that this item need not be a number; it can be any unique
identifier.
0
diffrn_reflns
Data items in the DIFFRN_REFLNS category record details about
the set of intensities measured in the diffraction experiment.
The DIFFRN_REFLN data items refer to individual intensity
measurements and must be included in looped lists.
The DIFFRN_REFLNS data items specify the parameters that apply
to all intensity measurements in a diffraction data set.
0
1
0
1
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1
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1
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1
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1
0
1
0
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0
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1
diffrn_reflnsCategory
This property indicates that datablock
has a category holder diffrn_reflnsCategory.
diffrn_reflnsCategory
This property indicates that diffrn_reflnsCategory.
has a category diffrn_reflns.
diffrn_reflnsItem
Abstract datatype property for diffrn_reflns items.
reference_to_diffrn_reflns
cross-reference to diffrn_reflns.
referenced_by_diffrn_reflns
cross-reference from diffrn_reflns.
diffrn_reflns.av_R_equivalents
The residual [sum|avdel(I)| / sum|av(I)|] for symmetry-equivalent
reflections used to calculate the average intensity av(I). The
avdel(I) term is the average absolute difference between av(I)
and the individual symmetry-equivalent intensities.
diffrn_reflns.av_sigmaI_over_netI
Measure [sum|sigma(I)|/sum|net(I)|] for all measured reflections.
diffrn_reflns.av_unetI_over_netI
Measure [sum u(net I)|/sum|net I|] for all measured reflections.
diffrn_reflns.limit_h_max
The maximum value of the Miller index h for the
reflection data specified by attribute index_h in category diffrn_refln.
diffrn_reflns.limit_h_min
The minimum value of the Miller index h for the
reflection data specified by attribute index_h in category diffrn_refln.
diffrn_reflns.limit_k_max
The maximum value of the Miller index k for the
reflection data specified by attribute index_k in category diffrn_refln.
diffrn_reflns.limit_k_min
The minimum value of the Miller index k for the
reflection data specified by attribute index_k in category diffrn_refln.
diffrn_reflns.limit_l_max
The maximum value of the Miller index l for the
reflection data specified by attribute index_l in category diffrn_refln.
diffrn_reflns.limit_l_min
The minimum value of the Miller index l for the
reflection data specified by attribute index_l in category diffrn_refln.
diffrn_reflns.number
The total number of measured intensities, excluding reflections
that are classified as systematically absent.
diffrn_reflns.pdbx_Rmerge_I_obs
The R factor for merging the reflections that satisfy the
resolution limits established by attribute d_resolution_high
in category diffrn_reflns and attribute d_resolution_low in category diffrn_reflns and the observation limit
established by attribute observed_criterion.
in category diffrn_reflns
Rmerge(I) = [sum~i~(sum~j~|I~j~ - |)] / [sum~i~(sum~j~)]
I~j~ = the intensity of the jth observation of reflection i
= the mean of the amplitudes of all observations of
reflection i
sum~i~ is taken over all reflections
sum~j~ is taken over all observations of each reflection
diffrn_reflns.pdbx_Rsym_value
The R factor for averaging the symmetry related reflections to a
unique data set.
diffrn_reflns.pdbx_chi_squared
Overall Chi-squared statistic for the data set.
diffrn_reflns.pdbx_d_res_high
The highest resolution for the interplanar spacings in the
reflection data set. This is the smallest d value.
diffrn_reflns.pdbx_d_res_low
The lowest resolution for the interplanar spacings in the
reflection data set. This is the largest d value.
diffrn_reflns.pdbx_number_obs
The number of reflections satisfying the observation criterion
as in attribute pdbx_observed_criterion in category diffrn_reflns
diffrn_reflns.pdbx_observed_criterion
The criterion used to classify a reflection as 'observed'. This
criterion is usually expressed in terms of a sigma(I) or
sigma(F) threshold.
diffrn_reflns.pdbx_percent_possible_obs
The percentage of geometrically possible reflections represented
by reflections that satisfy the resolution limits established
by _diffrn_reflns.d_resolution_high and _diffrn_reflns.d_resolution_low and
the observation limit established by attribute observed_criterion in category diffrn_reflns.
diffrn_reflns.pdbx_redundancy
The overall redundancy for the data set.
diffrn_reflns.pdbx_rejects
The number of rejected reflections in the data set.
The reflections may be rejected by setting the
observation criterion, attribute observed_criterion in category diffrn_reflns.
diffrn_reflns.reduction_process
A description of the process used to reduce the intensity data
into structure-factor magnitudes.
data averaged using Fisher test
diffrn_reflns.theta_max
Maximum theta angle in degrees for the measured diffraction
intensities.
diffrn_reflns.theta_min
Minimum theta angle in degrees for the measured diffraction
intensities.
diffrn_reflns.transf_matrix11
The [1][1] element of the 3x3 matrix used to transform Miller
indices in the DIFFRN_REFLN category into the Miller indices in
the REFLN category.
diffrn_reflns.transf_matrix12
The [1][2] element of the 3x3 matrix used to transform Miller
indices in the DIFFRN_REFLN category into the Miller indices in
the REFLN category.
diffrn_reflns.transf_matrix13
The [1][3] element of the 3x3 matrix used to transform Miller
indices in the DIFFRN_REFLN category into the Miller indices in
the REFLN category.
diffrn_reflns.transf_matrix21
The [2][1] element of the 3x3 matrix used to transform Miller
indices in the DIFFRN_REFLN category into the Miller indices in
the REFLN category.
diffrn_reflns.transf_matrix22
The [2][2] element of the 3x3 matrix used to transform Miller
indices in the DIFFRN_REFLN category into the Miller indices in
the REFLN category.
diffrn_reflns.transf_matrix23
The [2][3] element of the 3x3 matrix used to transform Miller
indices in the DIFFRN_REFLN category into the Miller indices in
the REFLN category.
diffrn_reflns.transf_matrix31
The [3][1] element of the 3x3 matrix used to transform Miller
indices in the DIFFRN_REFLN category into the Miller indices in
the REFLN category.
diffrn_reflns.transf_matrix32
The [3][2] element of the 3x3 matrix used to transform Miller
indices in the DIFFRN_REFLN category into the Miller indices in
the REFLN category.
diffrn_reflns.transf_matrix33
The [3][3] element of the 3x3 matrix used to transform Miller
indices in the DIFFRN_REFLN category into the Miller indices in
the REFLN category.
diffrn_reflns.diffrn_id
This data item is a pointer to attribute id in category diffrn in the DIFFRN
category.
0
diffrn_reflns_class
Data items in the DIFFRN_REFLNS_CLASS category record details
about the classes of reflections measured in the diffraction
experiment.
Example 1 - example corresponding to the one-dimensional incommensurately
modulated structure of K~2~SeO~4~. Each reflection class is
defined by the number m=sum|m~i~|, where the m~i~ are the
integer coefficients that, in addition to h,k,l, index the
corresponding diffraction vector in the basis defined for
the reciprocal lattice.
<PDBx:diffrn_reflns_classCategory>
<PDBx:diffrn_reflns_class code="Main">
<PDBx:av_R_eq>0.015</PDBx:av_R_eq>
<PDBx:d_res_high>0.551</PDBx:d_res_high>
<PDBx:d_res_low>6.136</PDBx:d_res_low>
<PDBx:description>m=0; main reflections</PDBx:description>
<PDBx:number>1580</PDBx:number>
</PDBx:diffrn_reflns_class>
<PDBx:diffrn_reflns_class code="Sat1">
<PDBx:av_R_eq>0.010</PDBx:av_R_eq>
<PDBx:d_res_high>0.551</PDBx:d_res_high>
<PDBx:d_res_low>6.136</PDBx:d_res_low>
<PDBx:description>m=1; first-order satellites</PDBx:description>
<PDBx:number>1045</PDBx:number>
</PDBx:diffrn_reflns_class>
</PDBx:diffrn_reflns_classCategory>
0
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0
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1
diffrn_reflns_classCategory
This property indicates that datablock
has a category holder diffrn_reflns_classCategory.
diffrn_reflns_classCategory
This property indicates that diffrn_reflns_classCategory.
has a category diffrn_reflns_class.
diffrn_reflns_classItem
Abstract datatype property for diffrn_reflns_class items.
reference_to_diffrn_reflns_class
cross-reference to diffrn_reflns_class.
referenced_by_diffrn_reflns_class
cross-reference from diffrn_reflns_class.
diffrn_reflns_class.av_R_eq
For each reflection class, the residual
[sum av|del(I)|/sum|av(I)|] for symmetry-equivalent reflections
used to calculate the average intensity av(I). The av|del(I)|
term is the average absolute difference between av(I) and the
individual intensities.
diffrn_reflns_class.av_sgI_over_I
Measure [sum|sigma(net I)|/sum|net I|] for all measured intensities
in a reflection class.
diffrn_reflns_class.av_uI_over_I
Measure [sum|u(net I)|/sum|net I|] for all measured intensities
in a reflection class.
diffrn_reflns_class.d_res_high
The smallest value in angstroms for the interplanar
spacings for the reflections in each measured reflection class.
This is called the highest resolution for this reflection class.
diffrn_reflns_class.d_res_low
The largest value in angstroms of the interplanar
spacings for the reflections for each measured reflection class.
This is called the lowest resolution for this reflection class.
diffrn_reflns_class.description
Description of each reflection class.
m=1 first order satellites
H0L0 common projection reflections
diffrn_reflns_class.number
The total number of measured intensities for each reflection
class, excluding the systematic absences arising from
centring translations.
diffrn_reflns_class.code
The code identifying a certain reflection class.
1
m1
s2
0
diffrn_scale_group
Data items in the DIFFRN_SCALE_GROUP category record details
of the scaling factors applied to place all intensities in the
reflection lists on a common scale.
Scaling groups might, for example, correspond to each film in a
multi-film data set or each crystal in a multi-crystal data set.
Example 1 - based on CAD-4 diffractometer data obtained for
Yb(S-C5H4N)2(THF)4.
<PDBx:diffrn_scale_groupCategory>
<PDBx:diffrn_scale_group code="A24">
<PDBx:I_net>1.021</PDBx:I_net>
</PDBx:diffrn_scale_group>
</PDBx:diffrn_scale_groupCategory>
0
1
1
diffrn_scale_groupCategory
This property indicates that datablock
has a category holder diffrn_scale_groupCategory.
diffrn_scale_groupCategory
This property indicates that diffrn_scale_groupCategory.
has a category diffrn_scale_group.
diffrn_scale_groupItem
Abstract datatype property for diffrn_scale_group items.
reference_to_diffrn_scale_group
cross-reference to diffrn_scale_group.
referenced_by_diffrn_scale_group
cross-reference from diffrn_scale_group.
diffrn_scale_group.I_net
The scale for a specific measurement group which is to be
multiplied with the net intensity to place all intensities
in the DIFFRN_REFLN or REFLN list on a common scale.
diffrn_scale_group.code
The value of attribute code in category diffrn_scale_group must uniquely identify a
record in the DIFFRN_SCALE_GROUP list.
Note that this item need not be a number; it can be any unique
identifier.
1
2
c1
c2
0
diffrn_scan
Data items in the DIFFRN_SCAN category describe the parameters of one
or more scans, relating axis positions to frames.
Example 1. derived from a suggestion by R. M. Sweet.
The vector of each axis is not given here, because it is provided in
the AXIS category. By making _diffrn_scan_axis.scan_id and
_diffrn_scan_axis.axis_id keys of the DIFFRN_SCAN_AXIS category,
an arbitrary number of scanning and fixed axes can be specified for a
scan. In this example, three rotation axes and one translation axis
at nonzero values are specified, with one axis stepping. There is no
reason why more axes could not have been specified to step. Range
information has been specified, but note that it can be calculated from
the number of frames and the increment, so the data item
_diffrn_scan_axis.angle_range could be dropped.
Both the sweep data and the data for a single frame are specified.
Note that the information on how the axes are stepped is given twice,
once in terms of the overall averages in the value of
_diffrn_scan.integration_time and the values for DIFFRN_SCAN_AXIS,
and precisely for the given frame in the value for
_diffrn_scan_frame.integration_time and the values for
DIFFRN_SCAN_FRAME_AXIS . If dose-related adjustments are made to
scan times and nonlinear stepping is done, these values may differ.
Therefore, in interpreting the data for a particular frame it is
important to use the frame-specific data.
There are three date/times in this set: *.date_start and
*. date_end_estimated, both of which are mandatory, because the former
is data which can be logged at the start of collection and the latter
is data that can be estimated at the same time, and *.date_end which
can only be logged exactly if the data collection completes normally.
<PDBx:diffrn_scanCategory>
<PDBx:diffrn_scan id="1">
<PDBx:date_end>2001-11-18T03:36:45</PDBx:date_end>
<PDBx:date_end_estimated>2001-11-18T03:36:45</PDBx:date_end_estimated>
<PDBx:date_start>2001-11-18T03:26:42</PDBx:date_start>
<PDBx:frame_id_end>mad_L2_200</PDBx:frame_id_end>
<PDBx:frame_id_start>mad_L2_000</PDBx:frame_id_start>
<PDBx:frames>201</PDBx:frames>
<PDBx:integration_time>3.0</PDBx:integration_time>
</PDBx:diffrn_scan>
</PDBx:diffrn_scanCategory>
<PDBx:diffrn_scan_axisCategory>
<PDBx:diffrn_scan_axis axis_id="omega" scan_id="1">
<PDBx:angle_increment>0.1</PDBx:angle_increment>
<PDBx:angle_range>20.0</PDBx:angle_range>
<PDBx:angle_start>200.0</PDBx:angle_start>
<PDBx:displacement_increment xsi:nil="true" />
<PDBx:displacement_range xsi:nil="true" />
<PDBx:displacement_start xsi:nil="true" />
</PDBx:diffrn_scan_axis>
<PDBx:diffrn_scan_axis axis_id="kappa" scan_id="1">
<PDBx:angle_increment>0.0</PDBx:angle_increment>
<PDBx:angle_range>0.0</PDBx:angle_range>
<PDBx:angle_start>-40.0</PDBx:angle_start>
<PDBx:displacement_increment xsi:nil="true" />
<PDBx:displacement_range xsi:nil="true" />
<PDBx:displacement_start xsi:nil="true" />
</PDBx:diffrn_scan_axis>
<PDBx:diffrn_scan_axis axis_id="phi" scan_id="1">
<PDBx:angle_increment>0.0</PDBx:angle_increment>
<PDBx:angle_range>0.0</PDBx:angle_range>
<PDBx:angle_start>127.5</PDBx:angle_start>
<PDBx:displacement_increment xsi:nil="true" />
<PDBx:displacement_range xsi:nil="true" />
<PDBx:displacement_start xsi:nil="true" />
</PDBx:diffrn_scan_axis>
<PDBx:diffrn_scan_axis axis_id="tranz" scan_id="1">
<PDBx:angle_increment xsi:nil="true" />
<PDBx:angle_range xsi:nil="true" />
<PDBx:angle_start xsi:nil="true" />
<PDBx:displacement_increment>0.0</PDBx:displacement_increment>
<PDBx:displacement_range>0.0</PDBx:displacement_range>
<PDBx:displacement_start>2.3</PDBx:displacement_start>
</PDBx:diffrn_scan_axis>
</PDBx:diffrn_scan_axisCategory>
<PDBx:diffrn_scan_frameCategory>
<PDBx:diffrn_scan_frame frame_id="mad_L2_018" scan_id="1">
<PDBx:date>2001-11-18T03:27:33</PDBx:date>
<PDBx:frame_number>18</PDBx:frame_number>
<PDBx:integration_time>3.0</PDBx:integration_time>
</PDBx:diffrn_scan_frame>
</PDBx:diffrn_scan_frameCategory>
<PDBx:diffrn_scan_frame_axisCategory>
<PDBx:diffrn_scan_frame_axis axis_id="omega" frame_id="mad_L2_018">
<PDBx:angle>201.8</PDBx:angle>
<PDBx:angle_increment>0.1</PDBx:angle_increment>
<PDBx:displacement xsi:nil="true" />
<PDBx:displacement_increment xsi:nil="true" />
</PDBx:diffrn_scan_frame_axis>
<PDBx:diffrn_scan_frame_axis axis_id="kappa" frame_id="mad_L2_018">
<PDBx:angle>-40.0</PDBx:angle>
<PDBx:angle_increment>0.0</PDBx:angle_increment>
<PDBx:displacement xsi:nil="true" />
<PDBx:displacement_increment xsi:nil="true" />
</PDBx:diffrn_scan_frame_axis>
<PDBx:diffrn_scan_frame_axis axis_id="phi" frame_id="mad_L2_018">
<PDBx:angle>127.5</PDBx:angle>
<PDBx:angle_increment>0.0</PDBx:angle_increment>
<PDBx:displacement xsi:nil="true" />
<PDBx:displacement_increment xsi:nil="true" />
</PDBx:diffrn_scan_frame_axis>
<PDBx:diffrn_scan_frame_axis axis_id="tranz" frame_id="mad_L2_018">
<PDBx:angle xsi:nil="true" />
<PDBx:angle_increment xsi:nil="true" />
<PDBx:displacement>2.3</PDBx:displacement>
<PDBx:displacement_increment>0.0</PDBx:displacement_increment>
</PDBx:diffrn_scan_frame_axis>
</PDBx:diffrn_scan_frame_axisCategory>
0
1
0
1
0
1
1
1
1
1
0
1
0
1
0
1
0
1
1
diffrn_scanCategory
This property indicates that datablock
has a category holder diffrn_scanCategory.
diffrn_scanCategory
This property indicates that diffrn_scanCategory.
has a category diffrn_scan.
diffrn_scanItem
Abstract datatype property for diffrn_scan items.
reference_to_diffrn_scan
cross-reference to diffrn_scan.
referenced_by_diffrn_scan
cross-reference from diffrn_scan.
diffrn_scan.date_end
The date and time of the end of the scan. Note that this
may be an estimate generated during the scan, before the
precise time of the end of the scan is known, in which
case attribute date_end_estimated in category diffrn_scan should be used instead.
diffrn_scan.date_end_estimated
The estimated date and time of the end of the scan. Note
that this may be generated at the start or during the scan,
before the precise time of the end of the scan is known.
diffrn_scan.date_start
The date and time of the start of the scan.
diffrn_scan.frame_id_end
The value of this data item is the identifier of the
last frame in the scan.
This item is a pointer to attribute id in category diffrn_data_frame in the
DIFFRN_DATA_FRAME category.
diffrn_scan.frame_id_start
The value of this data item is the identifier of the
first frame in the scan.
This item is a pointer to attribute id in category diffrn_data_frame in the
DIFFRN_DATA_FRAME category.
diffrn_scan.frames
The value of this data item is the number of frames in
the scan.
diffrn_scan.integration_time
Approximate average time in seconds to integrate each
step of the scan. The precise time for integration
of each particular step must be provided in
attribute integration_time in category diffrn_scan_frame, even
if all steps have the same integration time.
diffrn_scan.time_period
Approximate average time in seconds between the start
of each step of the scan. The precise start-to-start
time increment of each particular step may be provided in
attribute time_period in category diffrn_scan_frame.
diffrn_scan.time_rstrt_incr
Approximate average time in seconds between the end
of integration of each step of the scan and the start
of integration of the next step.
In general, this will agree with
attribute time_rstrt_incr in category diffrn_scan_frame . The
sum of the values of attribute integration_time
in category diffrn_scan_frame and attribute time_rstrt_incr in category diffrn_scan_frame is the
time from the start of integration of one frame and the start of
integration for the next frame and should equal the value of
attribute time_period in category diffrn_scan_frame for this
frame. If the individual frame values vary, then the value of
attribute time_rstrt_incr in category diffrn_scan will be
representative of the ensemble of values of
attribute time_rstrt_incr in category diffrn_scan_frame (e.g.
the mean).
diffrn_scan.id
The value of attribute id in category diffrn_scan uniquely identifies each
scan. The identifier is used to tie together all the
information about the scan.
0
diffrn_scan_axis
Data items in the DIFFRN_SCAN_AXIS category describe the settings of
axes for particular scans. Unspecified axes are assumed to be at
their zero points.
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
1
diffrn_scan_axisCategory
This property indicates that datablock
has a category holder diffrn_scan_axisCategory.
diffrn_scan_axisCategory
This property indicates that diffrn_scan_axisCategory.
has a category diffrn_scan_axis.
diffrn_scan_axisItem
Abstract datatype property for diffrn_scan_axis items.
reference_to_diffrn_scan_axis
cross-reference to diffrn_scan_axis.
referenced_by_diffrn_scan_axis
cross-reference from diffrn_scan_axis.
diffrn_scan_axis.angle_increment
The increment for each step for the specified axis
in degrees. In general, this will agree with
attribute angle_increment in category diffrn_scan_frame_axis . The
sum of the values of attribute angle in category diffrn_scan_frame_axis and
attribute angle_increment in category diffrn_scan_frame_axis is the
angular setting of the axis at the end of the integration
time for a given frame. If the individual frame values
vary, then the value of
attribute angle_increment in category diffrn_scan_axis will be
representative
of the ensemble of values of
attribute angle_increment in category diffrn_scan_frame_axis (e.g.
the mean).
diffrn_scan_axis.angle_range
The range from the starting position for the specified axis
in degrees.
diffrn_scan_axis.angle_rstrt_incr
The increment after each step for the specified axis
in degrees. In general, this will agree with
attribute angle_rstrt_incr in category diffrn_scan_frame_axis . The
sum of the values of attribute angle,
in category diffrn_scan_frame_axis attribute angle_increment
in category diffrn_scan_frame_axis and attribute angle_rstrt_incr in category diffrn_scan_frame_axis is the
angular setting of the axis at the start of the integration
time for the next frame relative to a given frame and
should equal attribute angle in category diffrn_scan_frame_axis for this
next frame. If the individual frame values
vary, then the value of
attribute angle_rstrt_incr in category diffrn_scan_axis will be
representative
of the ensemble of values of
attribute angle_rstrt_incr in category diffrn_scan_frame_axis (e.g.
the mean).
diffrn_scan_axis.angle_start
The starting position for the specified axis in degrees.
diffrn_scan_axis.displacement_increment
The increment for each step for the specified axis
in millimetres. In general, this will agree with
attribute displacement_increment.
in category diffrn_scan_frame_axis The sum of the values of
attribute displacement in category diffrn_scan_frame_axis and
attribute displacement_increment in category diffrn_scan_frame_axis is the
angular setting of the axis at the end of the integration
time for a given frame. If the individual frame values
vary, then the value of
attribute displacement_increment in category diffrn_scan_axis will be
representative of the ensemble of values of
attribute displacement_increment in category diffrn_scan_frame_axis (e.g.
the mean).
diffrn_scan_axis.displacement_range
The range from the starting position for the specified axis
in millimetres.
diffrn_scan_axis.displacement_rstrt_incr
The increment for each step for the specified axis
in millimetres. In general, this will agree with
attribute displacement_rstrt_incr.
in category diffrn_scan_frame_axis The sum of the values of
attribute displacement,
in category diffrn_scan_frame_axis attribute displacement_increment in category diffrn_scan_frame_axis and
attribute displacement_rstrt_incr in category diffrn_scan_frame_axis is the
angular setting of the axis at the start of the integration
time for the next frame relative to a given frame and
should equal attribute displacement
in category diffrn_scan_frame_axis for this next frame. If the individual frame values
vary, then the value of
attribute displacement_rstrt_incr in category diffrn_scan_axis will be
representative of the ensemble of values of
attribute displacement_rstrt_incr in category diffrn_scan_frame_axis (e.g.
the mean).
diffrn_scan_axis.displacement_start
The starting position for the specified axis in millimetres.
diffrn_scan_axis.reference_angle
The setting of the specified axis in degrees
against which measurements of the reference beam centre
and reference detector distance should be made.
In general, this will agree with
attribute reference_angle.
in category diffrn_scan_frame_axis
If the individual frame values vary, then the value of
attribute reference_angle in category diffrn_scan_axis will be
representative of the ensemble of values of
attribute reference_angle in category diffrn_scan_frame_axis (e.g.
the mean).
If not specified, the value defaults to zero.
diffrn_scan_axis.reference_displacement
The setting of the specified axis in millimetres
against which measurements of the reference beam centre
and reference detector distance should be made.
In general, this will agree with
attribute reference_displacement.
in category diffrn_scan_frame_axis
If the individual frame values vary, then the value of
attribute reference_displacement in category diffrn_scan_axis will be
representative of the ensemble of values of
attribute reference_displacement in category diffrn_scan_frame_axis (e.g.
the mean).
diffrn_scan_axis.axis_id
The value of this data item is the identifier of one of
the axes for the scan for which settings are being specified.
Multiple axes may be specified for the same value of
attribute id.
in category diffrn_scan
This item is a pointer to attribute id in category axis in the
AXIS category.
diffrn_scan_axis.scan_id
The value of this data item is the identifier of the
scan for which axis settings are being specified.
Multiple axes may be specified for the same value of
attribute id.
in category diffrn_scan
This item is a pointer to attribute id in category diffrn_scan in the
DIFFRN_SCAN category.
0
diffrn_scan_collection
Data items in the DIFFRN_SCAN_COLLECTION category describe
the collection strategy for each scan.
This category is a preliminary version being developed as
synchrotron and XFEL collection strategies evolve.
Example 1 - Describing a multi-wedge raster scan.
<PDBx:diffrn_scan_collectionCategory>
<PDBx:diffrn_scan_collection scan_id="multi_wedge">
<PDBx:details> scan 20 micrometre beam in 100 micrometre steps on 31
by 46 alternating raster of 20 degree wedges</PDBx:details>
</PDBx:diffrn_scan_collection>
</PDBx:diffrn_scan_collectionCategory>
0
1
0
1
0
1
1
diffrn_scan_collectionCategory
This property indicates that datablock
has a category holder diffrn_scan_collectionCategory.
diffrn_scan_collectionCategory
This property indicates that diffrn_scan_collectionCategory.
has a category diffrn_scan_collection.
diffrn_scan_collectionItem
Abstract datatype property for diffrn_scan_collection items.
reference_to_diffrn_scan_collection
cross-reference to diffrn_scan_collection.
referenced_by_diffrn_scan_collection
cross-reference from diffrn_scan_collection.
diffrn_scan_collection.details
The value of attribute details in category diffrn_scan_collection should give a
description of special aspects of each collection strategy.
diffrn_scan_collection.translation_width
The value of attribute translation_width
in category diffrn_scan_collection gives the average single step translation in micrometres
in collection strategies for which this information is
appropriate, e.g. 'vector'.
diffrn_scan_collection.type
The value of attribute type in category diffrn_scan_collection identifies
the strategy used in this scan, e.g. `rotation', 'raster',
'vector', 'still', etc.
The default is 'rotation'.
diffrn_scan_collection.scan_id
The value of attribute scan_id in category diffrn_scan_collection identifies the scan
containing this frame.
This item is a pointer to attribute id in category diffrn_scan in the
DIFFRN_SCAN category.
In the case of a single-scan dataset, the value is implicit.
0
diffrn_scan_frame
Data items in the DIFFRN_SCAN_FRAME category describe
the relationships of particular frames to scans.
0
1
0
1
1
1
0
1
0
1
0
1
1
1
diffrn_scan_frameCategory
This property indicates that datablock
has a category holder diffrn_scan_frameCategory.
diffrn_scan_frameCategory
This property indicates that diffrn_scan_frameCategory.
has a category diffrn_scan_frame.
diffrn_scan_frameItem
Abstract datatype property for diffrn_scan_frame items.
reference_to_diffrn_scan_frame
cross-reference to diffrn_scan_frame.
referenced_by_diffrn_scan_frame
cross-reference from diffrn_scan_frame.
diffrn_scan_frame.date
The date and time of the start of the frame being scanned.
diffrn_scan_frame.frame_number
The value of this data item is the number of the frame
within the scan, starting with 1. It is not necessarily
the same as the value of attribute frame_id,
in category diffrn_scan_frame but it may be.
diffrn_scan_frame.integration_time
The time in seconds to integrate this step of the scan.
This should be the precise time of integration of each
particular frame. The value of this data item should
be given explicitly for each frame and not inferred
from the value of attribute integration_time in category diffrn_scan.
diffrn_scan_frame.polarizn_Stokes_I
The quantity Ip+In+Inp, where Ip is the intensity (amplitude
squared) of the electric vector in the plane of polarization,
In is the intensity (amplitude squared) of the electric vector
in the plane of the normal to the plane of polarization,
and Inp is the intensity (amplitude squared) of the
non-polarized (incoherent) electric vector.
This is an average or other representative sample of the
frame.
This is the first of the Stokes polarization parameters,
I, Q, U, V [also known as I, M, C, S; see Berry et al. (1977)].
If the absolute intensity is not known, the value 1.0
is assumed for I, and all four Stokes parameters are
dimensionless. When the absolute intensity is known,
all four Stokes parameters are in units of watts per
square metre.
Note that, if the polarized intensity Ip+In is required,
(Ip+In)^2^ is the sum of Q^2^+U^2^+V^2^.
Reference:
Berry, H. H., Gabrielse, G. & Livingston, A. E. (1977).
'Measurement of the Stokes parameters of light',
Appl. Optics, 16:12, 3200--3205.
diffrn_scan_frame.time_period
The time in seconds between the start of this frame and the
start of the next frame, if any. If there is no next frame,
a null value should be given.
diffrn_scan_frame.time_rstrt_incr
The time in seconds between the end of integration of this step of the scan
and the start of integration of the next step.
The sum of the values of attribute integration_time
in category diffrn_scan_frame and attribute time_rstrt_incr in category diffrn_scan_frame is the
time from the start of integration of one frame and the start of
integration for the next frame and should equal the value of
attribute time_period in category diffrn_scan_frame for this
frame. The value of attribute time_rstrt_incr in category diffrn_scan will be
representative of the ensemble of values of
attribute time_rstrt_incr in category diffrn_scan_frame (e.g.
the mean).
If there is no next frame, a null value should be given.
diffrn_scan_frame.frame_id
The value of this data item is the identifier of the
frame being examined.
This item is a pointer to attribute id in category diffrn_data_frame in the
DIFFRN_DATA_FRAME category.
diffrn_scan_frame.scan_id
The value of attribute scan_id in category diffrn_scan_frame identifies the scan
containing this frame.
This item is a pointer to attribute id in category diffrn_scan in the
DIFFRN_SCAN category.
0
diffrn_scan_frame_axis
Data items in the DIFFRN_SCAN_FRAME_AXIS category describe the
settings of axes for particular frames. Unspecified axes are
assumed to be at their zero points. If, for any given frame,
nonzero values apply for any of the data items in this category,
those values should be given explicitly in this category and not
simply inferred from values in DIFFRN_SCAN_AXIS.
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
1
diffrn_scan_frame_axisCategory
This property indicates that datablock
has a category holder diffrn_scan_frame_axisCategory.
diffrn_scan_frame_axisCategory
This property indicates that diffrn_scan_frame_axisCategory.
has a category diffrn_scan_frame_axis.
diffrn_scan_frame_axisItem
Abstract datatype property for diffrn_scan_frame_axis items.
reference_to_diffrn_scan_frame_axis
cross-reference to diffrn_scan_frame_axis.
referenced_by_diffrn_scan_frame_axis
cross-reference from diffrn_scan_frame_axis.
diffrn_scan_frame_axis.angle
The setting of the specified axis in degrees for this frame.
This is the setting at the start of the integration time.
diffrn_scan_frame_axis.angle_increment
The increment for this frame for the angular setting of
the specified axis in degrees. The sum of the values
of attribute angle in category diffrn_scan_frame_axis and
attribute angle_increment in category diffrn_scan_frame_axis is the
angular setting of the axis at the end of the integration
time for this frame.
diffrn_scan_frame_axis.angle_rstrt_incr
The increment after this frame for the angular setting of
the specified axis in degrees. The sum of the values
of attribute angle,
in category diffrn_scan_frame_axis attribute angle_increment in category diffrn_scan_frame_axis and
attribute angle_rstrt_incr in category diffrn_scan_frame_axis is the
angular setting of the axis at the start of the integration
time for the next frame and should equal
attribute angle in category diffrn_scan_frame_axis for this next frame.
diffrn_scan_frame_axis.displacement
The setting of the specified axis in millimetres for this
frame. This is the setting at the start of the integration
time.
diffrn_scan_frame_axis.displacement_increment
The increment for this frame for the displacement setting of
the specified axis in millimetres. The sum of the values
of attribute displacement in category diffrn_scan_frame_axis and
attribute displacement_increment in category diffrn_scan_frame_axis is the
angular setting of the axis at the end of the integration
time for this frame.
diffrn_scan_frame_axis.displacement_rstrt_incr
The increment for this frame for the displacement setting of
the specified axis in millimetres. The sum of the values
of attribute displacement,
in category diffrn_scan_frame_axis attribute displacement_increment in category diffrn_scan_frame_axis and
attribute displacement_rstrt_incr in category diffrn_scan_frame_axis is the
angular setting of the axis at the start of the integration
time for the next frame and should equal
attribute displacement in category diffrn_scan_frame_axis for this next frame.
diffrn_scan_frame_axis.reference_angle
The setting of the specified axis in degrees
against which measurements of the reference beam centre
and reference detector distance should be made.
This is normally the same for all frames, but the
option is provided here of making changes when
needed.
If not provided, it is assumed to be zero.
diffrn_scan_frame_axis.reference_displacement
The setting of the specified axis in millimetres for this
frame against which measurements of the reference beam centre
and reference detector distance should be made.
This is normally the same for all frames, but the
option is provided here of making changes when
needed.
If not provided, it is assumed to be equal to
attribute displacement in category diffrn_scan_frame_axis.
diffrn_scan_frame_axis.axis_id
The value of this data item is the identifier of one of
the axes for the frame for which settings are being specified.
Multiple axes may be specified for the same value of
attribute frame_id.
in category diffrn_scan_frame
This item is a pointer to attribute id in category axis in the
AXIS category.
diffrn_scan_frame_axis.frame_id
The value of this data item is the identifier of the
frame for which axis settings are being specified.
Multiple axes may be specified for the same value of
attribute frame_id.
in category diffrn_scan_frame
This item is a pointer to attribute id in category diffrn_data_frame in the
DIFFRN_DATA_FRAME category.
0
diffrn_source
Data items in the DIFFRN_SOURCE category record details of
the source of radiation used in the diffraction experiment.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:diffrn_sourceCategory>
<PDBx:diffrn_source diffrn_id="s1">
<PDBx:current>180</PDBx:current>
<PDBx:power>50</PDBx:power>
<PDBx:size>8mm x 0.4 mm broad-focus</PDBx:size>
<PDBx:source>rotating anode</PDBx:source>
<PDBx:type>Rigaku RU-200</PDBx:type>
</PDBx:diffrn_source>
</PDBx:diffrn_sourceCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
diffrn_sourceCategory
This property indicates that datablock
has a category holder diffrn_sourceCategory.
diffrn_sourceCategory
This property indicates that diffrn_sourceCategory.
has a category diffrn_source.
diffrn_sourceItem
Abstract datatype property for diffrn_source items.
reference_to_diffrn_source
cross-reference to diffrn_source.
referenced_by_diffrn_source
cross-reference from diffrn_source.
diffrn_source.current
The current in milliamperes at which the radiation source
was operated.
diffrn_source.details
A description of special aspects of the radiation source used.
diffrn_source.pdbx_source_specific_beamline
Beamline for synchrotron source.
6A2
7.2
9.5
9.6
A-1
A1
BL-6A
BW6
BW7B
F-1
F1
PX7.2
PX9.6
UNDULATOR
W32
WIGGLER
X11
X12C
X25
X26-C
X31
X4A
X8C
diffrn_source.pdbx_synchrotron_beamline
Synchrotron beamline.
diffrn_source.pdbx_synchrotron_site
Synchrotron site.
diffrn_source.pdbx_synchrotron_y_n
Yes/No if synchrotron source was used or not.
Y
N
diffrn_source.pdbx_wavelength
Wavelength of radiation.
diffrn_source.pdbx_wavelength_list
Comma separated list of wavelengths or wavelength range.
diffrn_source.power
The power in kilowatts at which the radiation source
was operated.
diffrn_source.size
The dimensions of the source as viewed from the sample.
8mm x 0.4 mm fine-focus
broad focus
diffrn_source.source
The general class of the radiation source.
sealed X-ray tube
nuclear reactor
spallation source
electron microscope
rotating-anode X-ray tube
synchrotron
diffrn_source.take-off_angle
The complement of the angle in degrees between the normal
to the surface of the X-ray tube target and the primary
X-ray beam for beams generated by traditional X-ray tubes.
1.5
H
He
Li
Be
B
C
N
O
F
Ne
Na
Mg
Al
Si
P
S
Cl
Ar
K
Ca
Sc
Ti
V
Cr
Mn
Fe
Co
Ni
Cu
Zn
Ga
Ge
As
Se
Br
Kr
Rb
Sr
Y
Zr
Nb
Mo
Tc
Ru
Rh
Pd
Ag
Cd
In
Sn
Sb
Te
I
Xe
Cs
Ba
La
Ce
Pr
Nd
Pm
Sm
Eu
Gd
Tb
Dy
Ho
Er
Tm
Yb
Lu
Hf
Ta
W
Re
Os
Ir
Pt
Au
Hg
Tl
Pb
Bi
Po
At
Rn
Fr
Ra
Ac
Th
Pa
U
Np
Pu
Am
Cm
Bk
Cf
Es
Fm
Md
No
Lr
The chemical element symbol for the X-ray target
(usually the anode) used to generate X-rays.
This can also be used for spallation sources.
diffrn_source.type
The make, model or name of the source of radiation.
NSLS beamline X8C
Rigaku RU200
diffrn_source.voltage
The voltage in kilovolts at which the radiation source was
operated.
diffrn_source.diffrn_id
This data item is a pointer to attribute id in category diffrn in the DIFFRN
category.
0
diffrn_standard_refln
Data items in the DIFFRN_STANDARD_REFLN category record details
about the reflections treated as standards during the measurement
of a set of diffraction intensities.
Note that these are the individual standard reflections, not the
results of the analysis of the standard reflections.
Example 2 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
<PDBx:diffrn_standard_reflnCategory>
<PDBx:diffrn_standard_refln code="1" diffrn_id="s1">
<PDBx:index_h>3</PDBx:index_h>
<PDBx:index_k>2</PDBx:index_k>
<PDBx:index_l>4</PDBx:index_l>
</PDBx:diffrn_standard_refln>
<PDBx:diffrn_standard_refln code="1" diffrn_id="s1">
<PDBx:index_h>1</PDBx:index_h>
<PDBx:index_k>9</PDBx:index_k>
<PDBx:index_l>1</PDBx:index_l>
</PDBx:diffrn_standard_refln>
<PDBx:diffrn_standard_refln code="1" diffrn_id="s1">
<PDBx:index_h>3</PDBx:index_h>
<PDBx:index_k>0</PDBx:index_k>
<PDBx:index_l>10</PDBx:index_l>
</PDBx:diffrn_standard_refln>
</PDBx:diffrn_standard_reflnCategory>
1
1
1
1
1
1
1
1
diffrn_standard_reflnCategory
This property indicates that datablock
has a category holder diffrn_standard_reflnCategory.
diffrn_standard_reflnCategory
This property indicates that diffrn_standard_reflnCategory.
has a category diffrn_standard_refln.
diffrn_standard_reflnItem
Abstract datatype property for diffrn_standard_refln items.
reference_to_diffrn_standard_refln
cross-reference to diffrn_standard_refln.
referenced_by_diffrn_standard_refln
cross-reference from diffrn_standard_refln.
diffrn_standard_refln.index_h
Miller index h of a standard reflection used in the diffraction
measurement process.
diffrn_standard_refln.index_k
Miller index k of a standard reflection used in the diffraction
measurement process.
diffrn_standard_refln.index_l
Miller index l of a standard reflection used in the diffraction
measurement process.
diffrn_standard_refln.code
The code identifying a reflection measured as a standard
reflection with the indices attribute index_h,
in category diffrn_standard_refln attribute index_k in category diffrn_standard_refln and
attribute index_l in category diffrn_standard_refln. This is the same code as the
attribute standard_code in category diffrn_refln in the DIFFRN_REFLN list.
1
2
c1
c2
diffrn_standard_refln.diffrn_id
This data item is a pointer to attribute id in category diffrn in the DIFFRN
category.
0
diffrn_standards
Data items in the DIFFRN_STANDARDS category record details
about the set of standard reflections used to monitor intensity
stability during the measurement of diffraction intensities.
Note that these records describe properties common to the set of
standard reflections, not the standard reflections themselves.
Example 1 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
<PDBx:diffrn_standardsCategory>
<PDBx:diffrn_standards diffrn_id="s1">
<PDBx:decay_>0</PDBx:decay_>
<PDBx:interval_time>120</PDBx:interval_time>
<PDBx:number>3</PDBx:number>
</PDBx:diffrn_standards>
</PDBx:diffrn_standardsCategory>
0
1
0
1
0
1
0
1
0
1
0
1
1
diffrn_standardsCategory
This property indicates that datablock
has a category holder diffrn_standardsCategory.
diffrn_standardsCategory
This property indicates that diffrn_standardsCategory.
has a category diffrn_standards.
diffrn_standardsItem
Abstract datatype property for diffrn_standards items.
reference_to_diffrn_standards
cross-reference to diffrn_standards.
referenced_by_diffrn_standards
cross-reference from diffrn_standards.
diffrn_standards.decay_
The percentage decrease in the mean of the intensities
for the set of standard reflections from the start of the
measurement process to the end. This value usually
affords a measure of the overall decay in crystal quality
during the diffraction measurement process. Negative values
are used in exceptional instances where the final intensities
are greater than the initial ones.
diffrn_standards.interval_count
The number of reflection intensities between the measurement of
standard reflection intensities.
diffrn_standards.interval_time
The time in minutes between the measurement of standard
reflection intensities.
diffrn_standards.number
The number of unique standard reflections used during the
measurement of the diffraction intensities.
diffrn_standards.scale_sigma
The standard uncertainty (estimated standard deviation) of
the individual mean standard scales applied to the intensity
data.
diffrn_standards.scale_u
The standard uncertainty of the individual mean
standard scales applied to the intensity data.
diffrn_standards.diffrn_id
This data item is a pointer to attribute id in category diffrn in the DIFFRN
category.
0
em_2d_crystal_entity
Data items in the EM_SYMMETRY_2DX category record
2D crystal symmetry parameters utilized in a 3DEM reconstruction.
1
1
0
1
0
1
1
1
1
1
1
1
1
1
1
1
em_2d_crystal_entityCategory
This property indicates that datablock
has a category holder em_2d_crystal_entityCategory.
em_2d_crystal_entityCategory
This property indicates that em_2d_crystal_entityCategory.
has a category em_2d_crystal_entity.
em_2d_crystal_entityItem
Abstract datatype property for em_2d_crystal_entity items.
reference_to_em_2d_crystal_entity
cross-reference to em_2d_crystal_entity.
referenced_by_em_2d_crystal_entity
cross-reference from em_2d_crystal_entity.
em_2d_crystal_entity.angle_gamma
Unit-cell angle gamma in degrees.
em_2d_crystal_entity.c_sampling_length
Length used to sample the reciprocal lattice lines in the c-direction.
em_2d_crystal_entity.entity_assembly_id
Corresponding key in _em_entity_assembly category.
em_2d_crystal_entity.length_a
Unit-cell length a in angstroms.
62.4
em_2d_crystal_entity.length_b
Unit-cell length b in angstroms.
62.4
em_2d_crystal_entity.length_c
Thickness of 2D crystal
62.4
P 1
P 2
P 1 2
P 1 21
C 1 2
P 2 2 2
P 2 2 21
P 2 21 21
C 2 2 2
P 4
P 4 2 2
P 4 21 2
P 3
P 3 1 2
P 3 2 1
P 6
P 6 2 2
There are 17 plane groups classified as oblique, rectangular, square, and hexagonal.
To describe the symmetry of 2D crystals of biological molecules,
plane groups are expanded to equivalent noncentrosymmetric space groups.
The 2D crystal plane corresponds to the 'ab' plane of the space group.
Enumerated space group descriptions include the plane group number in parentheses,
the H-M plane group symbol, and the plane group class.
em_2d_crystal_entity.id
PRIMARY KEY
em_2d_crystal_entity.image_processing_id
pointer to attribute id in category em_image_processing in the EM_IMAGE_PROCESSING category.
0
em_2d_projection_selection
Data items in the EM_2D_PROJECTION_SELECTION category
record details of images from scanned micrographs and the
number of particles selected from a scanned set of micrographs.
Example 1
<PDBx:em_2d_projection_selectionCategory>
<PDBx:em_2d_projection_selection entry_id="1ABC">
<PDBx:details xsi:nil="true" />
<PDBx:method>INTERACTIVE</PDBx:method>
<PDBx:num_particles>52346</PDBx:num_particles>
<PDBx:software_name>EMAN2 BOXER</PDBx:software_name>
</PDBx:em_2d_projection_selection>
</PDBx:em_2d_projection_selectionCategory>
0
1
0
1
1
1
0
1
0
1
0
1
1
em_2d_projection_selectionCategory
This property indicates that datablock
has a category holder em_2d_projection_selectionCategory.
em_2d_projection_selectionCategory
This property indicates that em_2d_projection_selectionCategory.
has a category em_2d_projection_selection.
em_2d_projection_selectionItem
Abstract datatype property for em_2d_projection_selection items.
reference_to_em_2d_projection_selection
cross-reference to em_2d_projection_selection.
referenced_by_em_2d_projection_selection
cross-reference from em_2d_projection_selection.
em_2d_projection_selection.citation_id
This data item is a pointer to attribute id in category citation in the
CITATION category.
em_2d_projection_selection.details
Any additional details used for selecting observed assemblies.
negative monitor contrast facilitated particle picking
em_2d_projection_selection.id
unique identifier for each projection selection description
em_2d_projection_selection.method
The method used for selecting observed assemblies.
particles picked interactively from monitor
em_2d_projection_selection.num_particles
The number of particles selected from the projection set of images.
840
em_2d_projection_selection.software_name
The software used to select 2d projections.
em_2d_projection_selection.entry_id
entry id
0
em_3d_crystal_entity
Data items in the EM_SYMMETRY_3DX category record
3D crystal symmetry parameters utilized in 3DEM reconstruction averaging.
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
em_3d_crystal_entityCategory
This property indicates that datablock
has a category holder em_3d_crystal_entityCategory.
em_3d_crystal_entityCategory
This property indicates that em_3d_crystal_entityCategory.
has a category em_3d_crystal_entity.
em_3d_crystal_entityItem
Abstract datatype property for em_3d_crystal_entity items.
reference_to_em_3d_crystal_entity
cross-reference to em_3d_crystal_entity.
referenced_by_em_3d_crystal_entity
cross-reference from em_3d_crystal_entity.
em_3d_crystal_entity.angle_alpha
Unit-cell angle alpha in degrees.
120.0
em_3d_crystal_entity.angle_beta
Unit-cell angle beta in degrees.
120.0
em_3d_crystal_entity.angle_gamma
Unit-cell angle gamma in degrees.
120.0
em_3d_crystal_entity.length_a
Unit-cell length a in angstroms.
62.4
em_3d_crystal_entity.length_b
Unit-cell length b in angstroms.
62.4
em_3d_crystal_entity.length_c
Unit-cell length c in angstroms.
62.4
em_3d_crystal_entity.space_group_name
Space group name.
P 1
P 21 21 2
I 4
H 3
em_3d_crystal_entity.space_group_num
Space group number.
22
em_3d_crystal_entity.id
PRIMARY KEY
em_3d_crystal_entity.image_processing_id
pointer to attribute id in category em_image_processing in the EM_IMAGE_PROCESSING category.
0
em_3d_fitting
Data items in the 3D_FITTING category
record details of the method of fitting atomic
coordinates from a PDB file into a 3d-em
volume map file
Example 1 - based on PDB entry 1DYL and laboratory records for the
structure corresponding to PDB entry 1DYL
<PDBx:em_3d_fittingCategory>
<PDBx:em_3d_fitting entry_id="1DYL" id="1">
<PDBx:details> THE CRYSTAL STRUCTURE OF THE CAPSID
PROTEIN FROM CHOI ET AL (1997) PROTEINS 3 27:345-359
(SUBUNIT A OF PDB FILE 1VCQ) WAS PLACED INTO THE CRYO-EM
DENSITY MAP. THE CAPSID PROTEIN WAS FIRST MANUALLY POSITIONED
INTO THE CRYO-EM DENSITY CORRESPONDING TO POSITIONS OF THE
FOUR INDEPENDENT MONOMER DENSITIES BETWEEN THE INNER LEAFLET
OF THE BILAYER AND THE RNA. THESE POSITIONS WERE THEN REFINED
BY RIGID BODY REFINEMENT IN REAL SPACE WITH THE PROGRAM EMFIT
(CHENG ET AL. 1995, CELL 80, 621-630). THE QUALITY OF THE FIT
CAN BE SEEN FROM THE MAP DENSITY WITHIN THE PROTEIN. ALL 4563
ATOMS ARE IN DENSITY OF AT LEAST 4 SIGMA (96.73) ABOVE THE
AVERAGE (512.04), 1167 ATOMS ARE IN DENSITY BETWEEN 4 AND 5
SIGMA, 3174 ATOMS ARE IN DENSITY BETWEEN 5 AND 6 SIGMA, AND 222
ATOMS ARE IN DENSTY OF 6 SIGMA OR ABOVE. THE VARIATION IN
DENSITY OVER THE FITTED PROTEIN CAN BE VISUALIZED WITH THE
PSEUDO TEMPERATURE FACTOR. THE DENSITY VALUE AT EACH ATOM IS
GIVEN IN THE 8TH COLUM (USUALLY THE OCCUPANCY) AS THE NUMBER
OF STANDARD DEVIATION ABOVE BACKGROUND. COLUMN NINE (USUALLY
THE TEMPERATURE FACTOR) CONTAINS THE VALUE OF THE RELATIVE
DENSITY WITHIN THE FITTED PROTEIN SCALED LINEARLY SO THAT THE
MINIMUM DENSITY IS 100.0 AND THE MAXIMUM DENSITY IS 1.0. THE
ATOMS THAT LIE IN THE LOWER DENSITY REGIONS WILL HAVE THE
HIGHEST PSEUDO TEMPERATURE FACTORS.</PDBx:details>
<PDBx:method>AUTOMATIC</PDBx:method>
<PDBx:overall_b_value xsi:nil="true" />
<PDBx:ref_protocol>RIGID BODY REFINEMENT</PDBx:ref_protocol>
<PDBx:ref_space>REAL</PDBx:ref_space>
<PDBx:software_name>1</PDBx:software_name>
<PDBx:target_criteria>R-FACTOR</PDBx:target_criteria>
</PDBx:em_3d_fitting>
</PDBx:em_3d_fittingCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
1
em_3d_fittingCategory
This property indicates that datablock
has a category holder em_3d_fittingCategory.
em_3d_fittingCategory
This property indicates that em_3d_fittingCategory.
has a category em_3d_fitting.
em_3d_fittingItem
Abstract datatype property for em_3d_fitting items.
reference_to_em_3d_fitting
cross-reference to em_3d_fitting.
referenced_by_em_3d_fitting
cross-reference from em_3d_fitting.
em_3d_fitting.details
Any additional details regarding fitting of atomic coordinates into
the 3DEM volume, including data and considerations from other
methods used in computation of the model.
Initial local fitting was done using Chimera and then NMFF was used for flexible fitting.
em_3d_fitting.initial_refinement_model_id
The value of attribute initial_refinement_model_id in category em_3d_fitting itentifies the id
in the _pdbx_initial_refinement_model
em_3d_fitting.method
The method used to fit atomic coordinates
into the 3dem reconstructed map.
em_3d_fitting.overall_b_value
The overall B (temperature factor) value for the 3d-em volume.
200
RIGID BODY FIT
FLEXIBLE FIT
BACKBONE TRACE
AB INITIO MODEL
OTHER
The refinement protocol used.
REAL
RECIPROCAL
A flag to indicate whether fitting was carried out in real
or reciprocal refinement space.
em_3d_fitting.software_name
The software used for fitting atomic coordinates to the map.
Situs, NMFF, YUP.scx, etc.
em_3d_fitting.target_criteria
The measure used to assess quality of fit of the atomic coordinates in the
3DEM map volume.
Cross-correlation coefficient
em_3d_fitting.entry_id
This data item is a pointer to _entry_id in
the ENTRY category.
em_3d_fitting.id
The value of attribute id in category em_3d_fitting must uniquely identify
a fitting procedure of atomic coordinates
into 3dem reconstructed map volume.
0
em_3d_fitting_list
Data items in the 3D_FITTING_LIST category
lists the methods of fitting atomic coordinates from a PDB file
into a 3d-em volume map file
Example 1 - based on PDB entry 1DYL and laboratory records for the
structure corresponding to PDB entry 1DYL
<PDBx:em_3d_fitting_listCategory>
<PDBx:em_3d_fitting_list _3d_fitting_id="l" id="1">
<PDBx:pdb_chain_id xsi:nil="true" />
<PDBx:pdb_entry_id>1VCQ</PDBx:pdb_entry_id>
</PDBx:em_3d_fitting_list>
</PDBx:em_3d_fitting_listCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
1
em_3d_fitting_listCategory
This property indicates that datablock
has a category holder em_3d_fitting_listCategory.
em_3d_fitting_listCategory
This property indicates that em_3d_fitting_listCategory.
has a category em_3d_fitting_list.
em_3d_fitting_listItem
Abstract datatype property for em_3d_fitting_list items.
reference_to_em_3d_fitting_list
cross-reference to em_3d_fitting_list.
referenced_by_em_3d_fitting_list
cross-reference from em_3d_fitting_list.
em_3d_fitting_list.accession_code
This item identifies an accession code of the resource where the initial model
is used
em_3d_fitting_list.chain_id
The ID of the biopolymer chain used for fitting, e.g., A. Please note that
only one chain can be specified per instance. If all chains of a particular
structure have been used for fitting, this field can be left blank.
em_3d_fitting_list.chain_residue_range
The residue ranges of the initial model used in this fitting.
em_3d_fitting_list.details
Details about the model used in fitting.
The initial model consisted of the complete biological assembly for PDB entry 2GTL.
em_3d_fitting_list.initial_refinement_model_id
The value of attribute initial_refinement_model_id in category em_3d_fitting itentifies the id
in the _pdbx_initial_refinement_model
em_3d_fitting_list.pdb_chain_id
The ID of the biopolymer chain used for fitting, e.g., A. Please note that
only one chain can be specified per instance. If all chains of a particular
structure have been used for fitting, this field can be left blank.
The ID of the biopolymer chain used for fitting, e.g., A. Please note that only one chain can be specified per instance. If all chains of a particular structure have been used for fitting, this field can be left blank.
em_3d_fitting_list.pdb_chain_residue_range
Residue range for the identified chain.
5-545
em_3d_fitting_list.pdb_entry_id
The PDB code for the entry used in fitting.
1EHZ
PDB
AlphaFold
RoseTTAFold
ModelArchive
SwissModel
Modeller
ITasser
Other
This item identifies the resource of initial model used for refinement
in silico model
experimental model
integrative model
other
This item describes the type of the initial model was generated
em_3d_fitting_list._3d_fitting_id
The value of attribute 3d_fitting_id in category em_3d_fitting_list is a pointer
to attribute id in category em_3d_fitting in the 3d_fitting category
em_3d_fitting_list.id
PRIMARY KEY
0
em_3d_reconstruction
Data items in the EM_3D_RECONSTRUCTION category
record details of the 3D reconstruction procedure from 2D projections.
Example 1 - based on PDB entry 1DYL and laboratory records for the
structure corresponding to PDB entry 1DYL
<PDBx:em_3d_reconstructionCategory>
<PDBx:em_3d_reconstruction id="1">
<PDBx:actual_pixel_size>2.52</PDBx:actual_pixel_size>
<PDBx:ctf_correction_method xsi:nil="true" />
<PDBx:details xsi:nil="true" />
<PDBx:entry_id>1DYL</PDBx:entry_id>
<PDBx:method>CROSS-COMMON LINES</PDBx:method>
<PDBx:nominal_pixel_size>2.64</PDBx:nominal_pixel_size>
<PDBx:resolution>9</PDBx:resolution>
<PDBx:resolution_method xsi:nil="true" />
</PDBx:em_3d_reconstruction>
</PDBx:em_3d_reconstructionCategory>
0
1
0
1
0
1
0
1
0
1
1
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
1
em_3d_reconstructionCategory
This property indicates that datablock
has a category holder em_3d_reconstructionCategory.
em_3d_reconstructionCategory
This property indicates that em_3d_reconstructionCategory.
has a category em_3d_reconstruction.
em_3d_reconstructionItem
Abstract datatype property for em_3d_reconstruction items.
reference_to_em_3d_reconstruction
cross-reference to em_3d_reconstruction.
referenced_by_em_3d_reconstruction
cross-reference from em_3d_reconstruction.
em_3d_reconstruction.actual_pixel_size
The actual pixel size of the projection set of images in Angstroms.
2.8
5.76
em_3d_reconstruction.algorithm
The reconstruction algorithm/technique used to generate the map.
em_3d_reconstruction.citation_id
This data item is a pointer to attribute id in category citation in the
CITATION category.
em_3d_reconstruction.ctf_correction_method
The CTF-correction method.
The Contrast Transfer Function CTF compensation for low contrast
specimens (e.g. frozen-hydrated), for which phase contrast is the only
significant mechanism, then higher defocus levels must be used to
achieve any significant transfer, and several images at different
focus levels must be combined to complete the information lost from
the transfer gaps of any one image. The CTF correction can be applied
to each extracted particle separately or to the whole micrograph after
digitisation. The simplest level of compensation is to reverse phases
at the negative lobes of the CTF.
The volumes were CTF-corrected in defocus groups, with an average of approximately 999 individual images per group
em_3d_reconstruction.details
Any additional details used in the 3d reconstruction.
a modified version of SPIDER program was used for the reconstruction
em_3d_reconstruction.entry_id
This data item is a pointer to attribute id in category entry in the ENTRY category.
em_3d_reconstruction.euler_angles_details
euler angles details
EVEN/ODD MAPS REFINED TOTALLY INDEPENDENT (GOLD STANDARD)
EVEN/ODD MAPS REFINED AGAINST THE SAME MODEL (SEMI-INDEPENDENT)
Half-set refinement protocol (semi-independent or gold standard)
em_3d_reconstruction.magnification_calibration
The magnification calibration method for the 3d reconstruction.
TMV images
em_3d_reconstruction.method
The algorithm method used for the 3d-reconstruction.
cross-common lines
polar Fourier transform (PFT)
em_3d_reconstruction.nominal_pixel_size
The nominal pixel size of the projection set of images in Angstroms.
3.11
6.78
em_3d_reconstruction.num_class_averages
The number of classes used in the final 3d reconstruction
300
em_3d_reconstruction.num_particles
The number of 2D projections or 3D subtomograms used in the 3d reconstruction
300
HALF-MAPS REFINED AGAINST SAME DATA
HALF-MAPS REFINED INDEPENDENTLY
HALF-MAPS REFINED WITH FREQUENCY RANGE OMITTED
HALF-MAPS REFINED INDEPENDENTLY WITH FREQUENCY RANGE OMITTED
OTHER
Indicates details on how the half-map used for resolution determination (usually by FSC) have been generated.
em_3d_reconstruction.resolution
The final resolution (in angstroms) of the 3D reconstruction.
8.9
10.0
em_3d_reconstruction.resolution_method
The method used to determine the final resolution
of the 3d reconstruction.
The Fourier Shell Correlation criterion as a measure of
resolution is based on the concept of splitting the (2D)
data set into two halves; averaging each and comparing them
using the Fourier Ring Correlation (FRC) technique.
FSC at 0.5 cut-off
em_3d_reconstruction.software
software name
POINT
HELICAL
2D CRYSTAL
3D CRYSTAL
The type of symmetry applied to the reconstruction
em_3d_reconstruction.id
PRIMARY KEY
em_3d_reconstruction.image_processing_id
Foreign key to the EM_IMAGE_PROCESSING category
0
em_admin
Administration-related data items
Example 1
<PDBx:em_adminCategory>
<PDBx:em_admin entry_id="D_100005">
<PDBx:current_status>REL</PDBx:current_status>
<PDBx:deposition_date>2008-12-01</PDBx:deposition_date>
<PDBx:details xsi:nil="true" />
<PDBx:last_update>2011-05-22</PDBx:last_update>
<PDBx:map_release_date>2009-12-01</PDBx:map_release_date>
</PDBx:em_admin>
</PDBx:em_adminCategory>
0
1
1
1
1
1
1
1
0
1
0
1
1
1
0
1
0
1
0
1
0
1
0
1
1
1
1
em_adminCategory
This property indicates that datablock
has a category holder em_adminCategory.
em_adminCategory
This property indicates that em_adminCategory.
has a category em_admin.
em_adminItem
Abstract datatype property for em_admin items.
reference_to_em_admin
cross-reference to em_admin.
referenced_by_em_admin
cross-reference from em_admin.
YES
NO
Indicates whether the authors have declared that this is a composite map deposition
PROC
WAIT
AUTH
REUP
REPL
AUXU
AUXS
AUCO
REFI
POLC
HPUB
HOLD
HOLD8W
REL
WDRN
OBS
This data item indicates the current status of the EMDB entry.
em_admin.deposition_date
date of the entry deposition
PDBE
RCSB
PDBJ
PDBC
entry deposition site
em_admin.details
EMDB administration details
em_admin.header_release_date
date of header information release for this entry
em_admin.last_update
date of last update to the file
em_admin.map_hold_date
Date when the map is due to be released after a specific hold period.
em_admin.map_release_date
date of map release for this entry
em_admin.obsoleted_date
date that map entry was obsoleted
RCSB
PDBE
PDBJ
PDBC
The site where the file was deposited.
RCSB
PDBE
PDBJ
PDBC
YES
NO
Please indicate whether the current entry is intended to supersede a
previously released entry. Please contact wwPDB annotation staff using the
"Communication" page if you have any questions regarding how to answer this
question.
em_admin.title
Title for the EMDB entry.
em_admin.entry_id
This data item is a pointer to attribute id in category entry.
0
em_assembly
Data items in the EM_ASSEMBLY category record details
about the imaged EM sample.
Example 1 - based on PDB entry 1DYL and laboratory records for the
structure corresponding to PDB entry 1DYL
<PDBx:em_assemblyCategory>
<PDBx:em_assembly entry_id="1DYL" id="1">
<PDBx:aggregation_state>PARTICLE</PDBx:aggregation_state>
<PDBx:composition>virus</PDBx:composition>
<PDBx:details xsi:nil="true" />
<PDBx:mol_wt_exp xsi:nil="true" />
<PDBx:mol_wt_method xsi:nil="true" />
<PDBx:mol_wt_theo xsi:nil="true" />
<PDBx:name>virus</PDBx:name>
<PDBx:num_components>1</PDBx:num_components>
</PDBx:em_assembly>
</PDBx:em_assemblyCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
1
em_assemblyCategory
This property indicates that datablock
has a category holder em_assemblyCategory.
em_assemblyCategory
This property indicates that em_assemblyCategory.
has a category em_assembly.
em_assemblyItem
Abstract datatype property for em_assembly items.
reference_to_em_assembly
cross-reference to em_assembly.
referenced_by_em_assembly
cross-reference from em_assembly.
2D CRYSTAL
3D CRYSTAL
INDIVIDUAL STRUCTURE
FILAMENT
ICOSAHEDRAL
PARTICLE
TISSUE
CELL
A description of the aggregation state of the assembly.
em_assembly.composition
The composition of the assembly.
Protein/DNA complex
Virus
em_assembly.details
Any additional details describing the imaged sample.
The sample was monodisperse
em_assembly.mol_wt_exp
The value (in megadaltons) of the experimentally
determined molecular weight of the assembly.
3.5
em_assembly.mol_wt_method
The method used to determine the molecular weight.
em_assembly.mol_wt_theo
The value (in megadaltons) of the theoretically
determined molecular weight of the assembly.
3.5
em_assembly.name
The name of the assembly of observed complexes.
MaB1 Fab Fragment bound to Human Rhinovirus
em_assembly.num_components
The number of components of the biological assembly.
3
em_assembly.entry_id
This data item is a pointer to attribute id in category entry in the ENTRY category.
em_assembly.id
The value of attribute id in category em_assembly must uniquely identify
a collection of observed complexes.
0
em_author_list
Category to collect the authors of this entry
Example 1
<PDBx:em_author_listCategory>
<PDBx:em_author_list ordinal="1">
<PDBx:author>Miller, A.</PDBx:author>
</PDBx:em_author_list>
<PDBx:em_author_list ordinal="2">
<PDBx:author>Smith, J.T.</PDBx:author>
</PDBx:em_author_list>
</PDBx:em_author_listCategory>
1
1
0
1
1
em_author_listCategory
This property indicates that datablock
has a category holder em_author_listCategory.
em_author_listCategory
This property indicates that em_author_listCategory.
has a category em_author_list.
em_author_listItem
Abstract datatype property for em_author_list items.
reference_to_em_author_list
cross-reference to em_author_list.
referenced_by_em_author_list
cross-reference from em_author_list.
em_author_list.author
Author of the EMDB entry in PDB format: Taylor, T.J.
Taylor, D.J.
em_author_list.identifier_ORCID
The Open Researcher and Contributor ID (ORCID).
0000-0002-6681-547X
em_author_list.ordinal
ID 1 corresponds to the main author of the entry
0
em_buffer
Data items in the BUFFER category
record details of the sample buffer.
0
1
0
1
0
1
1
1
em_bufferCategory
This property indicates that datablock
has a category holder em_bufferCategory.
em_bufferCategory
This property indicates that em_bufferCategory.
has a category em_buffer.
em_bufferItem
Abstract datatype property for em_buffer items.
reference_to_em_buffer
cross-reference to em_buffer.
referenced_by_em_buffer
cross-reference from em_buffer.
em_buffer.details
Additional details about the buffer.
20mM NaCl, 10mM Tris-HCL,1mM MgCl2,1mM EDTA
em_buffer.name
The name of the buffer.
Polymix buffer
em_buffer.pH
The pH of the sample buffer.
5.5
em_buffer.id
PRIMARY KEY
em_buffer.specimen_id
pointer to attribute id in category em_specimen
0
em_buffer_component
Buffer category
0
1
0
1
0
1
0
1
1
1
em_buffer_componentCategory
This property indicates that datablock
has a category holder em_buffer_componentCategory.
em_buffer_componentCategory
This property indicates that em_buffer_componentCategory.
has a category em_buffer_component.
em_buffer_componentItem
Abstract datatype property for em_buffer_component items.
reference_to_em_buffer_component
cross-reference to em_buffer_component.
referenced_by_em_buffer_component
cross-reference from em_buffer_component.
em_buffer_component.concentration
The concentration of the sample (arbitrary units).
1.35
em_buffer_component.concentration_units
Units for the sample concentration value.
mg/mL
em_buffer_component.formula
formula for buffer component
NaCl
em_buffer_component.name
name of the buffer component
sodium chloride
em_buffer_component.buffer_id
Foreign key to the entry category.
em_buffer_component.id
PRIMARY KEY
0
em_crystal_formation
Description of growth of a 2D, 3D, or helical crystal array.
0
1
0
1
0
1
0
1
0
1
1
1
0
1
0
1
0
1
1
em_crystal_formationCategory
This property indicates that datablock
has a category holder em_crystal_formationCategory.
em_crystal_formationCategory
This property indicates that em_crystal_formationCategory.
has a category em_crystal_formation.
em_crystal_formationItem
Abstract datatype property for em_crystal_formation items.
reference_to_em_crystal_formation
cross-reference to em_crystal_formation.
referenced_by_em_crystal_formation
cross-reference from em_crystal_formation.
em_crystal_formation.atmosphere
The type of atmosphere in which crystals were grown
Crystallization was performed in an environmental chamber with constant nitrogen gas flow.
em_crystal_formation.details
Description of growth of a 2D, 3D, or helical crystal array.
Lysozyme (200 mg/ml) was mixed 1 to 1 with precipitant solution (3.5M sodium chloride,
15% PEG5000, 50 mM sodium acetate pH 4.5). Microcrystals were grown by the hanging drop method.
em_crystal_formation.instrument
Instrument used to prepare the crystalline array
Langmuir trough
Gryphon LCP
em_crystal_formation.lipid_mixture
Description of the lipid mixture used for crystallization
monoolein and monopalmitolein were mixed 1:1
em_crystal_formation.lipid_protein_ratio
The molar ratio of lipid to protein in the crystallized sample
5.0
em_crystal_formation.specimen_id
Foreign key relationship to the em_specimen category
em_crystal_formation.temperature
The value of the temperature in kelvin used for
growing the crystals.
298
em_crystal_formation.time
Time period for array crystallization, in time unit indicated (min, hr, day, month, year)
50
MINUTE
HOUR
DAY
MONTH
YEAR
Time unit for array crystallization
em_crystal_formation.id
PRIMARY KEY
0
em_ctf_correction
Description of the Contrast Transfer Function (CTF) correction
Example 1
<PDBx:em_ctf_correctionCategory>
<PDBx:em_ctf_correction id="1">
<PDBx:em_image_processing_id>1</PDBx:em_image_processing_id>
<PDBx:type>PHASE FLIPPING ONLY</PDBx:type>
</PDBx:em_ctf_correction>
</PDBx:em_ctf_correctionCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
em_ctf_correctionCategory
This property indicates that datablock
has a category holder em_ctf_correctionCategory.
em_ctf_correctionCategory
This property indicates that em_ctf_correctionCategory.
has a category em_ctf_correction.
em_ctf_correctionItem
Abstract datatype property for em_ctf_correction items.
reference_to_em_ctf_correction
cross-reference to em_ctf_correction.
referenced_by_em_ctf_correction
cross-reference from em_ctf_correction.
YES
NO
Yes if CTF amplitude correction was performed
em_ctf_correction.amplitude_correction_factor
Amplitude correction factor used in CTF correction
REAL
RECIPROCAL
CTF amplitude correction space
MULTIPLICATION
DIVISION
CTF correction operation
em_ctf_correction.details
Any additional details about CTF correction
CTF amplitude correction was performed following 3D reconstruction
em_ctf_correction.em_image_processing_id
Foreign key to the EM_IMAGE_PROCESSING category
YES
NO
Yes if Phase reversal (flipping) was performed
YES
NO
Yes if Anisotropic phase reversal (flipping) was performed
REAL
RECIPROCAL
CTF phase reversal correction space
em_ctf_correction.type
Type of CTF correction applied
em_ctf_correction.id
PRIMARY KEY
0
em_db_reference
Category holds links to raw data sources for the entry, e.g.,
held by a remote server.
Example 1
<PDBx:em_db_referenceCategory>
<PDBx:em_db_reference id="1">
<PDBx:access_code>1ABC</PDBx:access_code>
<PDBx:db_name>PDB</PDBx:db_name>
</PDBx:em_db_reference>
</PDBx:em_db_referenceCategory>
1
1
1
1
0
1
0
1
1
em_db_referenceCategory
This property indicates that datablock
has a category holder em_db_referenceCategory.
em_db_referenceCategory
This property indicates that em_db_referenceCategory.
has a category em_db_reference.
em_db_referenceItem
Abstract datatype property for em_db_reference items.
reference_to_em_db_reference
cross-reference to em_db_reference.
referenced_by_em_db_reference
cross-reference from em_db_reference.
em_db_reference.access_code
Unique identifier for a provided link.
1ABC
EMD-5002
PDB
EMDB
The name of the database containing the related entry.
em_db_reference.details
A description of the related entry.
map derived from same data with D7 symmetry imposed
model derived from X-ray crystal structure 1ABC
IN FRAME
OTHER
Indicates relationship of this entry with other entries in PDB and EMDB.
em_db_reference.id
PRIMARY KEY
0
em_db_reference_auxiliary
Category holds links to raw data sources for the entry, e.g.,
held by a remote server.
Example 1
<PDBx:em_db_reference_auxiliaryCategory>
<PDBx:em_db_reference_auxiliary id="1">
<PDBx:link>http://www.ebi.ac.uk/pdbe/emdb/singleParticledir/SPIDER_FRANK_data</PDBx:link>
<PDBx:link_type>2D EM DATA</PDBx:link_type>
</PDBx:em_db_reference_auxiliary>
</PDBx:em_db_reference_auxiliaryCategory>
1
1
1
1
1
em_db_reference_auxiliaryCategory
This property indicates that datablock
has a category holder em_db_reference_auxiliaryCategory.
em_db_reference_auxiliaryCategory
This property indicates that em_db_reference_auxiliaryCategory.
has a category em_db_reference_auxiliary.
em_db_reference_auxiliaryItem
Abstract datatype property for em_db_reference_auxiliary items.
reference_to_em_db_reference_auxiliary
cross-reference to em_db_reference_auxiliary.
referenced_by_em_db_reference_auxiliary
cross-reference from em_db_reference_auxiliary.
em_db_reference_auxiliary.link
Hyperlink to the auxiliary data.
2D EM DATA
CORRELATIVE LIGHT MICROSCOPY
Type of auxiliary data stored at the indicated link.
em_db_reference_auxiliary.id
PRIMARY KEY
0
em_depositor_info
Data items in the EM_DEPOSITOR INFO category record parameters for EM depositions
that are provided by the depositor
Example 1
<PDBx:em_depositor_infoCategory>
<PDBx:em_depositor_info entry_id="D_10005049">
<PDBx:em_method_selection>yes</PDBx:em_method_selection>
<PDBx:molecular_description_flag>yes</PDBx:molecular_description_flag>
</PDBx:em_depositor_info>
</PDBx:em_depositor_infoCategory>
1
1
0
1
1
em_depositor_infoCategory
This property indicates that datablock
has a category holder em_depositor_infoCategory.
em_depositor_infoCategory
This property indicates that em_depositor_infoCategory.
has a category em_depositor_info.
em_depositor_infoItem
Abstract datatype property for em_depositor_info items.
reference_to_em_depositor_info
cross-reference to em_depositor_info.
referenced_by_em_depositor_info
cross-reference from em_depositor_info.
Helical
Single particle
Subtomogram averaging
Tomography
Electron Diffraction
The selected EM experimental method.
yes
no
Records whether molecular/polymer entities of the EM sample will be described.
em_depositor_info.entry_id
This data item is a pointer to the ENTRY category.
0
em_depui
Some internal items to power the deposition interface
Example 1
<PDBx:em_depuiCategory>
<PDBx:em_depui entry_id="1ABC">
<PDBx:depositor_hold_instructions>HOLD</PDBx:depositor_hold_instructions>
<PDBx:macromolecule_description>YES</PDBx:macromolecule_description>
<PDBx:obsolete_instructions xsi:nil="true" />
<PDBx:same_authors_as_pdb>NO</PDBx:same_authors_as_pdb>
<PDBx:same_title_as_pdb>NO</PDBx:same_title_as_pdb>
</PDBx:em_depui>
</PDBx:em_depuiCategory>
0
1
1
1
1
1
0
1
1
1
1
1
1
em_depuiCategory
This property indicates that datablock
has a category holder em_depuiCategory.
em_depuiCategory
This property indicates that em_depuiCategory.
has a category em_depui.
em_depuiItem
Abstract datatype property for em_depui items.
reference_to_em_depui
cross-reference to em_depui.
referenced_by_em_depui
cross-reference from em_depui.
COMPOSITE MAP
NO
Indicates whether the authors have declared that this is a composite map deposition
REL
HOLD
HOLD8W
HPUB
Choose the manner in which you would like the map and associated files (half
maps, additional maps, masks, FSC curves, structure factors, layer lines, and
images) to be released. Release of these files can be delayed either until
publication of the associated primary citation or until one year after completion
of the deposition. It is the responsibility of the depositor to notify the EMDB when
the primary citation has been published. Please note that map-associated
experimental information and metadata (header data) are made available to the
public when an entry is placed on hold.
YES
NO
Indicates whether the authors are providing a macromolecule level description of their sample
em_depui.obsolete_instructions
Instruction for annotators on why a previous released entry should be obsoleted.
Example of valid request:
* Author wants to replace a map that has already been released, following discovery of a processing error
Examples of invalid requests:
* Someone other than the author wants to obsolete a map.
* Legal conflict of interest
Obsoletion is not required for the following actions:
* to change released metadata info.
* to update the map of an HPUB entry.
* to change the hand of a released map.
* to deposit an improved version of a released map.
YES
NO
Indicates whether the authors for the EMDB entry are the same as for the PDB entry
in a joint map + model deposition
YES
NO
Indicates whether the title for the EMDB entry is the same as for the PDB entry
in a joint map + model deposition
em_depui.entry_id
PRIMARY KEY
0
em_detector
Data items in the EM_DETECTOR category record details
of the image detector type.
Example 1 - based on PDB entry 1DYL and laboratory records for the
structure corresponding to PDB entry 1DYL
<PDBx:em_detectorCategory>
<PDBx:em_detector entry_id="1DYL" id="1">
<PDBx:details xsi:nil="true" />
<PDBx:detective_quantum_efficiency xsi:nil="true" />
<PDBx:type>KODAK SO163 FILM</PDBx:type>
</PDBx:em_detector>
</PDBx:em_detectorCategory>
0
1
0
1
0
1
0
1
1
1
em_detectorCategory
This property indicates that datablock
has a category holder em_detectorCategory.
em_detectorCategory
This property indicates that em_detectorCategory.
has a category em_detector.
em_detectorItem
Abstract datatype property for em_detector items.
reference_to_em_detector
cross-reference to em_detector.
referenced_by_em_detector
cross-reference from em_detector.
em_detector.details
Any additional information about the detection system.
Any other details regarding the detector.
em_detector.detective_quantum_efficiency
The detective_quantum_efficiency (DQE)is defined as the
square of the signal-to-noise ratio in the recording device
divided by the square of the signal-to-ratio in the electron beam:
(SIGNAL/NOISE)2 recording device
DQE = -------------------------------
(SIGNAL/NOISE)2 electron beam
A DQE value of 1 indicates a perfect recorder. "DQE = 0.25" menas
that the signal-to-noise ratio is reduced by half in the
recording step.
(0.5)**2
DQE = --------- = 0.25.
(1.0)**2
0.25
COUNTING
INTEGRATING
SUPER-RESOLUTION
OTHER
The detector mode used during image recording.
em_detector.type
The detector type used for recording images.
Usually film or CCD camera.
em_detector.entry_id
This data item is a pointer to attribute id in category entry in the ENTRY category.
em_detector.id
The value of attribute id in category em_detector must uniquely identify
the detector used for imaging.
0
em_diffraction
Microscopy parameters relevant only for crystallography
Example 1
<PDBx:em_diffractionCategory>
<PDBx:em_diffraction id="1">
<PDBx:camera_length>800</PDBx:camera_length>
<PDBx:imaging_id>1</PDBx:imaging_id>
</PDBx:em_diffraction>
<PDBx:em_diffraction id="2">
<PDBx:camera_length>750</PDBx:camera_length>
<PDBx:imaging_id>2</PDBx:imaging_id>
</PDBx:em_diffraction>
</PDBx:em_diffractionCategory>
1
1
1
1
0
1
1
em_diffractionCategory
This property indicates that datablock
has a category holder em_diffractionCategory.
em_diffractionCategory
This property indicates that em_diffractionCategory.
has a category em_diffraction.
em_diffractionItem
Abstract datatype property for em_diffraction items.
reference_to_em_diffraction
cross-reference to em_diffraction.
referenced_by_em_diffraction
cross-reference from em_diffraction.
em_diffraction.camera_length
The camera length (in millimeters). The camera length is the
product of the objective focal length and the combined magnification
of the intermediate and projector lenses when the microscope is
operated in the diffraction mode.
800
em_diffraction.imaging_id
Foreign key to the EM_IMAGING category
em_diffraction.tilt_angle_list
Comma-separated list of tilt angles (in degrees) used in the electron diffraction experiment.
20,40,50,55
em_diffraction.id
PRIMARY KEY
0
em_diffraction_shell
Statistical parameters for electron diffraction measurements
within a resolution shell
Example 1
<PDBx:em_diffraction_shellCategory>
<PDBx:em_diffraction_shell id="1">
<PDBx:fourier_space_coverage>93.0</PDBx:fourier_space_coverage>
<PDBx:high_resolution>7.5</PDBx:high_resolution>
<PDBx:low_resolution>45</PDBx:low_resolution>
<PDBx:multiplicity>2.3</PDBx:multiplicity>
<PDBx:num_structure_factors>327</PDBx:num_structure_factors>
<PDBx:phase_residual>13.5</PDBx:phase_residual>
</PDBx:em_diffraction_shell>
</PDBx:em_diffraction_shellCategory>
0
1
1
1
1
1
1
1
1
1
1
1
1
1
1
em_diffraction_shellCategory
This property indicates that datablock
has a category holder em_diffraction_shellCategory.
em_diffraction_shellCategory
This property indicates that em_diffraction_shellCategory.
has a category em_diffraction_shell.
em_diffraction_shellItem
Abstract datatype property for em_diffraction_shell items.
reference_to_em_diffraction_shell
cross-reference to em_diffraction_shell.
referenced_by_em_diffraction_shell
cross-reference from em_diffraction_shell.
em_diffraction_shell.em_diffraction_stats_id
Pointer to EM CRYSTALLOGRAPHY STATS
em_diffraction_shell.fourier_space_coverage
Completeness of the structure factor data within this resolution shell, in percent
93.2
em_diffraction_shell.high_resolution
High resolution limit for this shell (angstroms)
3.0
em_diffraction_shell.low_resolution
Low resolution limit for this shell (angstroms)
5.5
em_diffraction_shell.multiplicity
Multiplicity (average number of measurements) for the structure factors in this resolution shell
2.5
em_diffraction_shell.num_structure_factors
Number of measured structure factors in this resolution shell
244
em_diffraction_shell.phase_residual
Phase residual for this resolution shell, in degrees
13.5
em_diffraction_shell.id
PRIMARY KEY
0
em_diffraction_stats
Statistical parameters for electron diffraction measurements
Example 1
<PDBx:em_diffraction_statsCategory>
<PDBx:em_diffraction_stats id="1">
<PDBx:fourier_space_coverage>92</PDBx:fourier_space_coverage>
<PDBx:high_resolution>7.2</PDBx:high_resolution>
<PDBx:num_intensities_measured>1524</PDBx:num_intensities_measured>
<PDBx:num_structure_factors>325</PDBx:num_structure_factors>
<PDBx:overall_phase_error>18.6</PDBx:overall_phase_error>
<PDBx:overall_phase_residual>9.5</PDBx:overall_phase_residual>
<PDBx:phase_error_rejection_criteria>None</PDBx:phase_error_rejection_criteria>
<PDBx:r_merge>19.5</PDBx:r_merge>
<PDBx:r_sym>23.2</PDBx:r_sym>
</PDBx:em_diffraction_stats>
</PDBx:em_diffraction_statsCategory>
0
1
1
1
1
1
0
1
1
1
1
1
0
1
0
1
1
1
1
1
0
1
1
em_diffraction_statsCategory
This property indicates that datablock
has a category holder em_diffraction_statsCategory.
em_diffraction_statsCategory
This property indicates that em_diffraction_statsCategory.
has a category em_diffraction_stats.
em_diffraction_statsItem
Abstract datatype property for em_diffraction_stats items.
reference_to_em_diffraction_stats
cross-reference to em_diffraction_stats.
referenced_by_em_diffraction_stats
cross-reference from em_diffraction_stats.
em_diffraction_stats.details
Any addition details about the structure factor measurements
Phases were obtained from micrograph images of the 2D crystals
em_diffraction_stats.fourier_space_coverage
Completeness of the structure factor data within the defined space group
at the reported resolution (percent).
89.3
em_diffraction_stats.high_resolution
High resolution limit of the structure factor data, in angstroms
7.5
em_diffraction_stats.image_processing_id
Pointer to attribute id in category em_image_processing
em_diffraction_stats.num_intensities_measured
Total number of diffraction intensities measured (before averaging)
1590
em_diffraction_stats.num_structure_factors
Number of structure factors obtained (merged amplitudes + phases)
325
em_diffraction_stats.overall_phase_error
Overall phase error in degrees
17.5
em_diffraction_stats.overall_phase_residual
Overall phase residual in degrees
17.5
em_diffraction_stats.phase_error_rejection_criteria
Criteria used to reject phases
Structure factors with phase errors higher than 20 degrees were omitted from refinement
em_diffraction_stats.r_merge
Rmerge value (percent)
19.8
em_diffraction_stats.r_sym
Rsym value (percent)
24.4
em_diffraction_stats.id
PRIMARY KEY
0
em_embedding
Sugar embedding category
0
1
1
1
1
1
1
em_embeddingCategory
This property indicates that datablock
has a category holder em_embeddingCategory.
em_embeddingCategory
This property indicates that em_embeddingCategory.
has a category em_embedding.
em_embeddingItem
Abstract datatype property for em_embedding items.
reference_to_em_embedding
cross-reference to em_embedding.
referenced_by_em_embedding
cross-reference from em_embedding.
em_embedding.details
Staining procedure used in the specimen preparation.
The crystal suspension was injected into the lens of a drop of buffer containing
1 % tannin sitting on a carbon film supported by a molybdenum grid. An equal volume
of 1% glucose was then added and the solution thoroughly but gently mixed. The grid
was then blotted, air dried, and frozen in LN2.
em_embedding.material
The embedding material.
tannin and glucose
em_embedding.specimen_id
Foreign key relationship to the EM SPECIMEN category
em_embedding.id
PRIMARY KEY
0
em_entity_assembly
Data items in the EM_ENTITY_ASSEMBLY category
record details about each component of
the complex.
Example 1 -- based on PDB entry 1C2W
<PDBx:em_entity_assemblyCategory>
<PDBx:em_entity_assembly id="1">
<PDBx:name>50S Ribosomal Subunit</PDBx:name>
<PDBx:parent_id>0</PDBx:parent_id>
<PDBx:type>RIBOSOME</PDBx:type>
</PDBx:em_entity_assembly>
</PDBx:em_entity_assemblyCategory>
Example 2 -- based on PDB entry 3IY7
<PDBx:em_entity_assemblyCategory>
<PDBx:em_entity_assembly id="1">
<PDBx:name>Fab fragment from MAb F interacting with feline panleukopenia virus (FPV)</PDBx:name>
<PDBx:parent_id>0</PDBx:parent_id>
<PDBx:type>COMPLEX</PDBx:type>
</PDBx:em_entity_assembly>
<PDBx:em_entity_assembly id="2">
<PDBx:name>feline panleukopenia virus</PDBx:name>
<PDBx:parent_id>1</PDBx:parent_id>
<PDBx:synonym>FPV</PDBx:synonym>
<PDBx:type>VIRUS</PDBx:type>
</PDBx:em_entity_assembly>
<PDBx:em_entity_assembly id="3">
<PDBx:name>Fab fragment from Mab F</PDBx:name>
<PDBx:parent_id>1</PDBx:parent_id>
<PDBx:synonym>Fab</PDBx:synonym>
<PDBx:type>COMPLEX</PDBx:type>
</PDBx:em_entity_assembly>
</PDBx:em_entity_assemblyCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
1
0
1
0
1
1
1
0
1
0
1
0
1
1
em_entity_assemblyCategory
This property indicates that datablock
has a category holder em_entity_assemblyCategory.
em_entity_assemblyCategory
This property indicates that em_entity_assemblyCategory.
has a category em_entity_assembly.
em_entity_assemblyItem
Abstract datatype property for em_entity_assembly items.
reference_to_em_entity_assembly
cross-reference to em_entity_assembly.
referenced_by_em_entity_assembly
cross-reference from em_entity_assembly.
em_entity_assembly.assembly_id
This data item is a pointer to attribute id in category em_assembly in the
ASSEMBLY category.
YES
NO
An indication if an assembly is contains a chimeric polymer
em_entity_assembly.details
Additional details about the sample or sample subcomponent.
Fab fragment generated by proteolytic cleavage of LA2 IgG antibody.
em_entity_assembly.ebi_cell
The cell from which the component was
obtained.
CHO
HELA
3T3
em_entity_assembly.ebi_cellular_location
The cellular location of the component.
cytoplasm
endoplasmic reticulum
plasma membrane
YES
NO
A flag to indicate whether the component is engineered.
em_entity_assembly.ebi_expression_system
The expression system used to produce the component.
eschericia coli
saccharomyces cerevisiae
em_entity_assembly.ebi_expression_system_plasmid
The plasmid used to produce the component.
pBR322
pMB9
em_entity_assembly.ebi_organelle
The organelle from which the component was
obtained.
golgi
mitochondrion
cytoskeleton
em_entity_assembly.ebi_organism_common
The common name of the species of the natural organism from which
the component was obtained.
em_entity_assembly.ebi_organism_scientific
The species of the natural organism from which the component
was obtained.
em_entity_assembly.ebi_strain
The strain of the natural organism from which the component was
obtained, if relevant.
DH5a
BMH 71-18
em_entity_assembly.ebi_tissue
The tissue of the natural organism from which the component was
obtained.
heart
liver
eye lens
em_entity_assembly.entity_id_list
macromolecules associated with this component, if defined
as comma separated list of entity ids (integers).
1,2,3,4
em_entity_assembly.go_id
The Gene Ontology (GO) identifier for the component.
The GO id is the appropriate identifier used by the Gene Ontology
Consortium. Reference: Nature Genetics vol 25:25-29 (2000).
GO:0005876
GO:0015630
em_entity_assembly.ipr_id
The InterPro (IPR) identifier for the component.
The IPR id is the appropriate identifier used by the Interpro Resource.
Reference: Nucleic Acid Research vol 29(1):37-40(2001).
001304
002353
YES
NO
mutant flag
em_entity_assembly.name
The name of the sample or sample subcomponent.
Ternary complex of alpha-tubulin with tubulin folding cofactors TBCE and TBCB
80S Ribosome bound to emetine
messenger RNA
initiation factor 2
GroEL
antibody Fab fragment
em_entity_assembly.number_of_copies
number of copies
em_entity_assembly.oligomeric_details
oligomeric details
em_entity_assembly.parent_id
The parent of this assembly.
This data item is an internal category pointer to attribute id.
in category em_entity_assembly By convention, the full assembly (top of hierarchy) is assigned parent id 0 (zero).
NATURAL
RECOMBINANT
MULTIPLE SOURCES
SYNTHETIC
The type of source (e.g., natural source) for the component (sample or sample
subcomponent)
em_entity_assembly.synonym
Alternative name of the component.
FADV-1
em_entity_assembly.type
The general type of the sample or sample subcomponent.
em_entity_assembly.id
PRIMARY KEY
0
em_entity_assembly_molwt
Data items in this category record details about the molecular weight of
an assembly component of the sample.
Example 1 - based on PDB entry 1DYL and laboratory records for the
structure corresponding to PDB entry 1DYL
<PDBx:em_entity_assembly_molwtCategory>
<PDBx:em_entity_assembly_molwt entity_assembly_id="1" id="1">
<PDBx:units>MEGADALTONS</PDBx:units>
<PDBx:value>30.5</PDBx:value>
</PDBx:em_entity_assembly_molwt>
</PDBx:em_entity_assembly_molwtCategory>
0
1
0
1
0
1
0
1
1
1
em_entity_assembly_molwtCategory
This property indicates that datablock
has a category holder em_entity_assembly_molwtCategory.
em_entity_assembly_molwtCategory
This property indicates that em_entity_assembly_molwtCategory.
has a category em_entity_assembly_molwt.
em_entity_assembly_molwtItem
Abstract datatype property for em_entity_assembly_molwt items.
reference_to_em_entity_assembly_molwt
cross-reference to em_entity_assembly_molwt.
referenced_by_em_entity_assembly_molwt
cross-reference from em_entity_assembly_molwt.
YES
NO
Identifies whether the given molecular weight was derived experimentally.
em_entity_assembly_molwt.method
The method used to determine the molecular weight.
MEGADALTONS
KILODALTONS/NANOMETER
Molecular weight units.
em_entity_assembly_molwt.value
The molecular weight of the sample or sample subcomponent
0.53
em_entity_assembly_molwt.entity_assembly_id
A reference to em_entity_assembly.id which uniquely identifies one sample or sample subcomponent of the imaged specimen.
em_entity_assembly_molwt.id
PRIMARY KEY
0
em_entity_assembly_naturalsource
Data items in this category record taxonomic details about the natural source for EM
assemblies and assembly components.
Example 1
<PDBx:em_entity_assembly_naturalsourceCategory>
<PDBx:em_entity_assembly_naturalsource entity_assembly_id="8333" id="1">
<PDBx:cellular_location xsi:nil="true" />
<PDBx:ncbi_tax_id>Escherichia coli</PDBx:ncbi_tax_id>
<PDBx:organ xsi:nil="true" />
<PDBx:organelle>cytoplasm</PDBx:organelle>
<PDBx:organism>K12</PDBx:organism>
<PDBx:strain xsi:nil="true" />
<PDBx:tissue xsi:nil="true" />
</PDBx:em_entity_assembly_naturalsource>
</PDBx:em_entity_assembly_naturalsourceCategory>
0
1
0
1
0
1
1
1
0
1
0
1
1
1
0
1
0
1
1
1
em_entity_assembly_naturalsourceCategory
This property indicates that datablock
has a category holder em_entity_assembly_naturalsourceCategory.
em_entity_assembly_naturalsourceCategory
This property indicates that em_entity_assembly_naturalsourceCategory.
has a category em_entity_assembly_naturalsource.
em_entity_assembly_naturalsourceItem
Abstract datatype property for em_entity_assembly_naturalsource items.
reference_to_em_entity_assembly_naturalsource
cross-reference to em_entity_assembly_naturalsource.
referenced_by_em_entity_assembly_naturalsource
cross-reference from em_entity_assembly_naturalsource.
em_entity_assembly_naturalsource.cell
The cell type from which the component was obtained.
CHO
HELA
3T3
em_entity_assembly_naturalsource.cellular_location
The cellular location of the component.
cytoplasm
endoplasmic reticulum
plasma membrane
em_entity_assembly_naturalsource.details
Additional details describing this natural source.
em_entity_assembly_naturalsource.ncbi_tax_id
The NCBI taxonomy id for the natural organism source of the component.
10804
9606
em_entity_assembly_naturalsource.organ
The organ of the organism from which the component was obtained.
heart
em_entity_assembly_naturalsource.organelle
The organelle from which the component was obtained.
Golgi
Mitochondrion
Cytoskeleton
em_entity_assembly_naturalsource.organism
The scientific name of the source organism for the component
Homo sapiens
Gallus gallus
em_entity_assembly_naturalsource.strain
The strain of the natural organism from which the component was
obtained, if relevant.
DH5a
BMH 71-18
em_entity_assembly_naturalsource.tissue
The tissue of the natural organism from which the component was obtained.
Cartilage
Liver
Eye lens
em_entity_assembly_naturalsource.entity_assembly_id
Pointer to the assembly component defined in the EM ENTITY ASSEMBLY category.
em_entity_assembly_naturalsource.id
PRIMARY KEY
0
em_entity_assembly_recombinant
Data items in this category record details
about recombinant expression of the assembly or assembly component.
Example 1
<PDBx:em_entity_assembly_recombinantCategory>
<PDBx:em_entity_assembly_recombinant entity_assembly_id="1" id="1">
<PDBx:organism>Escherichia coli</PDBx:organism>
<PDBx:plasmid>pET17c</PDBx:plasmid>
</PDBx:em_entity_assembly_recombinant>
</PDBx:em_entity_assembly_recombinantCategory>
0
1
1
1
1
1
0
1
0
1
1
1
em_entity_assembly_recombinantCategory
This property indicates that datablock
has a category holder em_entity_assembly_recombinantCategory.
em_entity_assembly_recombinantCategory
This property indicates that em_entity_assembly_recombinantCategory.
has a category em_entity_assembly_recombinant.
em_entity_assembly_recombinantItem
Abstract datatype property for em_entity_assembly_recombinant items.
reference_to_em_entity_assembly_recombinant
cross-reference to em_entity_assembly_recombinant.
referenced_by_em_entity_assembly_recombinant
cross-reference from em_entity_assembly_recombinant.
em_entity_assembly_recombinant.cell
The cell of the host organism from which the expressed component was
obtained, if relevant.
Potato root
em_entity_assembly_recombinant.ncbi_tax_id
The NCBI taxonomy id of the expression host used to produce the component.
em_entity_assembly_recombinant.organism
Expression system host organism used to produce the component.
escherichia coli
saccharomyces cerevisiae
em_entity_assembly_recombinant.plasmid
The plasmid used to produce the component in the expression system.
pBR322
pMB9
em_entity_assembly_recombinant.strain
The strain of the host organism from which the expresed component was
obtained, if relevant.
DH5a
BMH 71-18
em_entity_assembly_recombinant.entity_assembly_id
Pointer to the expressed component described in the EM ENTITY ASSEMBLY category.
em_entity_assembly_recombinant.id
PRIMARY KEY
0
em_entity_assembly_synthetic
Data items in this category record taxonomic details about the synthetic source for EM
assemblies and assembly components.
Example 1
<PDBx:em_entity_assembly_syntheticCategory>
<PDBx:em_entity_assembly_synthetic entity_assembly_id="1" id="1">
<PDBx:cellular_location xsi:nil="true" />
<PDBx:ncbi_tax_id>8333</PDBx:ncbi_tax_id>
<PDBx:organ xsi:nil="true" />
<PDBx:organelle xsi:nil="true" />
<PDBx:organism>Escherichia coli</PDBx:organism>
<PDBx:strain>K12</PDBx:strain>
<PDBx:tissue xsi:nil="true" />
</PDBx:em_entity_assembly_synthetic>
</PDBx:em_entity_assembly_syntheticCategory>
0
1
0
1
1
1
0
1
0
1
1
1
0
1
0
1
1
1
em_entity_assembly_syntheticCategory
This property indicates that datablock
has a category holder em_entity_assembly_syntheticCategory.
em_entity_assembly_syntheticCategory
This property indicates that em_entity_assembly_syntheticCategory.
has a category em_entity_assembly_synthetic.
em_entity_assembly_syntheticItem
Abstract datatype property for em_entity_assembly_synthetic items.
reference_to_em_entity_assembly_synthetic
cross-reference to em_entity_assembly_synthetic.
referenced_by_em_entity_assembly_synthetic
cross-reference from em_entity_assembly_synthetic.
em_entity_assembly_synthetic.cell
The cell type from which the component was obtained.
CHO
HELA
3T3
em_entity_assembly_synthetic.cellular_location
The cellular location of the component.
cytoplasm
endoplasmic reticulum
plasma membrane
em_entity_assembly_synthetic.ncbi_tax_id
The NCBI taxonomy id for the synthetic organism source of the component.
10804
9606
em_entity_assembly_synthetic.organ
The organ of the organism from which the component was obtained.
heart
em_entity_assembly_synthetic.organelle
The organelle from which the component was obtained.
Golgi
Mitochondrion
Cytoskeleton
em_entity_assembly_synthetic.organism
The scientific name of the source organism for the component
Homo sapiens
Gallus gallus
em_entity_assembly_synthetic.strain
The strain of the synthetic organism from which the component was
obtained, if relevant.
DH5a
BMH 71-18
em_entity_assembly_synthetic.tissue
The tissue of the synthetic organism from which the component was obtained.
Cartilage
Liver
Eye lens
em_entity_assembly_synthetic.entity_assembly_id
Pointer to the assembly component defined in the EM ENTITY ASSEMBLY category.
em_entity_assembly_synthetic.id
PRIMARY KEY
0
em_euler_angle_assignment
Category to describe the euler angle assignement
Example 1
<PDBx:em_euler_angle_assignmentCategory>
<PDBx:em_euler_angle_assignment id="1">
<PDBx:image_processing_id>1</PDBx:image_processing_id>
<PDBx:order>FINAL</PDBx:order>
<PDBx:type>COMMON LINE</PDBx:type>
</PDBx:em_euler_angle_assignment>
</PDBx:em_euler_angle_assignmentCategory>
0
1
1
1
1
1
0
1
0
1
0
1
1
1
1
em_euler_angle_assignmentCategory
This property indicates that datablock
has a category holder em_euler_angle_assignmentCategory.
em_euler_angle_assignmentCategory
This property indicates that em_euler_angle_assignmentCategory.
has a category em_euler_angle_assignment.
em_euler_angle_assignmentItem
Abstract datatype property for em_euler_angle_assignment items.
reference_to_em_euler_angle_assignment
cross-reference to em_euler_angle_assignment.
referenced_by_em_euler_angle_assignment
cross-reference from em_euler_angle_assignment.
em_euler_angle_assignment.details
Any additional details about euler angle assignment
em_euler_angle_assignment.image_processing_id
Foreign key to the EM_IMAGE_PROCESSING category
INITIAL
FINAL
Stage of the reconstruction in which the angle assignments were made.
em_euler_angle_assignment.proj_matching_angular_sampling
Angular sampling of projection matching
1.5
em_euler_angle_assignment.proj_matching_merit_function
Overall figure of merit for projection matching
Correlation coeficient (CC)
em_euler_angle_assignment.proj_matching_num_projections
Number of reference projections used for euler angle assignment
PROJECTION MATCHING
COMMON LINE
ANGULAR RECONSTITUTION
RANDOM ASSIGNMENT
NOT APPLICABLE
MAXIMUM LIKELIHOOD
OTHER
The procedure used to assigned euler angles.
em_euler_angle_assignment.id
PRIMARY KEY
0
em_experiment
Data items in the EM_EXPERIMENT category provide
high-level classification of the EM experiment.
Example 1 - based on PDB entry 1EG0
<PDBx:em_experimentCategory>
<PDBx:em_experiment entry_id="1EG0">
<PDBx:aggregation_state>PARTICLE</PDBx:aggregation_state>
<PDBx:reconstruction_method>SINGLE PARTICLE</PDBx:reconstruction_method>
<PDBx:specimen_type>VITREOUS ICE (CRYO EM)</PDBx:specimen_type>
</PDBx:em_experiment>
</PDBx:em_experimentCategory>
1
1
1
1
1
1
1
1
0
1
1
em_experimentCategory
This property indicates that datablock
has a category holder em_experimentCategory.
em_experimentCategory
This property indicates that em_experimentCategory.
has a category em_experiment.
em_experimentItem
Abstract datatype property for em_experiment items.
reference_to_em_experiment
cross-reference to em_experiment.
referenced_by_em_experiment
cross-reference from em_experiment.
2D ARRAY
3D ARRAY
HELICAL ARRAY
FILAMENT
PARTICLE
TISSUE
CELL
The aggregation/assembly state of the imaged specimen.
em_experiment.entity_assembly_id
Foreign key to the EM_ENTITY_ASSEMBLY category
em_experiment.id
PRIMARY KEY
SINGLE PARTICLE
HELICAL
CRYSTALLOGRAPHY
SUBTOMOGRAM AVERAGING
TOMOGRAPHY
The reconstruction method used in the EM experiment.
em_experiment.specimen_type
The specimen type used in the EM experiment.
VITREOUS ICE (CRYO EM)
NEGATIVE STAIN
FREEZE SUBSTITUTION
em_experiment.entry_id
This data item is a pointer to attribute id in category entry in the ENTRY category.
0
em_fiducial_markers
Description of fiducial markers.
1
1
1
1
1
1
1
em_fiducial_markersCategory
This property indicates that datablock
has a category holder em_fiducial_markersCategory.
em_fiducial_markersCategory
This property indicates that em_fiducial_markersCategory.
has a category em_fiducial_markers.
em_fiducial_markersItem
Abstract datatype property for em_fiducial_markers items.
reference_to_em_fiducial_markers
cross-reference to em_fiducial_markers.
referenced_by_em_fiducial_markers
cross-reference from em_fiducial_markers.
em_fiducial_markers.diameter
Diameter of the fiducial markers
14
em_fiducial_markers.em_tomography_specimen_id
Foreign key relationship to the EM TOMOGRAPHY SPECIMEN category
em_fiducial_markers.manufacturer
Manufacturer source for the fiducial markers
nanoprobes
em_fiducial_markers.id
PRIMARY KEY
0
em_figure_depositor_info
Listing of image files (figures) associated with an EMDB entry
Example 1
<PDBx:em_figure_depositor_infoCategory>
<PDBx:em_figure_depositor_info id="1">
<PDBx:details xsi:nil="true" />
<PDBx:experiment_id>1</PDBx:experiment_id>
<PDBx:upload_file_name>groel-chimera-image.png</PDBx:upload_file_name>
</PDBx:em_figure_depositor_info>
</PDBx:em_figure_depositor_infoCategory>
0
1
0
1
1
1
1
em_figure_depositor_infoCategory
This property indicates that datablock
has a category holder em_figure_depositor_infoCategory.
em_figure_depositor_infoCategory
This property indicates that em_figure_depositor_infoCategory.
has a category em_figure_depositor_info.
em_figure_depositor_infoItem
Abstract datatype property for em_figure_depositor_info items.
reference_to_em_figure_depositor_info
cross-reference to em_figure_depositor_info.
referenced_by_em_figure_depositor_info
cross-reference from em_figure_depositor_info.
em_figure_depositor_info.details
Details about the image file.
em_figure_depositor_info.experiment_id
This data item optionally associates an image (figure) with an experiment.
em_figure_depositor_info.upload_file_name
The name of the image file associated with the map entry
em_figure_depositor_info.id
This data item is the unique identifier for an image file.
0
em_final_classification
Information about the final image classification
Example 1
<PDBx:em_final_classificationCategory>
<PDBx:em_final_classification id="1">
<PDBx:image_processing_id>1</PDBx:image_processing_id>
</PDBx:em_final_classification>
</PDBx:em_final_classificationCategory>
0
1
0
1
1
1
0
1
0
1
1
em_final_classificationCategory
This property indicates that datablock
has a category holder em_final_classificationCategory.
em_final_classificationCategory
This property indicates that em_final_classificationCategory.
has a category em_final_classification.
em_final_classificationItem
Abstract datatype property for em_final_classification items.
reference_to_em_final_classification
cross-reference to em_final_classification.
referenced_by_em_final_classification
cross-reference from em_final_classification.
em_final_classification.avg_num_images_per_class
The average number of images per class in the final 2D/3D classification
75
em_final_classification.details
Additional details about the final 2D/3D classification
The final 2D classification had a highly asymmetric distribution owing to preferred orientations
in the prepared specimen
em_final_classification.image_processing_id
Foreign key to the EM_IMAGE_PROCESSING category
em_final_classification.num_classes
The number of classes used in the final 2D/3D classification
2D
3D
Space (2D/3D) for the classification.
em_final_classification.id
PRIMARY KEY
0
em_focused_ion_beam
Description of sectioning by focused_ion_beam
1
1
0
1
0
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
em_focused_ion_beamCategory
This property indicates that datablock
has a category holder em_focused_ion_beamCategory.
em_focused_ion_beamCategory
This property indicates that em_focused_ion_beamCategory.
has a category em_focused_ion_beam.
em_focused_ion_beamItem
Abstract datatype property for em_focused_ion_beam items.
reference_to_em_focused_ion_beam
cross-reference to em_focused_ion_beam.
referenced_by_em_focused_ion_beam
cross-reference from em_focused_ion_beam.
em_focused_ion_beam.current
Current of the ion beam, in nanoamperes (nA)
em_focused_ion_beam.details
Additional details about FIB milling
em_focused_ion_beam.dose_rate
ions per sq centimetre per second
em_focused_ion_beam.duration
Milling time in seconds
em_focused_ion_beam.em_tomography_specimen_id
Foreign key relationship to the EM TOMOGRAPHY SPECIMEN category
em_focused_ion_beam.final_thickness
Final sample thickness
em_focused_ion_beam.initial_thickness
Initial sample thickness
em_focused_ion_beam.instrument
The instrument used for focused ion beam sectioning
FEI Quanta FIB
em_focused_ion_beam.ion
The ion source used to ablate the specimen
gallium ion
gold ion
iridium ion
em_focused_ion_beam.temperature
Temperature of the sample during milling, in kelvins
100
em_focused_ion_beam.voltage
Voltage applied to the ion source, in kilovolts
30
em_focused_ion_beam.id
PRIMARY KEY
0
em_fsc_curve
Data items in the EMD_VALIDATION_FSC_CURVE category
record details of the Fourier Shell Correlation (FSC) curve file.
Example 1
<PDBx:em_fsc_curveCategory>
<PDBx:em_fsc_curve id="1">
<PDBx:file>fsc_curve.txt</PDBx:file>
</PDBx:em_fsc_curve>
</PDBx:em_fsc_curveCategory>
0
1
0
1
1
em_fsc_curveCategory
This property indicates that datablock
has a category holder em_fsc_curveCategory.
em_fsc_curveCategory
This property indicates that em_fsc_curveCategory.
has a category em_fsc_curve.
em_fsc_curveItem
Abstract datatype property for em_fsc_curve items.
reference_to_em_fsc_curve
cross-reference to em_fsc_curve.
referenced_by_em_fsc_curve
cross-reference from em_fsc_curve.
em_fsc_curve.details
Details about the FSC file.
em_fsc_curve.file
FSC file name.
emd-5470-fsc.txt
em_fsc_curve.id
PRIMARY KEY
0
em_grid_pretreatment
Data items describing glow discharge pretreatment for an EM grid
Example 1
<PDBx:em_grid_pretreatmentCategory>
<PDBx:em_grid_pretreatment id="1">
<PDBx:sample_support_id>1</PDBx:sample_support_id>
<PDBx:time>12</PDBx:time>
<PDBx:type>GLOW DISCHARGE</PDBx:type>
</PDBx:em_grid_pretreatment>
</PDBx:em_grid_pretreatmentCategory>
0
1
0
1
1
1
0
1
0
1
1
em_grid_pretreatmentCategory
This property indicates that datablock
has a category holder em_grid_pretreatmentCategory.
em_grid_pretreatmentCategory
This property indicates that em_grid_pretreatmentCategory.
has a category em_grid_pretreatment.
em_grid_pretreatmentItem
Abstract datatype property for em_grid_pretreatment items.
reference_to_em_grid_pretreatment
cross-reference to em_grid_pretreatment.
referenced_by_em_grid_pretreatment
cross-reference from em_grid_pretreatment.
em_grid_pretreatment.atmosphere
The atmosphere used for glow discharge of the em grid.
AIR
AMYLAMINE
em_grid_pretreatment.pressure
Pressure of the glow discharge chamber, in pascals
em_grid_pretreatment.sample_support_id
Pointer to EM SAMPLE SUPPORT
em_grid_pretreatment.time
Time period for glow discharge of the em grid, in seconds
60
GLOW DISCHARGE
PLASMA CLEANING
Type of grid pretreatment
em_grid_pretreatment.id
PRIMARY KEY
0
em_helical_entity
Data items in the EM_HELICAL_ENTITY category record details
for a helical or filament type of assembly component.
0
1
0
1
1
1
0
1
0
1
0
1
0
1
1
1
em_helical_entityCategory
This property indicates that datablock
has a category holder em_helical_entityCategory.
em_helical_entityCategory
This property indicates that em_helical_entityCategory.
has a category em_helical_entity.
em_helical_entityItem
Abstract datatype property for em_helical_entity items.
reference_to_em_helical_entity
cross-reference to em_helical_entity.
referenced_by_em_helical_entity
cross-reference from em_helical_entity.
em_helical_entity.angular_rotation_per_subunit
The angular rotation per helical subunit in degrees. Negative values indicate left-handed helices; positive values indicate right handed helices.
-34.616000
em_helical_entity.axial_rise_per_subunit
The axial rise per subunit in the helical assembly.
17.400000
em_helical_entity.axial_symmetry
Symmetry of the helical axis, either cyclic (Cn) or dihedral (Dn), where n>=1.
C1
D2
C7
em_helical_entity.details
Any other details regarding the helical assembly
Dihedral symmetry
YES
NO
Value should be YES if a the filament has two-fold symmetry perpendicular to the helical axis.
em_helical_entity.entity_assembly_id
The value of attribute entity_assembly_id
in category em_helical_entity identifies a particular assembly component.
This data item is a pointer to attribute id
in category em_entity_assembly in the EM_ENTITY_ASSEMBLY category.
em_helical_entity.hand
Handedness of the helix: right handed or left handed
Right
Left
em_helical_entity.id
PRIMARY KEY
em_helical_entity.image_processing_id
This data item is a pointer to attribute id in category em_image_processing.
0
em_high_pressure_freezing
Description of high pressure freezing
0
1
1
1
1
1
1
em_high_pressure_freezingCategory
This property indicates that datablock
has a category holder em_high_pressure_freezingCategory.
em_high_pressure_freezingCategory
This property indicates that em_high_pressure_freezingCategory.
has a category em_high_pressure_freezing.
em_high_pressure_freezingItem
Abstract datatype property for em_high_pressure_freezing items.
reference_to_em_high_pressure_freezing
cross-reference to em_high_pressure_freezing.
referenced_by_em_high_pressure_freezing
cross-reference from em_high_pressure_freezing.
em_high_pressure_freezing.details
Additional details about high pressure freezing.
High pressure freezing chamber was 250 um thick, 3.0 mm diameter,
with central cavities 1.5 mm x 0.5 mm x 200 um deep. The chamber
was pre-coated with 0.5% lecithin in chloroform.
em_high_pressure_freezing.em_tomography_specimen_id
Foreign key relationship to the EM TOMOGRAPHY SPECIMEN category
em_high_pressure_freezing.instrument
The instrument used for high pressure freezing.
Leica EM HP100
em_high_pressure_freezing.id
PRIMARY KEY
0
em_image_processing
Data items in the EM_IMAGE_PROCESSING category
record details of the EM image processing procedure.
Example 1
<PDBx:em_image_processingCategory>
<PDBx:em_image_processing id="1" image_recording_id="1">
<PDBx:details>The selected images were high-pass filtered and normalized</PDBx:details>
</PDBx:em_image_processing>
</PDBx:em_image_processingCategory>
0
1
1
1
em_image_processingCategory
This property indicates that datablock
has a category holder em_image_processingCategory.
em_image_processingCategory
This property indicates that em_image_processingCategory.
has a category em_image_processing.
em_image_processingItem
Abstract datatype property for em_image_processing items.
reference_to_em_image_processing
cross-reference to em_image_processing.
referenced_by_em_image_processing
cross-reference from em_image_processing.
em_image_processing.details
Method details.
The selected images were high-pass filtered and normalized
em_image_processing.id
PRIMARY KEY
em_image_processing.image_recording_id
Foreign key to the EM_IMAGE_RECORDING
0
em_image_recording
Data items in the EM_IMAGE_RECORDING category record details
of the image recording (either film/microdensitometer or electronic detector)
and parameters for image digitization.
Example 1 - images collected on film
<PDBx:em_image_recordingCategory>
<PDBx:em_image_recording id="1" imaging_id="1">
<PDBx:avg_electron_dose_per_image>0.9</PDBx:avg_electron_dose_per_image>
<PDBx:film_or_detector_model>GENERIC FILM</PDBx:film_or_detector_model>
<PDBx:num_diffraction_images>48</PDBx:num_diffraction_images>
</PDBx:em_image_recording>
</PDBx:em_image_recordingCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
1
em_image_recordingCategory
This property indicates that datablock
has a category holder em_image_recordingCategory.
em_image_recordingCategory
This property indicates that em_image_recordingCategory.
has a category em_image_recording.
em_image_recordingItem
Abstract datatype property for em_image_recording items.
reference_to_em_image_recording
cross-reference to em_image_recording.
referenced_by_em_image_recording
cross-reference from em_image_recording.
em_image_recording.average_exposure_time
The average exposure time for each image.
2.0
em_image_recording.avg_electron_dose_per_image
The electron dose received by the specimen per image (electrons per square angstrom).
30.0
em_image_recording.avg_electron_dose_per_subtomogram
The average total electron dose received by the specimen for each subtomogram (electrons per square angstrom).
em_image_recording.details
Any additional details about image recording.
Images were collected in movie-mode at 17 frames per second
COUNTING
INTEGRATING
SUPER-RESOLUTION
OTHER
The detector mode used during image recording.
em_image_recording.film_or_detector_model
The detector type used for recording images.
Usually film , CCD camera or direct electron detector.
em_image_recording.num_diffraction_images
The number of diffraction images collected.
em_image_recording.num_grids_imaged
Number of grids in the microscopy session
em_image_recording.num_real_images
The number of micrograph images collected.
em_image_recording.id
PRIMARY KEY
em_image_recording.imaging_id
This data item the id of the microscopy settings used in the imaging.
0
em_image_scans
Data items in the EM_IMAGE_SCANS category record details
of the image scanning device (microdensitometer)
and parameters for digitization of the image.
Example 1 - based on PDB entry 1DYL and laboratory records for the
structure corresponding to PDB entry 1DYL
<PDBx:em_image_scansCategory>
<PDBx:em_image_scans id="2">
<PDBx:details xsi:nil="true" />
<PDBx:entry_id>1DYL</PDBx:entry_id>
<PDBx:number_digital_images>48</PDBx:number_digital_images>
<PDBx:od_range xsi:nil="true" />
<PDBx:quant_bit_size xsi:nil="true" />
<PDBx:sampling_size xsi:nil="true" />
<PDBx:scanner_model xsi:nil="true" />
</PDBx:em_image_scans>
</PDBx:em_image_scansCategory>
0
1
0
1
0
1
0
1
1
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
1
em_image_scansCategory
This property indicates that datablock
has a category holder em_image_scansCategory.
em_image_scansCategory
This property indicates that em_image_scansCategory.
has a category em_image_scans.
em_image_scansItem
Abstract datatype property for em_image_scans items.
reference_to_em_image_scans
cross-reference to em_image_scans.
referenced_by_em_image_scans
cross-reference from em_image_scans.
em_image_scans.citation_id
This data item is a pointer to attribute id
in category citation in the CITATION category.
em_image_scans.details
Any additional details about image recording.
em_image_scans.dimension_height
Height of scanned image, in pixels
em_image_scans.dimension_width
Width of scanned image, in pixels
em_image_scans.entry_id
This data item is a pointer to attribute id in category entry in the
ENTRY category.
em_image_scans.frames_per_image
Total number of time-slice (movie) frames taken per image.
10
em_image_scans.number_digital_images
The number of real images.
em_image_scans.od_range
The optical density range (OD=-log 10 transmission).
To the eye OD=1 appears light grey and OD=3 is opaque.
1.4
em_image_scans.quant_bit_size
The number of bits per pixel.
8
em_image_scans.sampling_size
The sampling step size (microns) set on the scanner.
ZEISS SCAI
EMIL 10
OPTRONICS
PERKIN ELMER
TEMSCAN
EIKONIX IEEE 488
NIKON COOLSCAN
NIKON SUPER COOLSCAN 9000
IMAGE SCIENCE PATCHWORK DENSITOMETER
PRIMESCAN
OTHER
The scanner model.
em_image_scans.used_frames_per_image
Range of time-slice (movie) frames used for the reconstruction.
2-10
em_image_scans.id
The value of attribute id in category em_image_scans must uniquely identify
the images scanned.
em_image_scans.image_recording_id
foreign key linked to _em_image_recording
0
em_imaging
Data items in the EM_IMAGING category record details about
the parameters used in imaging the sample in the electron microscope.
Example 1 - based on PDB entry 1DYL and laboratory records for the
structure corresponding to PDB entry 1DYL
<PDBx:em_imagingCategory>
<PDBx:em_imaging entry_id="1DYL" id="1">
<PDBx:accelerating_voltage>200</PDBx:accelerating_voltage>
<PDBx:calibrated_magnification xsi:nil="true" />
<PDBx:date>1998-15-06</PDBx:date>
<PDBx:details xsi:nil="true" />
<PDBx:detector_distance xsi:nil="true" />
<PDBx:electron_source>FEG</PDBx:electron_source>
<PDBx:energy_filter xsi:nil="true" />
<PDBx:energy_window xsi:nil="true" />
<PDBx:illumination_mode>bright field</PDBx:illumination_mode>
<PDBx:microscope_model>FEI/PHILIPS CM200 FEG</PDBx:microscope_model>
<PDBx:mode>low dose</PDBx:mode>
<PDBx:nominal_cs>2.0</PDBx:nominal_cs>
<PDBx:nominal_defocus_max>7600</PDBx:nominal_defocus_max>
<PDBx:nominal_defocus_min>975</PDBx:nominal_defocus_min>
<PDBx:nominal_magnification>50000</PDBx:nominal_magnification>
<PDBx:recording_temperature_maximum xsi:nil="true" />
<PDBx:recording_temperature_minimum xsi:nil="true" />
<PDBx:sample_support_id>1</PDBx:sample_support_id>
<PDBx:specimen_holder_model>gatan 626-0300</PDBx:specimen_holder_model>
<PDBx:specimen_holder_type>cryotransfer</PDBx:specimen_holder_type>
<PDBx:temperature>95</PDBx:temperature>
<PDBx:tilt_angle_max>0</PDBx:tilt_angle_max>
<PDBx:tilt_angle_min>0</PDBx:tilt_angle_min>
</PDBx:em_imaging>
</PDBx:em_imagingCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
1
0
1
1
1
1
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
1
0
1
0
1
0
1
1
1
em_imagingCategory
This property indicates that datablock
has a category holder em_imagingCategory.
em_imagingCategory
This property indicates that em_imagingCategory.
has a category em_imaging.
em_imagingItem
Abstract datatype property for em_imaging items.
reference_to_em_imaging
cross-reference to em_imaging.
referenced_by_em_imaging
cross-reference from em_imaging.
em_imaging.accelerating_voltage
A value of accelerating voltage (in kV) used for imaging.
300
NONE
BASIC
ZEMLIN TABLEAU
COMA FREE
OTHER
The type of procedure used to align the microscope electron beam.
em_imaging.astigmatism
astigmatism
em_imaging.c2_aperture_diameter
The open diameter of the c2 condenser lens,
in microns.
100
em_imaging.calibrated_defocus_max
The maximum calibrated defocus value of the objective lens (in nanometers) used
to obtain the recorded images. Negative values refer to overfocus.
5000
em_imaging.calibrated_defocus_min
The minimum calibrated defocus value of the objective lens (in nanometers) used
to obtain the recorded images. Negative values refer to overfocus.
1200
em_imaging.calibrated_magnification
The magnification value obtained for a known standard just
prior to, during or just after the imaging experiment.
61200
em_imaging.citation_id
This data item is a pointer to attribute id in category citation in
the CITATION category.
NITROGEN
HELIUM
Cryogen type used to maintain the specimen stage temperature during imaging
in the microscope.
em_imaging.date
Date (YYYY-MM-DD) of imaging experiment or the date at which
a series of experiments began.
2001-05-08
em_imaging.details
Any additional imaging details.
Preliminary grid screening was performed manually.
em_imaging.detector_distance
The camera length (in millimeters). The camera length is the
product of the objective focal length and the combined magnification
of the intermediate and projector lenses when the microscope is
operated in the diffraction mode.
em_imaging.detector_id
The value of attribute detector_id in category em_imaging must uniquely identify
the type of detector used in the experiment.
em_imaging.electron_beam_tilt_params
electron beam tilt params
em_imaging.electron_dose
The electron dose received by the specimen (electrons per square angstrom).
0.9
em_imaging.electron_source
The source of electrons. The electron gun.
em_imaging.energy_filter
The type of energy filter spectrometer apparatus.
FEI
em_imaging.energy_window
The energy filter range in electron volts (eV)set by spectrometer.
0 - 15
FLOOD BEAM
SPOT SCAN
OTHER
The mode of illumination.
em_imaging.microscope_id
This data item is a pointer to attribute id in category em_microscope in
the EM_MICROSCOPE category.
FEI MORGAGNI
FEI POLARA 300
FEI TALOS ARCTICA
FEI TECNAI 10
FEI TECNAI 12
FEI TECNAI 20
FEI TECNAI F20
FEI TECNAI F30
FEI TECNAI ARCTICA
FEI TECNAI SPHERA
FEI TECNAI SPIRIT
FEI TITAN
FEI TITAN KRIOS
FEI/PHILIPS CM10
FEI/PHILIPS CM12
FEI/PHILIPS CM120T
FEI/PHILIPS CM200FEG
FEI/PHILIPS CM200FEG/SOPHIE
FEI/PHILIPS CM200FEG/ST
FEI/PHILIPS CM200FEG/UT
FEI/PHILIPS CM200T
FEI/PHILIPS CM300FEG/HE
FEI/PHILIPS CM300FEG/ST
FEI/PHILIPS CM300FEG/T
FEI/PHILIPS EM400
FEI/PHILIPS EM420
HITACHI EF2000
HITACHI EF3000
HITACHI H7600
HITACHI HF2000
HITACHI HF3000
HITACHI H3000 UHVEM
HITACHI H-9500SD
JEOL 100B
JEOL 100CX
JEOL 1000EES
JEOL 1010
JEOL 1200
JEOL 1200EX
JEOL 1200EXII
JEOL 1230
JEOL 1400
JEOL 1400/HR + YPS FEG
JEOL 2000EX
JEOL 2000EXII
JEOL 2010
JEOL 2010F
JEOL 2010HT
JEOL 2010HC
JEOL 2010UHR
JEOL 2011
JEOL 2100
JEOL 2100F
JEOL 2200FS
JEOL 2200FSC
JEOL 3000SFF
JEOL 3100FEF
JEOL 3100FFC
JEOL 3200FS
JEOL 3200FSC
JEOL KYOTO-3000SFF
JEOL 4000
JEOL 4000EX
JEOL CRYO ARM 200
JEOL CRYO ARM 300
SIEMENS SULEIKA
TFS GLACIOS
TFS KRIOS
TFS TALOS
TFS TALOS F200C
TFS TALOS L120C
TFS TUNDRA
ZEISS LEO912
ZEISS LIBRA120PLUS
The name of the model of microscope.
4D-STEM
BRIGHT FIELD
DARK FIELD
DIFFRACTION
OTHER
The mode of imaging.
em_imaging.nominal_cs
The spherical aberration coefficient (Cs) in millimeters,
of the objective lens.
2.0
em_imaging.nominal_defocus_max
The maximum defocus value of the objective lens (in nanometers) used
to obtain the recorded images. Negative values refer to overfocus.
5000
em_imaging.nominal_defocus_min
The minimum defocus value of the objective lens (in nanometers) used
to obtain the recorded images. Negative values refer to overfocus.
1200
em_imaging.nominal_magnification
The magnification indicated by the microscope readout.
60000
em_imaging.recording_temperature_maximum
The specimen temperature maximum (kelvin) for the duration
of imaging.
70
em_imaging.recording_temperature_minimum
The specimen temperature minimum (kelvin) for the duration
of imaging.
em_imaging.residual_tilt
Residual tilt of the electron beam (in miliradians)
em_imaging.sample_support_id
This data item is a pointer to attribute id in category em_sample_support in
the EM_SAMPLE_SUPPORT category.
em_imaging.scans_id
The value of attribute scans_id in category em_imaging must uniquely identify
the image_scans used in the experiment.
FEI TITAN KRIOS AUTOGRID HOLDER
FISCHIONE 2550
FISCHIONE INSTRUMENTS DUAL AXIS TOMOGRAPHY HOLDER
GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
GATAN 910 MULTI-SPECIMEN SINGLE TILT CRYO TRANSFER HOLDER
GATAN 914 HIGH TILT LIQUID NITROGEN CRYO TRANSFER TOMOGRAPHY HOLDER
GATAN 915 DOUBLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
GATAN CHDT 3504 DOUBLE TILT HIGH RESOLUTION NITROGEN COOLING HOLDER
GATAN CT3500 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
GATAN CT3500TR SINGLE TILT ROTATION LIQUID NITROGEN CRYO TRANSFER HOLDER
GATAN ELSA 698 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
GATAN HC 3500 SINGLE TILT HEATING/NITROGEN COOLING HOLDER
GATAN HCHDT 3010 DOUBLE TILT HIGH RESOLUTION HELIUM COOLING HOLDER
GATAN HCHST 3008 SINGLE TILT HIGH RESOLUTION HELIUM COOLING HOLDER
GATAN HELIUM
GATAN LIQUID NITROGEN
GATAN UHRST 3500 SINGLE TILT ULTRA HIGH RESOLUTION NITROGEN COOLING HOLDER
GATAN ULTDT ULTRA LOW TEMPERATURE DOUBLE TILT HELIUM COOLING HOLDER
GATAN ULTST ULTRA LOW TEMPERATURE SINGLE TILT HELIUM COOLING HOLDER
HOME BUILD
JEOL
JEOL CRYOSPECPORTER
JEOL 3200FSC CRYOHOLDER
PHILIPS ROTATION HOLDER
SIDE ENTRY, EUCENTRIC
OTHER
The name of the model of specimen holder used during imaging.
em_imaging.specimen_holder_type
The type of specimen holder used during imaging.
cryo
em_imaging.specimen_id
Foreign key to the EM_SPECIMEN category
em_imaging.temperature
The mean specimen stage temperature (in kelvin) during imaging
in the microscope.
70
em_imaging.tilt_angle_max
The maximum angle at which the specimen was tilted to obtain
recorded images.
70
em_imaging.tilt_angle_min
The minimum angle at which the specimen was tilted to obtain
recorded images.
-70
em_imaging.entry_id
This data item is a pointer to attribute id in category entry in the ENTRY category.
em_imaging.id
PRIMARY KEY
0
em_imaging_optics
Description of a few specialist optics apparatus
Example 1
<PDBx:em_imaging_opticsCategory>
<PDBx:em_imaging_optics id="1" imaging_id="1">
<PDBx:chr_aberration_corrector>CEOS manufactured Cc corrector</PDBx:chr_aberration_corrector>
<PDBx:energyfilter_lower>0</PDBx:energyfilter_lower>
<PDBx:energyfilter_name>FEI</PDBx:energyfilter_name>
<PDBx:energyfilter_upper>15</PDBx:energyfilter_upper>
</PDBx:em_imaging_optics>
</PDBx:em_imaging_opticsCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
1
em_imaging_opticsCategory
This property indicates that datablock
has a category holder em_imaging_opticsCategory.
em_imaging_opticsCategory
This property indicates that em_imaging_opticsCategory.
has a category em_imaging_optics.
em_imaging_opticsItem
Abstract datatype property for em_imaging_optics items.
reference_to_em_imaging_optics
cross-reference to em_imaging_optics.
referenced_by_em_imaging_optics
cross-reference from em_imaging_optics.
em_imaging_optics.chr_aberration_corrector
Chromatic aberration corrector information
CEOS manufactured Cc corrector
em_imaging_optics.details
Details on the use of the phase plate
Phase plate evolution varied between different microscopes used to collect data but positions were shifted once phase evolution progressed past 120 degrees.
em_imaging_optics.energyfilter_lower
The energy filter range lower value in electron volts (eV) set by spectrometer.
0
em_imaging_optics.energyfilter_name
The type of energy filter spectrometer
GIF 200
em_imaging_optics.energyfilter_slit_width
The energy filter range slit width in electron volts (eV).
35
em_imaging_optics.energyfilter_upper
The energy filter range upper value in electron volts (eV) set by spectrometer.
15
em_imaging_optics.phase_plate
Phase plate information
ZERNIKE PHASE PLATE
em_imaging_optics.sph_aberration_corrector
Spherical aberration corrector information
Microscope was modified with a Cs corrector with two hexapole elements.
em_imaging_optics.id
PRIMARY KEY
em_imaging_optics.imaging_id
Foreign key to the EM IMAGING category
0
em_interpret_figure
Listing of all layer line files associated with the EM entry
Example 1
<PDBx:em_interpret_figureCategory>
<PDBx:em_interpret_figure id="1">
<PDBx:details xsi:nil="true" />
<PDBx:file>emd-1234.png</PDBx:file>
</PDBx:em_interpret_figure>
</PDBx:em_interpret_figureCategory>
0
1
1
1
1
em_interpret_figureCategory
This property indicates that datablock
has a category holder em_interpret_figureCategory.
em_interpret_figureCategory
This property indicates that em_interpret_figureCategory.
has a category em_interpret_figure.
em_interpret_figureItem
Abstract datatype property for em_interpret_figure items.
reference_to_em_interpret_figure
cross-reference to em_interpret_figure.
referenced_by_em_interpret_figure
cross-reference from em_interpret_figure.
em_interpret_figure.details
Details about the image file.
em_interpret_figure.file
The name of the image file associated with the map entry
em_interpret_figure.id
PRIMARY KEY
0
em_layer_lines
Listing of all layer line files associated with the EM entry
Example 1
<PDBx:em_layer_linesCategory>
<PDBx:em_layer_lines experiment_id="1" id="1">
<PDBx:details xsi:nil="true" />
<PDBx:file>emd-1234-sf.cif</PDBx:file>
</PDBx:em_layer_lines>
</PDBx:em_layer_linesCategory>
0
1
1
1
1
1
em_layer_linesCategory
This property indicates that datablock
has a category holder em_layer_linesCategory.
em_layer_linesCategory
This property indicates that em_layer_linesCategory.
has a category em_layer_lines.
em_layer_linesItem
Abstract datatype property for em_layer_lines items.
reference_to_em_layer_lines
cross-reference to em_layer_lines.
referenced_by_em_layer_lines
cross-reference from em_layer_lines.
em_layer_lines.details
Details about the layer line file.
em_layer_lines.file
The name of the layer line file associated with the map entry
em_layer_lines.experiment_id
This data item is a pointer to the EM EXPERIMENT category.
em_layer_lines.id
PRIMARY KEY
0
em_layer_lines_depositor_info
Listing of layer line files associated with the EM entry
Example 1
<PDBx:em_layer_lines_depositor_infoCategory>
<PDBx:em_layer_lines_depositor_info id="1">
<PDBx:details xsi:nil="true" />
<PDBx:experiment_id>1</PDBx:experiment_id>
<PDBx:upload_file_name>emd-1234-ll.cif</PDBx:upload_file_name>
</PDBx:em_layer_lines_depositor_info>
</PDBx:em_layer_lines_depositor_infoCategory>
0
1
0
1
1
1
1
em_layer_lines_depositor_infoCategory
This property indicates that datablock
has a category holder em_layer_lines_depositor_infoCategory.
em_layer_lines_depositor_infoCategory
This property indicates that em_layer_lines_depositor_infoCategory.
has a category em_layer_lines_depositor_info.
em_layer_lines_depositor_infoItem
Abstract datatype property for em_layer_lines_depositor_info items.
reference_to_em_layer_lines_depositor_info
cross-reference to em_layer_lines_depositor_info.
referenced_by_em_layer_lines_depositor_info
cross-reference from em_layer_lines_depositor_info.
em_layer_lines_depositor_info.details
Details about the layer line file.
em_layer_lines_depositor_info.experiment_id
This data item is a pointer to the EMD_STRUCT category.
em_layer_lines_depositor_info.upload_file_name
The name of the layer line file associated with the map entry
em_layer_lines_depositor_info.id
This data item is the unique identifier for the layer line file.
0
em_map
Data items in the EMD_MAP category record parameters of the CCP4 binary-format map file header
(see ftp://ftp.wwpdb.org/pub/emdb/doc/map_format/EMDB_mapFormat_v1.0.pdf),
parameters derived from the map header, pixel size, contour level, and annotation details from the depositor.
The map is a three-dimensional array of data-values of the same data-type.
Important parameters are data-type and array size in three dimensions
(i.e. the number of columns, rows and sections).
Columns are the fastest changing, followed by rows and sections.
Example 1 - based on map entry EMD-5001
<PDBx:em_mapCategory>
<PDBx:em_map entry_id="1ABC" id="1">
<PDBx:annotation_details>D7 structure of Groel at 4.2 Angstrom resolution</PDBx:annotation_details>
<PDBx:axis_order_fast>X</PDBx:axis_order_fast>
<PDBx:axis_order_medium>Y</PDBx:axis_order_medium>
<PDBx:axis_order_slow>Z</PDBx:axis_order_slow>
<PDBx:cell_a>212.0</PDBx:cell_a>
<PDBx:cell_alpha>90.0</PDBx:cell_alpha>
<PDBx:cell_b>212.0</PDBx:cell_b>
<PDBx:cell_beta>90.0</PDBx:cell_beta>
<PDBx:cell_c>212.0</PDBx:cell_c>
<PDBx:cell_gamma>90.0</PDBx:cell_gamma>
<PDBx:data_type>Image stored as Reals</PDBx:data_type>
<PDBx:dimensions_col>200</PDBx:dimensions_col>
<PDBx:dimensions_row>200</PDBx:dimensions_row>
<PDBx:dimensions_sec>200</PDBx:dimensions_sec>
<PDBx:format>CCP4</PDBx:format>
<PDBx:origin_col>-100</PDBx:origin_col>
<PDBx:origin_row>-100</PDBx:origin_row>
<PDBx:origin_sec>-100</PDBx:origin_sec>
<PDBx:pixel_spacing_x>1.06</PDBx:pixel_spacing_x>
<PDBx:pixel_spacing_y>1.06</PDBx:pixel_spacing_y>
<PDBx:pixel_spacing_z>1.06</PDBx:pixel_spacing_z>
<PDBx:size_kb>32002</PDBx:size_kb>
<PDBx:spacing_x>200</PDBx:spacing_x>
<PDBx:spacing_y>200</PDBx:spacing_y>
<PDBx:spacing_z>200</PDBx:spacing_z>
<PDBx:statistics_average>0.0668982</PDBx:statistics_average>
<PDBx:statistics_maximum>2.42436</PDBx:statistics_maximum>
<PDBx:statistics_minimum>-0.965912</PDBx:statistics_minimum>
<PDBx:statistics_std>0.23771</PDBx:statistics_std>
<PDBx:symmetry_space_group>1</PDBx:symmetry_space_group>
</PDBx:em_map>
</PDBx:em_mapCategory>
0
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
0
1
0
1
1
1
1
1
1
1
1
1
1
1
0
1
1
1
0
1
0
1
0
1
0
1
1
1
1
1
1
1
0
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
0
1
0
1
0
1
0
1
1
1
1
1
1
1
em_mapCategory
This property indicates that datablock
has a category holder em_mapCategory.
em_mapCategory
This property indicates that em_mapCategory.
has a category em_map.
em_mapItem
Abstract datatype property for em_map items.
reference_to_em_map
cross-reference to em_map.
referenced_by_em_map
cross-reference from em_map.
em_map.annotation_details
map annotation details
X
Y
Z
The map axis that corresponds to Columns.
(CCP4 HEADER WORD 17 MAPC 1=x, 2=y, 3=z)
X
Y
Z
The map axis that corresponds to Rows.
(CCP4 map header word 18 MAPR 1=x, 2=y, 3=z)
X
Y
Z
The map axis that corresponds to Sections.
(CCP4 map header word 19 MAPS 1=x, 2=y, 3=z)
em_map.cell_a
Map unit cell length parameter a.
(CCP4 map header word 11)
em_map.cell_alpha
Value of map unit cell angle parameter alpha in degrees.
(CCP4 map header word 14)
em_map.cell_b
Map unit cell length parameter b.
(CCP4 map header word 12)
em_map.cell_beta
Value of map unit cell angle parameter beta in degrees.
(CCP4 map header word 15)
em_map.cell_c
Map unit cell length parameter c.
(CCP4 map header word 13)
em_map.cell_gamma
Value of map unit cell angle parameter gamma in degrees.
(CCP4 map header word 16)
em_map.contour_level
recommended contour level for viewing the map
author
emdb
software
source of the recommended contour level
author
Image stored as signed byte
Image stored as signed integer (2 bytes)
Image stored as floating point number (4 bytes)
The map data_type describes the data structure of the map voxels.
(CCP4 map header word 4 MODE)
EMDB currently holds MODE=0,1,and 2 maps; the majority are MODE=2.
MAPS with MODES other than 2 and 0 may not work in CCP4 programs.
MODE = 0: 8 bits, density stored as a signed byte (-128 to 127, ISO/IEC 10967)
MODE = 1: 16 bits, density stored as a signed integer (-32768 to 32767, ISO/IEC 10967)
MODE = 2: 32 bits, density stored as a floating point number (IEEE 754)
em_map.dimensions_col
The number of columns in the map.
(CCP4 map header word 1 NC)
em_map.dimensions_row
The number of rows in the map.
(CCP4 map header word 2 NR)
em_map.dimensions_sec
The number of sections in the map.
(CCP4 map header word 3 NS)
big
little
map file endian type
em_map.file
Map file name.
emd_5470.map.gz
CCP4
map format
em_map.label
text stored in the label field of the CCP4 map header
(WORDS 57-256)
em_map.limit_col
The final column position of the map relative to the
Cartesian coordinate origin in voxel grid units.
(derived = .origin_col + .dimensions_col -1)
em_map.limit_row
The final row position of the map relative to the
Cartesian coordinate origin in voxel grid units.
(derived = .origin_row + .dimensions_row -1)
em_map.limit_sec
The final section position of the map relative to the
Cartesian coordinate origin in voxel grid units.
(derived -- .origin_sec + .dimensions_sec -1)
em_map.origin_col
The position of the first column of the map relative to the
Cartesian coordinate origin in voxel grid units.
(CCP4 map header word 5 NCSTART)
em_map.origin_row
The position of the first row of the map relative to the
Cartesian coordinate origin in voxel grid units.
(CCP4 map header word 6 NRSTART)
em_map.origin_sec
The position of the first section of the map relative to the
Cartesian coordinate origin in voxel grid units.
(CCP4 map header word 7 NSSTART)
em_map.original_file
Depositiors original map file name.
emd_5470.map.gz
em_map.partition
Identifies the archive file partition number of any map file
em_map.pixel_spacing_x
The length in angstroms of one voxel along the X axis.
em_map.pixel_spacing_y
The length in angstroms of one voxel along the Y axis.
em_map.pixel_spacing_z
The length in angstroms of one voxel along the Z axis.
em_map.size_kb
map storage size in Kilobytes (before compression)
em_map.spacing_x
The number of intervals per cell repeat in X.
(CCP4 map header word 8 NX)
em_map.spacing_y
The number of intervals per cell repeat in Y.
(CCP4 map header word 9 NY)
em_map.spacing_z
The number of intervals per cell repeat in Z.
(CCP4 map header word 10 NZ)
em_map.statistics_average
Mean (average) density value of the map.
em_map.statistics_maximum
Maximum density value of the map.
em_map.statistics_minimum
Minimum density value of the map.
em_map.statistics_std
The standard deviation of the map density values.
em_map.symmetry_space_group
The space group number for the map.
The value is 1 unless the sample is crystalline.
(CCP4 map header word 23 ISPG)
primary map
half map
additional map
mask
raw map
FSC half map mask
FSC map-model mask
alignment mask
focused refinement mask
3D classification map
focus refinement map
segmentation
Map type
em_map.entry_id
This data item is a pointer to the ENTRY category.
em_map.id
PRIMARY KEY
0
em_map_depositor_info
Data items in the EM_MAP_DEPOSITOR INFO category record map parameters
that are provided by the depositor
Example 1 - based on map entry EMD-5001
<PDBx:em_map_depositor_infoCategory>
<PDBx:em_map_depositor_info entry_id="D_10005049" id="1">
<PDBx:annotation_details>D7 structure of Groel at 4.2 Angstrom resolution</PDBx:annotation_details>
<PDBx:contour_level>5.0</PDBx:contour_level>
<PDBx:experiment_id xsi:nil="true" />
<PDBx:map_type>primary</PDBx:map_type>
<PDBx:pixel_spacing_x>1.06</PDBx:pixel_spacing_x>
<PDBx:pixel_spacing_y>1.06</PDBx:pixel_spacing_y>
<PDBx:pixel_spacing_z>1.06</PDBx:pixel_spacing_z>
<PDBx:upload_file_name>GroelD7.mrc.gz</PDBx:upload_file_name>
<PDBx:upload_format>CCP4/MRC</PDBx:upload_format>
</PDBx:em_map_depositor_info>
</PDBx:em_map_depositor_infoCategory>
0
1
0
1
0
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
em_map_depositor_infoCategory
This property indicates that datablock
has a category holder em_map_depositor_infoCategory.
em_map_depositor_infoCategory
This property indicates that em_map_depositor_infoCategory.
has a category em_map_depositor_info.
em_map_depositor_infoItem
Abstract datatype property for em_map_depositor_info items.
reference_to_em_map_depositor_info
cross-reference to em_map_depositor_info.
referenced_by_em_map_depositor_info
cross-reference from em_map_depositor_info.
em_map_depositor_info.annotation_details
map annotation details
em_map_depositor_info.contour_level
recommended contour level for viewing the map
em_map_depositor_info.experiment_id
This data item optionally associates a map with a data item in the EM_EXPERIMENT category.
primary
additional
Primary map or additional map classification.
em_map_depositor_info.pixel_spacing_x
The length in angstroms of one voxel along the X axis.
em_map_depositor_info.pixel_spacing_y
The length in angstroms of one voxel along the Y axis.
em_map_depositor_info.pixel_spacing_z
The length in angstroms of one voxel along the Z axis.
em_map_depositor_info.upload_file_name
The name of a file containing the map.
CCP4/MRC
SPIDER
map format
em_map_depositor_info.entry_id
This data item is a pointer to the ENTRY category.
em_map_depositor_info.id
Unique identifier for each map listed.
0
em_mask_depositor_info
Data items in the EM_MASK_DEPOSITOR_INFO category record mask parameters
that are provided by the depositor
Example 1 - based on map entry EMD-5001
<PDBx:em_mask_depositor_infoCategory>
<PDBx:em_mask_depositor_info id="1">
<PDBx:annotation_details>D7 structure of Groel at 4.2 Angstrom resolution</PDBx:annotation_details>
<PDBx:contour_level>5.0</PDBx:contour_level>
<PDBx:pixel_spacing_x>1.06</PDBx:pixel_spacing_x>
<PDBx:pixel_spacing_y>1.06</PDBx:pixel_spacing_y>
<PDBx:pixel_spacing_z>1.06</PDBx:pixel_spacing_z>
<PDBx:upload_file_name>GroelD7.mrc.gz</PDBx:upload_file_name>
<PDBx:upload_format>CCP4/MRC</PDBx:upload_format>
</PDBx:em_mask_depositor_info>
</PDBx:em_mask_depositor_infoCategory>
0
1
0
1
1
1
1
1
1
1
1
1
1
1
1
em_mask_depositor_infoCategory
This property indicates that datablock
has a category holder em_mask_depositor_infoCategory.
em_mask_depositor_infoCategory
This property indicates that em_mask_depositor_infoCategory.
has a category em_mask_depositor_info.
em_mask_depositor_infoItem
Abstract datatype property for em_mask_depositor_info items.
reference_to_em_mask_depositor_info
cross-reference to em_mask_depositor_info.
referenced_by_em_mask_depositor_info
cross-reference from em_mask_depositor_info.
em_mask_depositor_info.annotation_details
map annotation details
em_mask_depositor_info.contour_level
recommended contour level for viewing the map
em_mask_depositor_info.pixel_spacing_x
The length in angstroms of one voxel along the X axis.
em_mask_depositor_info.pixel_spacing_y
The length in angstroms of one voxel along the Y axis.
em_mask_depositor_info.pixel_spacing_z
The length in angstroms of one voxel along the Z axis.
em_mask_depositor_info.upload_file_name
The name of a file containing the map.
CCP4/MRC
SPIDER
map format
em_mask_depositor_info.id
Unique identifier for each map listed.
0
em_obsolete
List of EMD entries made obsolete by this entry.
1
1
0
1
1
1
1
em_obsoleteCategory
This property indicates that datablock
has a category holder em_obsoleteCategory.
em_obsoleteCategory
This property indicates that em_obsoleteCategory.
has a category em_obsolete.
em_obsoleteItem
Abstract datatype property for em_obsolete items.
reference_to_em_obsolete
cross-reference to em_obsolete.
referenced_by_em_obsolete
cross-reference from em_obsolete.
em_obsolete.date
Dated when the entry made obsolete the other entry
em_obsolete.details
Description of the reason(s) for entry obsoletion
em_obsolete.entry
Entry made obsolete
em_obsolete.id
PRIMARY KEY
0
em_particle_selection
Data items in this category
record details of images from scanned micrographs and the
number of particles selected from a scanned set of micrographs.
Example 1 - based on PDB entry 1DYL and laboratory records for the
structure corresponding to PDB entry 1DYL
<PDBx:em_particle_selectionCategory>
<PDBx:em_particle_selection id="1" image_processing_id="1">
<PDBx:details xsi:nil="true" />
<PDBx:method>INTERACTIVE</PDBx:method>
<PDBx:num_particles_selected>5267</PDBx:num_particles_selected>
</PDBx:em_particle_selection>
</PDBx:em_particle_selectionCategory>
0
1
0
1
0
1
0
1
1
1
em_particle_selectionCategory
This property indicates that datablock
has a category holder em_particle_selectionCategory.
em_particle_selectionCategory
This property indicates that em_particle_selectionCategory.
has a category em_particle_selection.
em_particle_selectionItem
Abstract datatype property for em_particle_selection items.
reference_to_em_particle_selection
cross-reference to em_particle_selection.
referenced_by_em_particle_selection
cross-reference from em_particle_selection.
em_particle_selection.details
Additional detail such as description of filters used, if selection was
manual or automated, and/or template details.
negative monitor contrast facilitated particle picking
em_particle_selection.method
The method used for selecting particles
particles picked interactively from monitor
em_particle_selection.num_particles_selected
The number of particles selected from the projection set of images.
840
em_particle_selection.reference_model
Description of reference model used for particle selection
em_particle_selection.id
PRIMARY KEY
em_particle_selection.image_processing_id
The value of attribute image_processing_id in category em_particle_selection points to
the EM_IMAGE_PROCESSING category.
0
em_sample_preparation
Data items in the EM_SAMPLE_PREPARATION category
record details of sample conditions prior to and upon loading
onto grid support.
Example 1 - based on PDB entry 1DYL and laboratory records for the
structure corresponding to PDB entry 1DYL
<PDBx:em_sample_preparationCategory>
<PDBx:em_sample_preparation entry_id="1DYL" id="1">
<PDBx:_2d_crystal_grow_id xsi:nil="true" />
<PDBx:buffer_id>1</PDBx:buffer_id>
<PDBx:ph>7.6</PDBx:ph>
<PDBx:sample_concentration>5</PDBx:sample_concentration>
<PDBx:support_id>1</PDBx:support_id>
</PDBx:em_sample_preparation>
</PDBx:em_sample_preparationCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
1
em_sample_preparationCategory
This property indicates that datablock
has a category holder em_sample_preparationCategory.
em_sample_preparationCategory
This property indicates that em_sample_preparationCategory.
has a category em_sample_preparation.
em_sample_preparationItem
Abstract datatype property for em_sample_preparation items.
reference_to_em_sample_preparation
cross-reference to em_sample_preparation.
referenced_by_em_sample_preparation
cross-reference from em_sample_preparation.
em_sample_preparation._2d_crystal_grow_id
This data item is a pointer to attribute id
in category em_2d_crystal_grow in the 2D_CRYSTAL_GROW category.
em_sample_preparation.buffer_id
This data item is a pointer to attribute id in category em_buffer in the
BUFFER category.
em_sample_preparation.details
Details of the specimen preparation
1
Detergent-solubilized particles eluted from the cation-exchange
column were directly adsorbed for 1 min to parlodion carbon-coated
copper grids rendered hydrophilic by glow discharge at low pressure
in air. Grids were washed with 4 drops of double-distilled water
and stained with 2 drops of 0.75% uranyl formate.
2
Selectively stained by injection of horseradish peroxidase,
embedded in Spurr's resin and cut into 2-3 um thick sections.
3
S. cerevisiae PDC was purified to near homogeneity
from baker's yeast by modification of a published procedure. Highly
purified E1 was obtained by resolution of PDC with 2 M NaCl at pH 7.3
followed by FPLC on a Superdex 200 column. The weight-average molecular
weight of the PDC was determined by light scattering measurement to be
~8 x 106. On the basis of the known molecular weight of the complex and
its component enzymes and the experimentally determined polypeptide chain
ratios of E2/BP/E3, we estimated that the subunit composition of the
S. cerevisiae PDC is ~24 E1 tetramers, 60 E2 monomers, 12 BP monomers,
and 8 E3 dimers. Sufficient E1 was added to a sample of the PDC
preparation to increase the molar ratio of E1/E2 core to 60:1.
4
embedded in vitreous ice.
em_sample_preparation.entity_assembly_id
This data item is a pointer to attribute id in category entity_assembly in the em_entity_assembly category.
em_sample_preparation.ph
The pH value of the observed sample buffer.
5.5
em_sample_preparation.sample_concentration
The value of the concentration (mg per milliliter)
of the complex in the sample.
1.35
em_sample_preparation.support_id
This data item is a pointer to attribute id in category em_sample_support in the EM_SAMPLE_SUPPORT category.
em_sample_preparation.entry_id
This data item is a pointer to attribute id in category entry in the ENTRY category.
em_sample_preparation.id
The value of attribute id in category em_sample_preparation must
uniquely identify the sample preparation.
0
em_sample_support
Data items in the EM_SAMPLE_SUPPORT category record details
of the electron microscope grid type, grid support film and pretreatment
of whole before sample is applied
Example 1 - based on PDB entry 1DYL and laboratory records for the
structure corresponding to PDB entry 1DYL
<PDBx:em_sample_supportCategory>
<PDBx:em_sample_support id="1">
<PDBx:details>GLOW DISCHARGED 120 seconds</PDBx:details>
<PDBx:film_material>HOLEY CARBON</PDBx:film_material>
<PDBx:grid_material>COPPER</PDBx:grid_material>
<PDBx:grid_mesh_size>400</PDBx:grid_mesh_size>
</PDBx:em_sample_support>
</PDBx:em_sample_supportCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
1
em_sample_supportCategory
This property indicates that datablock
has a category holder em_sample_supportCategory.
em_sample_supportCategory
This property indicates that em_sample_supportCategory.
has a category em_sample_support.
em_sample_supportItem
Abstract datatype property for em_sample_support items.
reference_to_em_sample_support
cross-reference to em_sample_support.
referenced_by_em_sample_support
cross-reference from em_sample_support.
em_sample_support.citation_id
This data item is a pointer to attribute id
in category citation in the CITATION category.
em_sample_support.details
Any additional details concerning the sample support.
The grid was coated with gold prior to use
CARBON
FORMVAR PLUS CARBON
CELLULOSE ACETATE PLUS CARBON
PARLODION PLUS CARBON
HOLEY CARBON
The support material covering the em grid.
COPPER
COPPER/PALLADIUM
COPPER/RHODIUM
GOLD
GRAPHENE OXIDE
NICKEL
NICKEL/TITANIUM
PLATINUM
SILICON NITRIDE
TUNGSTEN
TITANIUM
MOLYBDENUM
The name of the material from which the grid is made.
em_sample_support.grid_mesh_size
The value of the mesh size (divisions per inch) of the em grid.
400
em_sample_support.grid_type
A description of the grid type.
em_sample_support.method
A description of the method used to produce the support film.
1%formvar in chloroform cast on distilled water
em_sample_support.pretreatment
A description of the grid plus support film pretreatment.
glow-discharged for 30 sec in argon
em_sample_support.id
PRIMARY KEY
em_sample_support.specimen_id
This data item is a pointer to attribute id in category em_sample_preparation in the EM_SPECIMEN category.
0
em_shadowing
Data items related to shadowing of an EM specimen
Example 1
<PDBx:em_shadowingCategory>
<PDBx:em_shadowing id="1" specimen_id="1">
<PDBx:angle>45</PDBx:angle>
<PDBx:details>shadowing was used to create a platinum replica</PDBx:details>
<PDBx:material>Platinum</PDBx:material>
<PDBx:thickness>3</PDBx:thickness>
</PDBx:em_shadowing>
</PDBx:em_shadowingCategory>
1
1
0
1
1
1
1
1
1
1
em_shadowingCategory
This property indicates that datablock
has a category holder em_shadowingCategory.
em_shadowingCategory
This property indicates that em_shadowingCategory.
has a category em_shadowing.
em_shadowingItem
Abstract datatype property for em_shadowing items.
reference_to_em_shadowing
cross-reference to em_shadowing.
referenced_by_em_shadowing
cross-reference from em_shadowing.
em_shadowing.angle
The shadowing angle (degrees)
20
em_shadowing.details
Additional details about specimen shadowing
rotary shadowing
directional shadowing
shadowing was used to create a carbon replica
em_shadowing.material
The chemical, compound or material used for shadowing
Platinum
em_shadowing.thickness
Thickness of the deposited shadow coat, in angstroms.
em_shadowing.id
PRIMARY KEY
em_shadowing.specimen_id
Foreign key relationship to the EM SPECIMEN category
0
em_single_particle_entity
Data items in the EM_SINGLE_PARTICLE_ENTITY category provide
the details of the symmetry for a single particle entity type.
Example
<PDBx:em_single_particle_entityCategory>
<PDBx:em_single_particle_entity id="1" image_processing_id="1">
<PDBx:point_symmetry>I</PDBx:point_symmetry>
</PDBx:em_single_particle_entity>
</PDBx:em_single_particle_entityCategory>
1
1
0
1
0
1
1
1
em_single_particle_entityCategory
This property indicates that datablock
has a category holder em_single_particle_entityCategory.
em_single_particle_entityCategory
This property indicates that em_single_particle_entityCategory.
has a category em_single_particle_entity.
em_single_particle_entityItem
Abstract datatype property for em_single_particle_entity items.
reference_to_em_single_particle_entity
cross-reference to em_single_particle_entity.
referenced_by_em_single_particle_entity
cross-reference from em_single_particle_entity.
em_single_particle_entity.entry_id
This data item is a pointer to attribute id in category entry in the ENTRY category.
em_single_particle_entity.point_symmetry
Point symmetry symbol, either Cn, Dn, T, O, or I
ASYMMETRIC
CYCLIC
DIHEDRAL
TETRAHEDRAL
OCTAHEDRAL
ICOSAHEDRAL
MIXED SYMMETRY
The single particle symmetry type.
em_single_particle_entity.id
PRIMARY KEY
em_single_particle_entity.image_processing_id
pointer to attribute id in category em_image_processing.
0
em_software
Description of the software that was used for data collection, data processing,
data analysis, structure calculations and refinement. The description should
include the name of the software, the author of the software and the version used.
Example 1
<PDBx:em_softwareCategory>
<PDBx:em_software id="1">
<PDBx:category>IMAGE ACQUISITION</PDBx:category>
<PDBx:details xsi:nil="true" />
<PDBx:name>Leginon</PDBx:name>
<PDBx:version>1.3</PDBx:version>
</PDBx:em_software>
<PDBx:em_software id="2">
<PDBx:category>PARTICLE SELECTION</PDBx:category>
<PDBx:details xsi:nil="true" />
<PDBx:name>X3D</PDBx:name>
<PDBx:version xsi:nil="true" />
</PDBx:em_software>
<PDBx:em_software id="3">
<PDBx:category>BACKGROUND MASKING</PDBx:category>
<PDBx:details xsi:nil="true" />
<PDBx:name>bsoft</PDBx:name>
<PDBx:version>1.1</PDBx:version>
</PDBx:em_software>
<PDBx:em_software id="4">
<PDBx:category>RECONSTRUCTION</PDBx:category>
<PDBx:details>em3dr2 -low 20</PDBx:details>
<PDBx:name>EM2DR2</PDBx:name>
<PDBx:version>3.2</PDBx:version>
</PDBx:em_software>
<PDBx:em_software id="5">
<PDBx:category>EULER ASSIGNMENT</PDBx:category>
<PDBx:details xsi:nil="true" />
<PDBx:name>erandom</PDBx:name>
<PDBx:version xsi:nil="true" />
</PDBx:em_software>
<PDBx:em_software id="6">
<PDBx:category>CTF CORRECTION</PDBx:category>
<PDBx:details xsi:nil="true" />
<PDBx:name>bctf</PDBx:name>
<PDBx:version xsi:nil="true" />
</PDBx:em_software>
<PDBx:em_software id="7">
<PDBx:category>MODEL FITTING</PDBx:category>
<PDBx:details xsi:nil="true" />
<PDBx:name>chimera</PDBx:name>
<PDBx:version>1.6</PDBx:version>
</PDBx:em_software>
</PDBx:em_softwareCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
em_softwareCategory
This property indicates that datablock
has a category holder em_softwareCategory.
em_softwareCategory
This property indicates that em_softwareCategory.
has a category em_software.
em_softwareItem
Abstract datatype property for em_software items.
reference_to_em_software
cross-reference to em_software.
referenced_by_em_software
cross-reference from em_software.
IMAGE ACQUISITION
PARTICLE SELECTION
VOLUME SELECTION
CLASSIFICATION
MASKING
RECONSTRUCTION
INITIAL EULER ASSIGNMENT
FINAL EULER ASSIGNMENT
CTF CORRECTION
LAYERLINE INDEXING
DIFFRACTION INDEXING
MODEL FITTING
MODEL REFINEMENT
SERIES ALIGNMENT
MOLECULAR REPLACEMENT
LATTICE DISTORTION CORRECTION
SYMMETRY DETERMINATION
CRYSTALLOGRAPHY MERGING
EWALD SPHERE CORRECTION
OTHER
The purpose of the software.
em_software.details
Details about the software used.
EMAN2 e2boxer.py was used to automatically select particle images.
em_software.fitting_id
pointer to attribute id in category em_3d_fitting in the EM_3D_FITTING category.
em_software.image_processing_id
pointer to attribute id in category em_image_processing in the EM_IMAGE_PROCESSING category.
em_software.imaging_id
pointer to attribute id in category em_imaging in the EM_IMAGING category.
em_software.name
The name of the software package used, e.g., RELION. Depositors are strongly
encouraged to provide a value in this field.
EMAN
Imagic
Spider
Bsoft
UCSF-Chimera
em_software.version
The version of the software.
9.03
2.1
em_software.id
PRIMARY KEY
0
em_specimen
Data items in the EMD_SPECIMEN category record details
about specimens prepared for imaging by electron microscopy.
Example 1 -- based on PDB 2FL8
<PDBx:em_specimenCategory>
<PDBx:em_specimen experiment_id="1" id="1">
<PDBx:embedding_applied>NO</PDBx:embedding_applied>
<PDBx:shadowing_applied>NO</PDBx:shadowing_applied>
<PDBx:staining_applied>NO</PDBx:staining_applied>
<PDBx:vitrification_applied>YES</PDBx:vitrification_applied>
</PDBx:em_specimen>
</PDBx:em_specimenCategory>
0
1
0
1
1
1
1
1
1
1
1
1
1
1
em_specimenCategory
This property indicates that datablock
has a category holder em_specimenCategory.
em_specimenCategory
This property indicates that em_specimenCategory.
has a category em_specimen.
em_specimenItem
Abstract datatype property for em_specimen items.
reference_to_em_specimen
cross-reference to em_specimen.
referenced_by_em_specimen
cross-reference from em_specimen.
em_specimen.concentration
The concentration (in milligrams per milliliter, mg/ml)
of the complex in the sample.
1.35
em_specimen.details
A description of any additional details of the specimen preparation.
This sample was monodisperse.
Au was deposited at a 30 degree angle to 15 nm thickness.
Colloidal gold particles were deposited by dipping into dilute solution.
The specimen was frozen at high pressure using the bal-tec hpm 010 instrument.
The embedded sample was sectioned at 100 K to 50 nm final thickness.
YES
NO
'YES' indicates that the specimen has been embedded.
YES
NO
'YES' indicates that the specimen has been shadowed.
YES
NO
'YES' indicates that the specimen has been stained.
YES
NO
'YES' indicates that the specimen was vitrified by cryopreservation.
em_specimen.experiment_id
Pointer to attribute id in category em_experiment.
em_specimen.id
PRIMARY KEY
0
em_staining
Staining category
Example 1
<PDBx:em_stainingCategory>
<PDBx:em_staining id="1">
<PDBx:material>Uranyl Acetate</PDBx:material>
<PDBx:specimen_id>1</PDBx:specimen_id>
<PDBx:type>NEGATIVE</PDBx:type>
</PDBx:em_staining>
</PDBx:em_stainingCategory>
0
1
1
1
1
1
1
1
1
em_stainingCategory
This property indicates that datablock
has a category holder em_stainingCategory.
em_stainingCategory
This property indicates that em_stainingCategory.
has a category em_staining.
em_stainingItem
Abstract datatype property for em_staining items.
reference_to_em_staining
cross-reference to em_staining.
referenced_by_em_staining
cross-reference from em_staining.
em_staining.details
Staining procedure used in the specimen preparation.
Negatively stained EM specimens were prepared using a carbon-sandwich technique
and uranyl-formate stain.
em_staining.material
The staining material.
Uranyl Acetate
em_staining.specimen_id
Foreign key relationship to the EM SPECIMEN category
NEGATIVE
POSITIVE
NONE
type of staining
em_staining.id
PRIMARY KEY
0
em_start_model
The startup model employed to begin refinement of the parameters for
a 3DEM reconstruction
Example 1 -- based on PDB 3IYD
<PDBx:em_start_modelCategory>
<PDBx:em_start_model id="1" image_processing_id="1">
<PDBx:details>a map created from PDB entry 3DXJ was gaussian blurred to 60 Angstroms</PDBx:details>
<PDBx:pdb_id>3DXJ</PDBx:pdb_id>
<PDBx:type>PDB ENTRY</PDBx:type>
</PDBx:em_start_model>
</PDBx:em_start_modelCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
1
1
1
em_start_modelCategory
This property indicates that datablock
has a category holder em_start_modelCategory.
em_start_modelCategory
This property indicates that em_start_modelCategory.
has a category em_start_model.
em_start_modelItem
Abstract datatype property for em_start_model items.
reference_to_em_start_model
cross-reference to em_start_model.
referenced_by_em_start_model
cross-reference from em_start_model.
em_start_model.details
Any additional details about generating the startup model
em_start_model.emdb_id
EMDB id of the map used as the startup model
EMD-12345
em_start_model.insilico_model
Description of the "in silico" model used to generate the startup model
em_start_model.orthogonal_tilt_angle1
Tilt angle for the 1st image set of the orthogonal tilt pairs
-45
em_start_model.orthogonal_tilt_angle2
Tilt angle for the 2nd image set of the orthogonal tilt pairs
45
em_start_model.orthogonal_tilt_num_images
number of images used to generate the orthogonal tilt startup model
40
em_start_model.other
Description of other method/source used to generate the startup model
em_start_model.pdb_id
PDB id of the model coordinates used to generate the startup model
em_start_model.random_conical_tilt_angle
Angular difference between the conical tilt images used to generate the startup model
60
em_start_model.random_conical_tilt_num_images
number of images used to generate the random conical tilt startup model
40
RANDOM CONICAL TILT
ORTHOGONAL TILT
EMDB MAP
PDB ENTRY
INSILICO MODEL
NONE
OTHER
Type of startup model (map density) used to initiate the reconstruction
em_start_model.id
PRIMARY KEY
em_start_model.image_processing_id
Foreign key to the EM_IMAGE_PROCESSING category
0
em_structure_factors
Listing of all structure factor files associated with the EM entry
Example 1
<PDBx:em_structure_factorsCategory>
<PDBx:em_structure_factors experiment_id="1" id="1">
<PDBx:details xsi:nil="true" />
<PDBx:file>emd-1234-sf.cif</PDBx:file>
</PDBx:em_structure_factors>
</PDBx:em_structure_factorsCategory>
0
1
1
1
1
1
em_structure_factorsCategory
This property indicates that datablock
has a category holder em_structure_factorsCategory.
em_structure_factorsCategory
This property indicates that em_structure_factorsCategory.
has a category em_structure_factors.
em_structure_factorsItem
Abstract datatype property for em_structure_factors items.
reference_to_em_structure_factors
cross-reference to em_structure_factors.
referenced_by_em_structure_factors
cross-reference from em_structure_factors.
em_structure_factors.details
Details about the structure factor file.
em_structure_factors.file
The name of the structure factor file associated with the map entry
em_structure_factors.experiment_id
This data item is a pointer to the EM EXPERIMENT category.
em_structure_factors.id
PRIMARY KEY
0
em_structure_factors_depositor_info
Structure factor files associated with the EM entry
Example 1
<PDBx:em_structure_factors_depositor_infoCategory>
<PDBx:em_structure_factors_depositor_info id="1">
<PDBx:details xsi:nil="true" />
<PDBx:experiment_id>1</PDBx:experiment_id>
<PDBx:upload_file_name>emd-1234-sf.cif</PDBx:upload_file_name>
</PDBx:em_structure_factors_depositor_info>
</PDBx:em_structure_factors_depositor_infoCategory>
0
1
0
1
1
1
1
em_structure_factors_depositor_infoCategory
This property indicates that datablock
has a category holder em_structure_factors_depositor_infoCategory.
em_structure_factors_depositor_infoCategory
This property indicates that em_structure_factors_depositor_infoCategory.
has a category em_structure_factors_depositor_info.
em_structure_factors_depositor_infoItem
Abstract datatype property for em_structure_factors_depositor_info items.
reference_to_em_structure_factors_depositor_info
cross-reference to em_structure_factors_depositor_info.
referenced_by_em_structure_factors_depositor_info
cross-reference from em_structure_factors_depositor_info.
em_structure_factors_depositor_info.details
Details about the structure factor file.
em_structure_factors_depositor_info.experiment_id
This data item is an optional pointer to the EM_EXPERIMENT category.
em_structure_factors_depositor_info.upload_file_name
The name of the structure factor file associated with the map entry
em_structure_factors_depositor_info.id
This data item is the unique identifier for the structure factor file.
0
em_supersede
List of newer entries that replace this entry.
1
1
0
1
1
1
1
em_supersedeCategory
This property indicates that datablock
has a category holder em_supersedeCategory.
em_supersedeCategory
This property indicates that em_supersedeCategory.
has a category em_supersede.
em_supersedeItem
Abstract datatype property for em_supersede items.
reference_to_em_supersede
cross-reference to em_supersede.
referenced_by_em_supersede
cross-reference from em_supersede.
em_supersede.date
Dated when the entry made supersede the other entry
em_supersede.details
Details
em_supersede.entry
Newer entry that replaces this entry
em_supersede.id
PRIMARY KEY
0
em_support_film
Data items to describe films supporting the specimen
Example 1 - based on PDB entry 1DYL and laboratory records for the
structure corresponding to PDB entry 1DYL
<PDBx:em_support_filmCategory>
<PDBx:em_support_film id="1">
<PDBx:material>CARBON</PDBx:material>
</PDBx:em_support_film>
</PDBx:em_support_filmCategory>
0
1
1
1
0
1
0
1
1
em_support_filmCategory
This property indicates that datablock
has a category holder em_support_filmCategory.
em_support_filmCategory
This property indicates that em_support_filmCategory.
has a category em_support_film.
em_support_filmItem
Abstract datatype property for em_support_film items.
reference_to_em_support_film
cross-reference to em_support_film.
referenced_by_em_support_film
cross-reference from em_support_film.
CARBON
FORMVAR
CELLULOSE ACETATE
PARLODION
GOLD
GRAPHENE
GRAPHENE OXIDE
The support material covering the em grid.
em_support_film.sample_support_id
Pointer to EM SAMPLE SUPPORT
em_support_film.thickness
Thickness of the support film, in angstroms
CONTINUOUS
LACEY
HOLEY
HOLEY ARRAY
The topology of the material from which the grid is made.
em_support_film.id
PRIMARY KEY
0
em_tomography
Microscopy parameters only relevant for tomography
Example 1
<PDBx:em_tomographyCategory>
<PDBx:em_tomography id="1" imaging_id="1">
<PDBx:axis1_angle_increment>2</PDBx:axis1_angle_increment>
<PDBx:axis1_max_angle>70.</PDBx:axis1_max_angle>
<PDBx:axis1_min_angle>-70.</PDBx:axis1_min_angle>
<PDBx:axis2_angle_increment>2</PDBx:axis2_angle_increment>
<PDBx:axis2_max_angle>70.</PDBx:axis2_max_angle>
<PDBx:axis2_min_angle>-70.</PDBx:axis2_min_angle>
<PDBx:dual_tilt_axis_rotation>90.</PDBx:dual_tilt_axis_rotation>
</PDBx:em_tomography>
</PDBx:em_tomographyCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
1
em_tomographyCategory
This property indicates that datablock
has a category holder em_tomographyCategory.
em_tomographyCategory
This property indicates that em_tomographyCategory.
has a category em_tomography.
em_tomographyItem
Abstract datatype property for em_tomography items.
reference_to_em_tomography
cross-reference to em_tomography.
referenced_by_em_tomography
cross-reference from em_tomography.
em_tomography.axis1_angle_increment
The angle increment of specimen tilting to obtain the
recorded images (axis 1).
2
em_tomography.axis1_max_angle
The maximum angle at which the specimen was tilted to obtain
recorded images (axis 1).
70
em_tomography.axis1_min_angle
The minimum angle at which the specimen was tilted to obtain
recorded images (axis 1).
-70
em_tomography.axis2_angle_increment
The angle increment of specimen tilting to obtain the
recorded images (axis 2).
2
em_tomography.axis2_max_angle
The maximum angle at which the specimen was tilted to obtain
recorded images (axis 2).
70
em_tomography.axis2_min_angle
The minimum angle at which the specimen was tilted to obtain
recorded images (axis 2).
-70
em_tomography.dual_tilt_axis_rotation
Angular difference between axis1 and axis2 in degrees
em_tomography.id
PRIMARY KEY
em_tomography.imaging_id
Foreign key to the EM IMAGING category
0
em_tomography_specimen
Description specimen preparation for imaging using tomography.
0
1
0
1
0
1
0
1
0
1
1
1
1
em_tomography_specimenCategory
This property indicates that datablock
has a category holder em_tomography_specimenCategory.
em_tomography_specimenCategory
This property indicates that em_tomography_specimenCategory.
has a category em_tomography_specimen.
em_tomography_specimenItem
Abstract datatype property for em_tomography_specimen items.
reference_to_em_tomography_specimen
cross-reference to em_tomography_specimen.
referenced_by_em_tomography_specimen
cross-reference from em_tomography_specimen.
em_tomography_specimen.cryo_protectant
The type of cryo-protectant used during specimen preparation.
2% glycerol
em_tomography_specimen.details
Any additional details about specimen preparation.
Axonemes were mixed with 15-nm colloidal gold suspension conjugated with BSA.
Suspended axonemes plus colloidal gold were loaded onto grids and plunge-frozen
in liquid ethane with a Leica EM GP automated plunge-freezing device.
YES
NO
'YES' indicates that fiducial markers were used in the specimen preparation
YES
NO
'YES' indicates that high pressure freezing was used in the specimen preparation
NO SECTIONING
ULTRAMICROTOMY
FOCUSED ION BEAM
The type of sectioning performed during specimen preparation.
em_tomography_specimen.specimen_id
Foreign key relationship to the EM SPECIMEN category
em_tomography_specimen.id
PRIMARY KEY
0
em_ultramicrotomy
Description of sectioning by ultramicrotomy
0
1
1
1
1
1
1
1
1
1
1
em_ultramicrotomyCategory
This property indicates that datablock
has a category holder em_ultramicrotomyCategory.
em_ultramicrotomyCategory
This property indicates that em_ultramicrotomyCategory.
has a category em_ultramicrotomy.
em_ultramicrotomyItem
Abstract datatype property for em_ultramicrotomy items.
reference_to_em_ultramicrotomy
cross-reference to em_ultramicrotomy.
referenced_by_em_ultramicrotomy
cross-reference from em_ultramicrotomy.
em_ultramicrotomy.details
Additional details about the ultramicrotomy sample preparation
em_ultramicrotomy.em_tomography_specimen_id
Foreign key relationship to the EM TOMOGRAPHY SPECIMEN category
em_ultramicrotomy.final_thickness
Final thickness of the sectioned sample, in nanometers
60
em_ultramicrotomy.instrument
Ultramicrotome instrument used for sectioning
Leica EM UC7
em_ultramicrotomy.temperature
Temperature of the sample during microtome sectioning, in kelvins
100
em_ultramicrotomy.id
PRIMARY KEY
0
em_virus_entity
Data items in the EM_VIRUS_ENTITY category record details
of the icosahedral virus.
Example 1 - based on PDB entry 1DYL and laboratory records for the
structure corresponding to PDB entry 1DYL
<PDBx:em_virus_entityCategory>
<PDBx:em_virus_entity entity_assembly_id="1" id="1">
<PDBx:empty>NO</PDBx:empty>
<PDBx:enveloped>YES</PDBx:enveloped>
<PDBx:ictvdb_id>00.073.0.01.023</PDBx:ictvdb_id>
<PDBx:virus_host_category>VERTERBRATES</PDBx:virus_host_category>
<PDBx:virus_host_species>HOMO SAPIENS</PDBx:virus_host_species>
<PDBx:virus_isolate>STRAIN</PDBx:virus_isolate>
<PDBx:virus_type>VIRUS</PDBx:virus_type>
</PDBx:em_virus_entity>
</PDBx:em_virus_entityCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
1
em_virus_entityCategory
This property indicates that datablock
has a category holder em_virus_entityCategory.
em_virus_entityCategory
This property indicates that em_virus_entityCategory.
has a category em_virus_entity.
em_virus_entityItem
Abstract datatype property for em_virus_entity items.
reference_to_em_virus_entity
cross-reference to em_virus_entity.
referenced_by_em_virus_entity
cross-reference from em_virus_entity.
em_virus_entity.details
Additional details about this virus entity
YES
NO
Flag to indicate if the virus is empty or not.
YES
NO
Flag to indicate if the virus is enveloped or not.
em_virus_entity.ictvdb_id
The International Committee on Taxonomy of Viruses
(ICTV) Taxon Identifier is the Virus Code used throughout the
ICTV database (ICTVdb). The ICTVdb id is the appropriate
identifier used by the International Committee on Taxonomy of Viruses
Resource. Reference: Virus Taxonomy, Academic Press (1999).
ISBN:0123702003.
NOTE: ICTV no longer maintains ids; maintained for legacy only.
NL-54
em_virus_entity.virus_host_category
The host category description for the virus.
ALGAE
ARCHAEA
BACTERIA(EUBACTERIA)
FUNGI
INVERTEBRATES
PLANTAE (HIGHER PLANTS)
PROTOZOA
VERTEBRATES
em_virus_entity.virus_host_growth_cell
The host cell from which the virus was isolated.
HELA
CHO
em_virus_entity.virus_host_species
The host species from which the virus was isolated.
homo sapiens
gallus gallus
STRAIN
SEROTYPE
SEROCOMPLEX
SUBSPECIES
SPECIES
OTHER
The isolate from which the virus was obtained.
VIRION
SATELLITE
PRION
VIROID
VIRUS-LIKE PARTICLE
The type of virus.
em_virus_entity.entity_assembly_id
This data item is a pointer to attribute id in category em_virus_entity in the
ENTITY_ASSEMBLY category.
em_virus_entity.id
PRIMARY KEY
0
em_virus_natural_host
Data items in this category record details of a virus entity.
0
1
0
1
0
1
1
1
em_virus_natural_hostCategory
This property indicates that datablock
has a category holder em_virus_natural_hostCategory.
em_virus_natural_hostCategory
This property indicates that em_virus_natural_hostCategory.
has a category em_virus_natural_host.
em_virus_natural_hostItem
Abstract datatype property for em_virus_natural_host items.
reference_to_em_virus_natural_host
cross-reference to em_virus_natural_host.
referenced_by_em_virus_natural_host
cross-reference from em_virus_natural_host.
em_virus_natural_host.ncbi_tax_id
The NCBI taxonomy id for the natural host organism of the virus
9606
9031
em_virus_natural_host.organism
The host organism from which the virus was isolated.
Homo sapiens
Gallus gallus
em_virus_natural_host.strain
The strain of the host organism from which the virus was
obtained, if relevant.
DH5a
BMH 71-18
em_virus_natural_host.entity_assembly_id
Pointer to attribute id in category em_entity_assembly.
em_virus_natural_host.id
PRIMARY KEY
0
em_virus_shell
Data items in the EMD_VIRUS_SHELL category record details
of the viral shell number, shell diameter, and icosahedral triangulation number.
Example 1 -- Bluetongue Virus
<PDBx:em_virus_shellCategory>
<PDBx:em_virus_shell entity_assembly_id="1" id="1">
<PDBx:diameter>348</PDBx:diameter>
<PDBx:name>VP7 layer</PDBx:name>
<PDBx:triangulation>13</PDBx:triangulation>
</PDBx:em_virus_shell>
<PDBx:em_virus_shell entity_assembly_id="1" id="2">
<PDBx:diameter>348</PDBx:diameter>
<PDBx:name>VP3 layer</PDBx:name>
<PDBx:triangulation>2</PDBx:triangulation>
</PDBx:em_virus_shell>
</PDBx:em_virus_shellCategory>
0
1
0
1
0
1
1
1
em_virus_shellCategory
This property indicates that datablock
has a category holder em_virus_shellCategory.
em_virus_shellCategory
This property indicates that em_virus_shellCategory.
has a category em_virus_shell.
em_virus_shellItem
Abstract datatype property for em_virus_shell items.
reference_to_em_virus_shell
cross-reference to em_virus_shell.
referenced_by_em_virus_shell
cross-reference from em_virus_shell.
em_virus_shell.diameter
The value of the diameter (in angstroms) for this virus shell.
524.0
em_virus_shell.name
The name for this virus shell.
em_virus_shell.triangulation
The triangulation number, T, describes the organization of subunits within an
icosahedron. T is defined as T= h^2 + h*k + k^2, where h and k are positive
integers that define the position of the five-fold vertex on the original
hexagonal net.
27
em_virus_shell.entity_assembly_id
The value of attribute entity_assembly_id in category em_virus_shell is
a pointer to attribute id
in category em_entity_assembly category.
em_virus_shell.id
PRIMARY KEY
0
em_virus_synthetic
Data items in this category record details of a synthetic virus entity.
0
1
0
1
0
1
1
1
em_virus_syntheticCategory
This property indicates that datablock
has a category holder em_virus_syntheticCategory.
em_virus_syntheticCategory
This property indicates that em_virus_syntheticCategory.
has a category em_virus_synthetic.
em_virus_syntheticItem
Abstract datatype property for em_virus_synthetic items.
reference_to_em_virus_synthetic
cross-reference to em_virus_synthetic.
referenced_by_em_virus_synthetic
cross-reference from em_virus_synthetic.
em_virus_synthetic.ncbi_tax_id
The NCBI taxonomy ID of the host species from which the virus was isolated
10804
9606
em_virus_synthetic.organism
The host organism from which the virus was isolated.
Homo sapiens
Gallus gallus
em_virus_synthetic.strain
The strain of the host organism from which the virus was
obtained, if relevant.
DH5a
BMH 71-18
em_virus_synthetic.entity_assembly_id
Pointer to attribute id in category em_entity_assembly.
em_virus_synthetic.id
PRIMARY KEY
0
em_vitrification
Data items in the EM_VITRIFICATION category
record details about the method and cryogen used in
rapid freezing of the sample on the grid prior to its
insertion in the electron microscope
Example 1 - based on PDB entry 1DYL and laboratory records for the
structure corresponding to PDB entry 1DYL
<PDBx:em_vitrificationCategory>
<PDBx:em_vitrification id="1">
<PDBx:cryogen_name>ETHANE</PDBx:cryogen_name>
<PDBx:details> SAMPLES WERE PREPARED AS THIN
LAYERS OF VITREOUS ICE AND
MAINTAINED AT NEAR LIQUID NITROGEN
TEMPERATURE IN THE ELECTRON MICROSCOPE
WITH A GATAN 626-0300 CRYOTRANSFER
HOLDER.</PDBx:details>
<PDBx:entry_id>1DYL</PDBx:entry_id>
<PDBx:humidity>90</PDBx:humidity>
<PDBx:instrument xsi:nil="true" />
<PDBx:method>PLUNGE VITRIFICATION</PDBx:method>
<PDBx:sample_preparation_id>1</PDBx:sample_preparation_id>
<PDBx:temp>95</PDBx:temp>
<PDBx:time_resolved_state xsi:nil="true" />
</PDBx:em_vitrification>
</PDBx:em_vitrificationCategory>
0
1
0
1
0
1
0
1
1
1
0
1
0
1
0
1
0
1
0
1
0
1
1
1
em_vitrificationCategory
This property indicates that datablock
has a category holder em_vitrificationCategory.
em_vitrificationCategory
This property indicates that em_vitrificationCategory.
has a category em_vitrification.
em_vitrificationItem
Abstract datatype property for em_vitrification items.
reference_to_em_vitrification
cross-reference to em_vitrification.
referenced_by_em_vitrification
cross-reference from em_vitrification.
em_vitrification.chamber_temperature
The temperature (in kelvin) of the sample just prior to vitrification.
298
em_vitrification.citation_id
This data item is a pointer to attribute id in category citation in the
CITATION category.
HELIUM
NITROGEN
PROPANE
ETHANE
ETHANE-PROPANE
METHANE
FREON 22
FREON 12
OTHER
This is the name of the cryogen.
em_vitrification.details
Any additional details relating to vitrification.
Vitrification carried out in argon atmosphere.
em_vitrification.entry_id
This data item is a pointer to attribute id in category entry in the ENTRY category.
em_vitrification.humidity
Relative humidity (%) of air surrounding the specimen just prior to
vitrification.
90
CRYOSOL VITROJET
EMS-002 RAPID IMMERSION FREEZER
FEI VITROBOT MARK I
FEI VITROBOT MARK II
FEI VITROBOT MARK III
FEI VITROBOT MARK IV
GATAN CRYOPLUNGE 3
HOMEMADE PLUNGER
LEICA PLUNGER
LEICA EM GP
LEICA EM CPC
LEICA KF80
REICHERT-JUNG PLUNGER
SPOTITON
ZEISS PLUNGE FREEZER CRYOBOX
The type of instrument used in the vitrification process.
em_vitrification.method
The procedure for vitrification.
plunge freezing
em_vitrification.sample_preparation_id
This data item is a pointer to attribute id in category em_sample_preparation in the
EM_SAMPLE_PREPARATION category.
em_vitrification.temp
The vitrification temperature (in kelvin), e.g.,
temperature of the plunge instrument cryogen bath.
90
em_vitrification.time_resolved_state
The length of time after an event effecting the sample that
vitrification was induced and a description of the event.
plunge 30 msec after spraying with effector
em_vitrification.id
PRIMARY KEY
em_vitrification.specimen_id
This data item is a pointer to attribute id in category em_specimen
0
em_volume_selection
Volume selection in image processing
Example 1 - based on PDB entry 1DYL and laboratory records for the
structure corresponding to PDB entry 1DYL
<PDBx:em_volume_selectionCategory>
<PDBx:em_volume_selection id="1" image_processing_id="1">
<PDBx:details xsi:nil="true" />
<PDBx:method>INTERACTIVE</PDBx:method>
<PDBx:num_volumes_extracted>5267</PDBx:num_volumes_extracted>
</PDBx:em_volume_selection>
</PDBx:em_volume_selectionCategory>
0
1
0
1
1
1
1
1
0
1
1
1
em_volume_selectionCategory
This property indicates that datablock
has a category holder em_volume_selectionCategory.
em_volume_selectionCategory
This property indicates that em_volume_selectionCategory.
has a category em_volume_selection.
em_volume_selectionItem
Abstract datatype property for em_volume_selection items.
reference_to_em_volume_selection
cross-reference to em_volume_selection.
referenced_by_em_volume_selection
cross-reference from em_volume_selection.
em_volume_selection.details
Any additional details used for selecting volumes.
negative monitor contrast facilitated volume picking
em_volume_selection.method
The method used for selecting volumes.
volumes picked interactively
em_volume_selection.num_tomograms
The number of tomograms used in the extraction/selection
20
em_volume_selection.num_volumes_extracted
The number of volumes selected from the projection set of images.
840
em_volume_selection.reference_model
Description of reference model used for volume selection
em_volume_selection.id
PRIMARY KEY
em_volume_selection.image_processing_id
The value of attribute image_processing_id in category em_volume_selection points to
the EM_IMAGE_PROCESSING category.
0
entity
Data items in the ENTITY category record details (such as
chemical composition, name and source) about the molecular
entities that are present in the crystallographic structure.
Items in the various ENTITY subcategories provide a full
chemical description of these molecular entities.
Entities are of three types: polymer, non-polymer and water.
Note that the water category includes only water; ordered
solvent such as sulfate ion or acetone would be described as
individual non-polymer entities.
The ENTITY category is specific to macromolecular CIF
applications and replaces the function of the CHEMICAL category
in the CIF core.
It is important to remember that the ENTITY data are not the
result of the crystallographic experiment; those results are
represented by the ATOM_SITE data items. ENTITY data items
describe the chemistry of the molecules under investigation
and can most usefully be thought of as the ideal groups to which
the structure is restrained or constrained during refinement.
It is also important to remember that entities do not correspond
directly to the enumeration of the contents of the asymmetric
unit. Entities are described only once, even in those structures
that contain multiple observations of an entity. The
STRUCT_ASYM data items, which reference the entity list,
describe and label the contents of the asymmetric unit.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:entityCategory>
<PDBx:entity id="1">
<PDBx:details> The enzymatically competent form of HIV
protease is a dimer. This entity
corresponds to one monomer of an active dimer.</PDBx:details>
<PDBx:formula_weight>10916</PDBx:formula_weight>
<PDBx:type>polymer</PDBx:type>
</PDBx:entity>
<PDBx:entity id="2">
<PDBx:details xsi:nil="true" />
<PDBx:formula_weight>762</PDBx:formula_weight>
<PDBx:type>non-polymer</PDBx:type>
</PDBx:entity>
<PDBx:entity id="3">
<PDBx:details xsi:nil="true" />
<PDBx:formula_weight>18</PDBx:formula_weight>
<PDBx:type>water</PDBx:type>
</PDBx:entity>
</PDBx:entityCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
entityCategory
This property indicates that datablock
has a category holder entityCategory.
entityCategory
This property indicates that entityCategory.
has a category entity.
entityItem
Abstract datatype property for entity items.
reference_to_entity
cross-reference to entity.
referenced_by_entity
cross-reference from entity.
entity.details
A description of special aspects of the entity.
entity.formula_weight
Formula mass in daltons of the entity.
entity.pdbx_description
A description of the entity.
Corresponds to the compound name in the PDB format.
DNA (5'-D(*GP*(CH3)CP*GP*(CH3)CP*GP*C)-3')
PROFLAVINE
PROTEIN (DEOXYRIBONUCLEASE I (E.C.3.1.21.1))
entity.pdbx_ec
Enzyme Commission (EC) number(s)
2.7.7.7
entity.pdbx_entities_per_biological_unit
Number of entity molecules in the biological assembly.
1
2
3
entity.pdbx_formula_weight_exptl
Experimentally determined formula mass in daltons of the entity
MASS SPEC
Method used to determine attribute pdbx_formula_weight_exptl in category entity.
MASS SPEC
entity.pdbx_fragment
Entity fragment description(s).
KLENOW FRAGMENT
REPLICASE OPERATOR HAIRPIN
C-TERMINAL DOMAIN
entity.pdbx_modification
Description(s) of any chemical or post-translational modifications
entity.pdbx_mutation
Details about any entity mutation(s).
Y31H
DEL(298-323)
entity.pdbx_number_of_molecules
A place holder for the number of molecules of the entity in
the entry.
1
2
3
entity.pdbx_parent_entity_id
An identifier for the parent entity if this entity
is part of a complex entity. For instance a chimeric
entity may be decomposed into several independent
chemical entities where each component entity was
obtained from a different source.
1
2
3
entity.pdbx_target_id
The value of attribute target_id in category entity points to a TARGETDB target idenitifier
from which this entity was generated.
nat
man
syn
The method by which the sample for the entity was produced.
Entities isolated directly from natural sources (tissues, soil
samples etc.) are expected to have further information in the
ENTITY_SRC_NAT category. Entities isolated from genetically
manipulated sources are expected to have further information in
the ENTITY_SRC_GEN category.
polymer
non-polymer
macrolide
water
branched
Defines the type of the entity.
Polymer entities are expected to have corresponding
ENTITY_POLY and associated entries.
Non-polymer entities are expected to have corresponding
CHEM_COMP and associated entries.
Water entities are not expected to have corresponding
entries in the ENTITY category.
entity.id
The value of attribute id in category entity must uniquely identify a record in the
ENTITY list.
Note that this item need not be a number; it can be any unique
identifier.
0
entity_keywords
Data items in the ENTITY_KEYWORDS category specify keywords
relevant to the molecular entities. Note that this list of
keywords is separate from the list that is used for the
STRUCT_BIOL data items and is intended to provide only the
information that one would know about the molecular entity *if
one did not know its structure*. Hence polypeptides are simply
polypeptides, not cytokines or beta-alpha-barrels, and
polyribonucleic acids are simply poly-RNA, not transfer-
RNA.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:entity_keywordsCategory>
<PDBx:entity_keywords entity_id="2">
<PDBx:text>natural product, inhibitor, reduced peptide</PDBx:text>
</PDBx:entity_keywords>
</PDBx:entity_keywordsCategory>
0
1
0
1
0
1
0
1
0
1
1
entity_keywordsCategory
This property indicates that datablock
has a category holder entity_keywordsCategory.
entity_keywordsCategory
This property indicates that entity_keywordsCategory.
has a category entity_keywords.
entity_keywordsItem
Abstract datatype property for entity_keywords items.
reference_to_entity_keywords
cross-reference to entity_keywords.
referenced_by_entity_keywords
cross-reference from entity_keywords.
entity_keywords.pdbx_antibody_isotype
PDB placeholder.
entity_keywords.pdbx_ec
Enzyme Commission (EC) number(s)
2.7.7.7
entity_keywords.pdbx_fragment
Entity fragment description(s).
KLENOW FRAGMENT
REPLICASE OPERATOR HAIRPIN
C-TERMINAL DOMAIN
entity_keywords.pdbx_mutation
Entity mutation description(s).
Y31H
DEL(298-323)
entity_keywords.text
Keywords describing this entity.
polypeptide
natural product
polysaccharide
entity_keywords.entity_id
This data item is a pointer to attribute id in category entity in the ENTITY category.
0
entity_link
Data items in the ENTITY_LINK category give details about
the links between entities.
0
1
1
1
1
1
0
1
0
1
1
entity_linkCategory
This property indicates that datablock
has a category holder entity_linkCategory.
entity_linkCategory
This property indicates that entity_linkCategory.
has a category entity_link.
entity_linkItem
Abstract datatype property for entity_link items.
reference_to_entity_link
cross-reference to entity_link.
referenced_by_entity_link
cross-reference from entity_link.
entity_link.details
A description of special aspects of a link between
chemical components in the structure.
entity_link.entity_id_1
The entity ID of the first of the two entities joined by the
link.
This data item is a pointer to attribute id in category entity in the ENTITY
category.
entity_link.entity_id_2
The entity ID of the second of the two entities joined by the
link.
This data item is a pointer to attribute id in category entity in the ENTITY
category.
entity_link.entity_seq_num_1
For a polymer entity, the sequence number in the first of
the two entities containing the link.
This data item is a pointer to attribute num in category entity_poly_seq in the
ENTITY_POLY_SEQ category.
entity_link.entity_seq_num_2
For a polymer entity, the sequence number in the second of
the two entities containing the link.
This data item is a pointer to attribute num in category entity_poly_seq in the
ENTITY_POLY_SEQ category.
entity_link.link_id
This data item is a pointer to attribute id in category chem_link in the
CHEM_LINK category.
0
entity_name_com
Data items in the ENTITY_NAME_COM category record the common name
or names associated with the entity. In some cases, the entity
name may not be the same as the name of the biological structure.
For example, haemoglobin alpha chain would be the entity common
name, not haemoglobin.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:entity_name_comCategory>
<PDBx:entity_name_com entity_id="1">
<PDBx:name>HIV-1 protease monomer</PDBx:name>
</PDBx:entity_name_com>
<PDBx:entity_name_com entity_id="1">
<PDBx:name>HIV-1 PR monomer</PDBx:name>
</PDBx:entity_name_com>
<PDBx:entity_name_com entity_id="2">
<PDBx:name>acetyl-pepstatin</PDBx:name>
</PDBx:entity_name_com>
<PDBx:entity_name_com entity_id="2">
<PDBx:name>acetyl-Ile-Val-Asp-Statine-Ala-Ile-Statine</PDBx:name>
</PDBx:entity_name_com>
<PDBx:entity_name_com entity_id="3">
<PDBx:name>water</PDBx:name>
</PDBx:entity_name_com>
</PDBx:entity_name_comCategory>
0
1
0
1
1
entity_name_comCategory
This property indicates that datablock
has a category holder entity_name_comCategory.
entity_name_comCategory
This property indicates that entity_name_comCategory.
has a category entity_name_com.
entity_name_comItem
Abstract datatype property for entity_name_com items.
reference_to_entity_name_com
cross-reference to entity_name_com.
referenced_by_entity_name_com
cross-reference from entity_name_com.
entity_name_com.name
A common name for the entity.
HIV protease monomer
hemoglobin alpha chain
2-fluoro-1,4-dichloro benzene
arbutin
UNIPROT
AUTHOR
Provides the provenance of the name in the attribute name in category entity_name_com field
entity_name_com.entity_id
This data item is a pointer to attribute id in category entity in the ENTITY category.
0
entity_name_sys
Data items in the ENTITY_NAME_SYS category record the systematic
name or names associated with the entity and the system that
was used to construct the systematic name. In some cases, the
entity name may not be the same as the name of the biological
structure.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:entity_name_sysCategory>
<PDBx:entity_name_sys entity_id="1">
<PDBx:name>EC 3.4.23.16</PDBx:name>
</PDBx:entity_name_sys>
<PDBx:entity_name_sys entity_id="2">
<PDBx:name>acetyl-Ile-Val-Asp-Sta-Ala-Ile-Sta</PDBx:name>
</PDBx:entity_name_sys>
<PDBx:entity_name_sys entity_id="3">
<PDBx:name>water</PDBx:name>
</PDBx:entity_name_sys>
</PDBx:entity_name_sysCategory>
0
1
0
1
1
entity_name_sysCategory
This property indicates that datablock
has a category holder entity_name_sysCategory.
entity_name_sysCategory
This property indicates that entity_name_sysCategory.
has a category entity_name_sys.
entity_name_sysItem
Abstract datatype property for entity_name_sys items.
reference_to_entity_name_sys
cross-reference to entity_name_sys.
referenced_by_entity_name_sys
cross-reference from entity_name_sys.
entity_name_sys.name
The systematic name for the entity.
hydroquinone-beta-D-pyranoside
EC 2.1.1.1
2-fluoro-1,4-dichlorobenzene
entity_name_sys.system
The system used to generate the systematic name of the entity.
Chemical Abstracts conventions
enzyme convention
Sigma catalog
entity_name_sys.entity_id
This data item is a pointer to attribute id in category entity in the ENTITY category.
0
entity_poly
Data items in the ENTITY_POLY category record details about the
polymer, such as the type of the polymer, the number of
monomers and whether it has nonstandard features.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:entity_polyCategory>
<PDBx:entity_poly entity_id="1">
<PDBx:nstd_chirality>no</PDBx:nstd_chirality>
<PDBx:nstd_linkage>no</PDBx:nstd_linkage>
<PDBx:nstd_monomer>no</PDBx:nstd_monomer>
<PDBx:type>polypeptide(L)</PDBx:type>
<PDBx:type_details xsi:nil="true" />
</PDBx:entity_poly>
</PDBx:entity_polyCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
entity_polyCategory
This property indicates that datablock
has a category holder entity_polyCategory.
entity_polyCategory
This property indicates that entity_polyCategory.
has a category entity_poly.
entity_polyItem
Abstract datatype property for entity_poly items.
reference_to_entity_poly
cross-reference to entity_poly.
referenced_by_entity_poly
cross-reference from entity_poly.
no
n
yes
y
A flag to indicate whether the polymer contains at least
one monomer unit with chirality different from that specified in
attribute type in category entity_poly.
no
n
yes
y
A flag to indicate whether the polymer contains at least
one monomer-to-monomer link different from that implied by
attribute type in category entity_poly.
no
n
yes
y
A flag to indicate whether the polymer contains at least
one monomer that is not considered standard.
entity_poly.number_of_monomers
The number of monomers in the polymer.
entity_poly.pdbx_C_terminal_seq_one_letter_code
C-terminal cloning artifacts and/or HIS tag.
HHHHHH
entity_poly.pdbx_N_terminal_seq_one_letter_code
N-terminal cloning artifacts and/or HIS tag.
HHHHHH
Y
N
A code to indicate that this sequence should be assigned
a PDB sequence reference.
Y
Y
N
A flag to indicate that linking data is explicitly provided for this polymer
in the PDBX_ENTITY_POLY_COMP_LINK_LIST category
entity_poly.pdbx_seq_align_begin
The sequence position in the database sequence at which the
alignment with your sequence begins.
59
entity_poly.pdbx_seq_align_end
The sequence position in the database sequence at which the
alignment with your sequence ends.
685
entity_poly.pdbx_seq_db_id
The identifier for this sequence in the sequence data base.
P00730
EMBL
GB
PIR
SWS
UNP
The name of the sequence data base containing a database entry
for this sequence.
Enter UNP for a Uniport entry
Enter SWS for a Swiss-Prot entry
Enter GB for a GenBank entry
Enter EMBL for an European Molecular Biology Laboratory entry
Enter PIR for a Protein Information Resource entry
entity_poly.pdbx_seq_one_letter_code
Sequence of protein or nucleic acid polymer in standard one-letter
codes of amino acids or nucleotides. Non-standard amino
acids/nucleotides are represented by their Chemical
Component Dictionary (CCD) codes in
parenthesis. Deoxynucleotides are represented by the
specially-assigned 2-letter CCD codes in parenthesis,
with 'D' prefix added to their ribonucleotide
counterparts. For hybrid polymer, each residue is
represented by the code of its individual type. A
cyclic polymer is represented in linear sequence from
the chosen start to end.
A for Alanine or Adenosine-5'-monophosphate
C for Cysteine or Cytidine-5'-monophosphate
D for Aspartic acid
E for Glutamic acid
F for Phenylalanine
G for Glycine or Guanosine-5'-monophosphate
H for Histidine
I for Isoleucine or Inosinic Acid
L for Leucine
K for Lysine
M for Methionine
N for Asparagine or Unknown ribonucleotide
O for Pyrrolysine
P for Proline
Q for Glutamine
R for Arginine
S for Serine
T for Threonine
U for Selenocysteine or Uridine-5'-monophosphate
V for Valine
W for Tryptophan
Y for Tyrosine
(DA) for 2'-deoxyadenosine-5'-monophosphate
(DC) for 2'-deoxycytidine-5'-monophosphate
(DG) for 2'-deoxyguanosine-5'-monophosphate
(DT) for Thymidine-5'-monophosphate
(MSE) for Selenomethionine
(SEP) for Phosphoserine
(TPO) for Phosphothreonine
(PTR) for Phosphotyrosine
(PCA) for Pyroglutamic acid
(UNK) for Unknown amino acid
(ACE) for Acetylation cap
(NH2) for Amidation cap
(MSE)SHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGAAFNVEFD
entity_poly.pdbx_seq_one_letter_code_can
Canonical sequence of protein or nucleic acid polymer in standard
one-letter codes of amino acids or nucleotides,
corresponding to the sequence in
attribute pdbx_seq_one_letter_code in category entity_poly. Non-standard
amino acids/nucleotides are represented by the codes of
their parents if parent is specified in
attribute mon_nstd_parent_comp_id in category chem_comp, or by letter 'X' if
parent is not specified. Deoxynucleotides are
represented by their canonical one-letter codes of A,
C, G, or T.
For modifications with several parent amino acids,
all corresponding parent amino acid codes will be listed
(ex. chromophores).
MSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGAAFNVEFD
entity_poly.pdbx_seq_one_letter_code_sample
For cases in which the sample and model sequence differ this item contains
the sample chemical sequence expressed as string of one-letter amino acid codes.
Modified may be include as 'X' or with their 3-letter codes in parentheses.
A for alanine or adenine
B for ambiguous asparagine/aspartic-acid
R for arginine
N for asparagine
D for aspartic-acid
C for cysteine or cystine or cytosine
Q for glutamine
E for glutamic-acid
Z for ambiguous glutamine/glutamic acid
G for glycine or guanine
H for histidine
I for isoleucine
L for leucine
K for lysine
M for methionine
F for phenylalanine
P for proline
S for serine
T for threonine or thymine
W for tryptophan
Y for tyrosine
V for valine
U for uracil
O for water
X for other
entity_poly.pdbx_seq_three_letter_code
Chemical sequence expressed as string of three-letter
amino acid codes.
alanine
ALA
arginine
ARG
asparagine
ASN
aspartic-acid
ASP
ambiguous asparagine/aspartic-acid
ASX
cysteine
CYS
glutamine
GLN
glutamic-acid
GLU
glycine
GLY
ambiguous glutamine/glutamic acid
GLX
histidine
HIS
isoleucine
ILE
leucine
LEU
lysine
LYS
methionine
MET
phenylalanine
PHE
proline
PRO
serine
SER
threonine
THR
tryptophan
TRP
tyrosine
TYR
valine
VAL
1-methyladenosine
1MA
5-methycytosine
5MC
2(prime)-O-methycytodine
OMC
1-methyguanosine
1MG
N(2)-methyguanosine
2MG
N(2)-dimethyguanosine
M2G
7-methyguanosine
7MG
2(prime)-O-methyguanosine
0MG
diydrouridine
H2U
ribosylthymidine
5MU
pseudouridine
PSU
acetic acid
ACE
formic acid
FOR
water
HOH
other
UNK
depositor provided
derived from coordinates
Evidence for the assignment of the polymer sequence.
entity_poly.pdbx_strand_id
The PDB strand/chain id(s) corresponding to this polymer entity.
A
B
A,B,C
entity_poly.pdbx_target_identifier
For Structural Genomics entries, the sequence's target identifier registered at the TargetTrack database.
356560
polypeptide(D)
polypeptide(L)
polydeoxyribonucleotide
polyribonucleotide
polydeoxyribonucleotide/polyribonucleotide hybrid
cyclic-pseudo-peptide
peptide nucleic acid
other
The type of the polymer.
entity_poly.type_details
A description of special aspects of the polymer type.
monomer Ala 16 is a D-amino acid
the oligomer contains alternating RNA and DNA units
entity_poly.entity_id
This data item is a pointer to attribute id in category entity in the ENTITY category.
0
entity_poly_seq
Data items in the ENTITY_POLY_SEQ category specify the sequence
of monomers in a polymer. Allowance is made for the possibility
of microheterogeneity in a sample by allowing a given sequence
number to be correlated with more than one monomer ID. The
corresponding ATOM_SITE entries should reflect this
heterogeneity.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:entity_poly_seqCategory>
<PDBx:entity_poly_seq entity_id="1" mon_id="PRO" num="1"></PDBx:entity_poly_seq>
<PDBx:entity_poly_seq entity_id="1" mon_id="GLN" num="2"></PDBx:entity_poly_seq>
<PDBx:entity_poly_seq entity_id="1" mon_id="ILE" num="3"></PDBx:entity_poly_seq>
<PDBx:entity_poly_seq entity_id="1" mon_id="THR" num="4"></PDBx:entity_poly_seq>
<PDBx:entity_poly_seq entity_id="1" mon_id="LEU" num="5"></PDBx:entity_poly_seq>
<PDBx:entity_poly_seq entity_id="1" mon_id="TRP" num="6"></PDBx:entity_poly_seq>
<PDBx:entity_poly_seq entity_id="1" mon_id="GLN" num="7"></PDBx:entity_poly_seq>
<PDBx:entity_poly_seq entity_id="1" mon_id="ARG" num="8"></PDBx:entity_poly_seq>
<PDBx:entity_poly_seq entity_id="1" mon_id="PRO" num="9"></PDBx:entity_poly_seq>
<PDBx:entity_poly_seq entity_id="1" mon_id="LEU" num="10"></PDBx:entity_poly_seq>
<PDBx:entity_poly_seq entity_id="1" mon_id="VAL" num="11"></PDBx:entity_poly_seq>
<PDBx:entity_poly_seq entity_id="1" mon_id="THR" num="12"></PDBx:entity_poly_seq>
<PDBx:entity_poly_seq entity_id="1" mon_id="ILE" num="13"></PDBx:entity_poly_seq>
<PDBx:entity_poly_seq entity_id="1" mon_id="LYS" num="14"></PDBx:entity_poly_seq>
<PDBx:entity_poly_seq entity_id="1" mon_id="ILE" num="15"></PDBx:entity_poly_seq>
<PDBx:entity_poly_seq entity_id="1" mon_id="GLY" num="16"></PDBx:entity_poly_seq>
<PDBx:entity_poly_seq entity_id="1" mon_id="GLY" num="17"></PDBx:entity_poly_seq>
<PDBx:entity_poly_seq entity_id="1" mon_id="GLN" num="18"></PDBx:entity_poly_seq>
<PDBx:entity_poly_seq entity_id="1" mon_id="LEU" num="19"></PDBx:entity_poly_seq>
<PDBx:entity_poly_seq entity_id="1" mon_id="LYS" num="20"></PDBx:entity_poly_seq>
<PDBx:entity_poly_seq entity_id="1" mon_id="GLU" num="21"></PDBx:entity_poly_seq>
<PDBx:entity_poly_seq entity_id="1" mon_id="ALA" num="22"></PDBx:entity_poly_seq>
<PDBx:entity_poly_seq entity_id="1" mon_id="LEU" num="23"></PDBx:entity_poly_seq>
<PDBx:entity_poly_seq entity_id="1" mon_id="LEU" num="24"></PDBx:entity_poly_seq>
<PDBx:entity_poly_seq entity_id="1" mon_id="ASP" num="25"></PDBx:entity_poly_seq>
</PDBx:entity_poly_seqCategory>
0
1
1
1
1
entity_poly_seqCategory
This property indicates that datablock
has a category holder entity_poly_seqCategory.
entity_poly_seqCategory
This property indicates that entity_poly_seqCategory.
has a category entity_poly_seq.
entity_poly_seqItem
Abstract datatype property for entity_poly_seq items.
reference_to_entity_poly_seq
cross-reference to entity_poly_seq.
referenced_by_entity_poly_seq
cross-reference from entity_poly_seq.
no
n
yes
y
A flag to indicate whether this monomer in the polymer is
heterogeneous in sequence.
entity_poly_seq.entity_id
This data item is a pointer to attribute id in category entity in the ENTITY category.
entity_poly_seq.mon_id
This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP
category.
entity_poly_seq.num
The value of attribute num in category entity_poly_seq must uniquely and sequentially
identify a record in the ENTITY_POLY_SEQ list.
Note that this item must be a number and that the sequence
numbers must progress in increasing numerical order.
0
entity_src_gen
Data items in the ENTITY_SRC_GEN category record details of
the source from which the entity was obtained in cases
where the source was genetically manipulated. The
following are treated separately: items pertaining to the tissue
from which the gene was obtained, items pertaining to the host
organism for gene expression and items pertaining to the actual
producing organism (plasmid).
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:entity_src_genCategory>
<PDBx:entity_src_gen entity_id="1" pdbx_src_id="1">
<PDBx:gene_src_common_name>HIV-1</PDBx:gene_src_common_name>
<PDBx:gene_src_strain>NY-5</PDBx:gene_src_strain>
<PDBx:host_org_common_name>bacteria</PDBx:host_org_common_name>
<PDBx:host_org_genus>Escherichia</PDBx:host_org_genus>
<PDBx:host_org_species>coli</PDBx:host_org_species>
<PDBx:plasmid_name>pB322</PDBx:plasmid_name>
</PDBx:entity_src_gen>
</PDBx:entity_src_genCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
1
entity_src_genCategory
This property indicates that datablock
has a category holder entity_src_genCategory.
entity_src_genCategory
This property indicates that entity_src_genCategory.
has a category entity_src_gen.
entity_src_genItem
Abstract datatype property for entity_src_gen items.
reference_to_entity_src_gen
cross-reference to entity_src_gen.
referenced_by_entity_src_gen
cross-reference from entity_src_gen.
entity_src_gen.expression_system_id
A unique identifier for the expression system. This
should be extracted from a local list of expression
systems.
entity_src_gen.gene_src_common_name
The common name of the natural organism from which the gene was
obtained.
man
yeast
bacteria
entity_src_gen.gene_src_details
A description of special aspects of the natural organism from
which the gene was obtained.
entity_src_gen.gene_src_dev_stage
A string to indicate the life-cycle or cell development
cycle in which the gene is expressed and the mature
protein is active.
entity_src_gen.gene_src_genus
The genus of the natural organism from which the gene was
obtained.
Homo
Saccharomyces
Escherichia
entity_src_gen.gene_src_species
The species of the natural organism from which the gene was
obtained.
sapiens
cerevisiae
coli
entity_src_gen.gene_src_strain
The strain of the natural organism from which the gene was
obtained, if relevant.
DH5a
BMH 71-18
entity_src_gen.gene_src_tissue
The tissue of the natural organism from which the gene was
obtained.
heart
liver
eye lens
entity_src_gen.gene_src_tissue_fraction
The subcellular fraction of the tissue of the natural organism
from which the gene was obtained.
mitochondria
nucleus
membrane
entity_src_gen.host_org_common_name
The common name of the organism that served as host for the
production of the entity. Where full details of the protein
production are available it would be expected that this item
be derived from attribute host_org_common_name
in category entity_src_gen_express or via attribute host_org_tax_id in category entity_src_gen_express
yeast
bacteria
entity_src_gen.host_org_details
A description of special aspects of the organism that served as
host for the production of the entity. Where full details of
the protein production are available it would be expected that
this item would derived from attribute host_org_details in category entity_src_gen_express
entity_src_gen.host_org_genus
The genus of the organism that served as host for the production
of the entity.
Saccharomyces
Escherichia
entity_src_gen.host_org_species
The species of the organism that served as host for the
production of the entity.
cerevisiae
coli
entity_src_gen.host_org_strain
The strain of the organism in which the entity was expressed.
Where full details of the protein production are available
it would be expected that this item be derived from
attribute host_org_strain in category entity_src_gen_express or via
attribute host_org_tax_id in category entity_src_gen_express
DH5a
BMH 71-18
sample
model
This data item identifies cases in which an alternative source
modeled.
entity_src_gen.pdbx_beg_seq_num
The beginning polymer sequence position for the polymer section corresponding
to this source.
A reference to the sequence position in the entity_poly category.
entity_src_gen.pdbx_description
Information on the source which is not given elsewhere.
entity_src_gen.pdbx_end_seq_num
The ending polymer sequence position for the polymer section corresponding
to this source.
A reference to the sequence position in the entity_poly category.
entity_src_gen.pdbx_gene_src_atcc
American Type Culture Collection tissue culture number.
6051
entity_src_gen.pdbx_gene_src_cell
Cell type.
ENDOTHELIAL
entity_src_gen.pdbx_gene_src_cell_line
The specific line of cells.
HELA CELLS
entity_src_gen.pdbx_gene_src_cellular_location
Identifies the location inside (or outside) the cell.
CYTOPLASM
NUCLEUS
entity_src_gen.pdbx_gene_src_culture_collection
Culture collection identifier.
6051
entity_src_gen.pdbx_gene_src_fragment
A domain or fragment of the molecule.
CYTOPLASM
NUCLEUS
entity_src_gen.pdbx_gene_src_gene
Identifies the gene.
entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id
NCBI Taxonomy identifier for the gene source organism.
Reference:
Wheeler DL, Chappey C, Lash AE, Leipe DD, Madden TL, Schuler GD,
Tatusova TA, Rapp BA (2000). Database resources of the National
Center for Biotechnology Information. Nucleic Acids Res 2000 Jan
1;28(1):10-4
Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Rapp BA,
Wheeler DL (2000). GenBank. Nucleic Acids Res 2000 Jan 1;28(1):15-18.
entity_src_gen.pdbx_gene_src_organ
Organized group of tissues that carries on a specialized function.
KIDNEY
LIVER
PANCREAS
entity_src_gen.pdbx_gene_src_organelle
Organized structure within cell.
MITOCHONDRIA
entity_src_gen.pdbx_gene_src_plasmid
The source plasmid.
entity_src_gen.pdbx_gene_src_plasmid_name
The source plasmid.
entity_src_gen.pdbx_gene_src_scientific_name
Scientific name of the organism.
ESCHERICHIA COLI
HOMO SAPIENS
SACCHAROMYCES CEREVISIAE
entity_src_gen.pdbx_gene_src_variant
Identifies the variant.
DELTAH1DELTATRP
entity_src_gen.pdbx_host_org_atcc
Americal Tissue Culture Collection of the expression system. Where
full details of the protein production are available it would
be expected that this item would be derived from
attribute host_org_culture_collection in category entity_src_gen_express
entity_src_gen.pdbx_host_org_cell
Cell type from which the gene is derived. Where
entity.target_id is provided this should be derived from
details of the target.
ENDOTHELIAL
entity_src_gen.pdbx_host_org_cell_line
A specific line of cells used as the expression system. Where
full details of the protein production are available it would
be expected that this item would be derived from
entity_src_gen_express.host_org_cell_line
HELA
entity_src_gen.pdbx_host_org_cellular_location
Identifies the location inside (or outside) the cell which
expressed the molecule.
CYTOPLASM
NUCLEUS
entity_src_gen.pdbx_host_org_culture_collection
Culture collection of the expression system. Where
full details of the protein production are available it would
be expected that this item would be derived somehwere, but
exactly where is not clear.
entity_src_gen.pdbx_host_org_gene
Specific gene which expressed the molecule.
HIV-1 POL
GLNS7
U1A (2-98, Y31H, Q36R)
entity_src_gen.pdbx_host_org_ncbi_taxonomy_id
NCBI Taxonomy identifier for the expression system organism.
Reference:
Wheeler DL, Chappey C, Lash AE, Leipe DD, Madden TL, Schuler GD,
Tatusova TA, Rapp BA (2000). Database resources of the National
Center for Biotechnology Information. Nucleic Acids Res 2000 Jan
1;28(1):10-4
Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Rapp BA,
Wheeler DL (2000). GenBank. Nucleic Acids Res 2000 Jan 1;28(1):15-18.
entity_src_gen.pdbx_host_org_organ
Specific organ which expressed the molecule.
KIDNEY
entity_src_gen.pdbx_host_org_organelle
Specific organelle which expressed the molecule.
MITOCHONDRIA
entity_src_gen.pdbx_host_org_scientific_name
The scientific name of the organism that served as host for the
production of the entity. Where full details of the protein
production are available it would be expected that this item
would be derived from attribute host_org_scientific_name
in category entity_src_gen_express or via attribute host_org_tax_id in category entity_src_gen_express
ESCHERICHIA COLI
SACCHAROMYCES CEREVISIAE
entity_src_gen.pdbx_host_org_strain
The strain of the organism in which the entity was
expressed.
AR120
entity_src_gen.pdbx_host_org_tissue
The specific tissue which expressed the molecule. Where full details
of the protein production are available it would be expected that this
item would be derived from attribute host_org_tissue in category entity_src_gen_express
heart
liver
eye lens
entity_src_gen.pdbx_host_org_tissue_fraction
The fraction of the tissue which expressed the
molecule.
mitochondria
nucleus
membrane
entity_src_gen.pdbx_host_org_variant
Variant of the organism used as the expression system. Where
full details of the protein production are available it would
be expected that this item be derived from
entity_src_gen_express.host_org_variant or via
attribute host_org_tax_id in category entity_src_gen_express
TRP-LAC
LAMBDA DE3
entity_src_gen.pdbx_host_org_vector
Identifies the vector used. Where full details of the protein
production are available it would be expected that this item
would be derived from attribute vector_name in category entity_src_gen_clone.
PBIT36
PET15B
PUC18
entity_src_gen.pdbx_host_org_vector_type
Identifies the type of vector used (plasmid, virus, or cosmid).
Where full details of the protein production are available it
would be expected that this item would be derived from
attribute vector_type in category entity_src_gen_express.
COSMID
PLASMID
N-terminal tag
C-terminal tag
Biological sequence
Linker
This data item povides additional information about the sequence type.
entity_src_gen.plasmid_details
A description of special aspects of the plasmid that produced the
entity in the host organism. Where full details of the protein
production are available it would be expected that this item
would be derived from attribute details in category pdbx_construct of the construct
pointed to from attribute plasmid_id in category entity_src_gen_express.
entity_src_gen.plasmid_name
The name of the plasmid that produced the entity in the host
organism. Where full details of the protein production are available
it would be expected that this item would be derived from
attribute name in category pdbx_construct of the construct pointed to from
attribute plasmid_id in category entity_src_gen_express.
pET3C
pT123sab
entity_src_gen.start_construct_id
A pointer to attribute id in category pdbx_construct in the PDBX_CONSTRUCT category.
The indentified sequence is the initial construct.
entity_src_gen.entity_id
This data item is a pointer to attribute id in category entity in the ENTITY category.
entity_src_gen.pdbx_src_id
This data item is an ordinal identifier for entity_src_gen data records.
0
entity_src_nat
Data items in the ENTITY_SRC_NAT category record details of
the source from which the entity was obtained in cases
where the entity was isolated directly from a natural tissue.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:entity_src_natCategory>
<PDBx:entity_src_nat entity_id="2" pdbx_src_id="1">
<PDBx:common_name>bacteria</PDBx:common_name>
<PDBx:details> Acetyl-pepstatin was isolated by Dr. K. Oda, Osaka
Prefecture University, and provided to us by Dr. Ben
Dunn, University of Florida, and Dr. J. Kay, University
of Wales.</PDBx:details>
<PDBx:genus>Actinomycetes</PDBx:genus>
</PDBx:entity_src_nat>
</PDBx:entity_src_natCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
1
entity_src_natCategory
This property indicates that datablock
has a category holder entity_src_natCategory.
entity_src_natCategory
This property indicates that entity_src_natCategory.
has a category entity_src_nat.
entity_src_natItem
Abstract datatype property for entity_src_nat items.
reference_to_entity_src_nat
cross-reference to entity_src_nat.
referenced_by_entity_src_nat
cross-reference from entity_src_nat.
entity_src_nat.common_name
The common name of the organism from which the entity
was isolated.
man
yeast
bacteria
entity_src_nat.details
A description of special aspects of the organism from which the
entity was isolated.
entity_src_nat.genus
The genus of the organism from which the entity was isolated.
Homo
Saccharomyces
Escherichia
sample
model
This data item identifies cases in which an alternative source
modeled.
entity_src_nat.pdbx_atcc
Americal Tissue Culture Collection number.
6051
entity_src_nat.pdbx_beg_seq_num
The beginning polymer sequence position for the polymer section corresponding
to this source.
A reference to the sequence position in the entity_poly category.
entity_src_nat.pdbx_cell
A particular cell type.
BHK-21
entity_src_nat.pdbx_cell_line
The specific line of cells.
HELA
entity_src_nat.pdbx_cellular_location
Identifies the location inside (or outside) the cell.
entity_src_nat.pdbx_culture_collection
Culture Collection identifier.
6051
entity_src_nat.pdbx_end_seq_num
The ending polymer sequence position for the polymer section corresponding
to this source.
A reference to the sequence position in the entity_poly category.
entity_src_nat.pdbx_fragment
A domain or fragment of the molecule.
entity_src_nat.pdbx_ncbi_taxonomy_id
NCBI Taxonomy identifier for the source organism.
Reference:
Wheeler DL, Chappey C, Lash AE, Leipe DD, Madden TL, Schuler GD,
Tatusova TA, Rapp BA (2000). Database resources of the National
Center for Biotechnology Information. Nucleic Acids Res 2000 Jan
1;28(1):10-4
Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Rapp BA,
Wheeler DL (2000). GenBank. Nucleic Acids Res 2000 Jan 1;28(1):15-18.
entity_src_nat.pdbx_organ
Organized group of tissues that carries on a specialized function.
KIDNEY
entity_src_nat.pdbx_organelle
Organized structure within cell.
MITOCHONDRIA
entity_src_nat.pdbx_organism_scientific
Scientific name of the organism of the natural source.
BOS TAURUS
SUS SCROFA
ASPERGILLUS ORYZAE
entity_src_nat.pdbx_plasmid_details
Details about the plasmid.
PLC28 DERIVATIVE
entity_src_nat.pdbx_plasmid_name
The plasmid containing the gene.
pB322
entity_src_nat.pdbx_secretion
Identifies the secretion from which the molecule was isolated.
saliva
urine
venom
entity_src_nat.pdbx_variant
Identifies the variant.
entity_src_nat.species
The species of the organism from which the entity was isolated.
sapiens
cerevisiae
coli
entity_src_nat.strain
The strain of the organism from which the entity was isolated.
DH5a
BMH 71-18
entity_src_nat.tissue
The tissue of the organism from which the entity was isolated.
heart
liver
eye lens
entity_src_nat.tissue_fraction
The subcellular fraction of the tissue of the organism from
which the entity was isolated.
mitochondria
nucleus
membrane
entity_src_nat.entity_id
This data item is a pointer to attribute id in category entity in the ENTITY category.
entity_src_nat.pdbx_src_id
This data item is an ordinal identifier for entity_src_nat data records.
0
entry
There is only one item in the ENTRY category, attribute id in category entry. This
data item gives a name to this entry and is indirectly a key to
the categories (such as CELL, GEOM, EXPTL) that describe
information pertinent to the entire data block.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:entryCategory>
<PDBx:entry id="5HVP"></PDBx:entry>
</PDBx:entryCategory>
Example 2 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
<PDBx:entryCategory>
<PDBx:entry id="TOZ"></PDBx:entry>
</PDBx:entryCategory>
0
1
1
entryCategory
This property indicates that datablock
has a category holder entryCategory.
entryCategory
This property indicates that entryCategory.
has a category entry.
entryItem
Abstract datatype property for entry items.
reference_to_entry
cross-reference to entry.
referenced_by_entry
cross-reference from entry.
entry.pdbx_DOI
Document Object Identifier (DOI) for this entry registered
with http://crossref.org.
entry.id
The value of attribute id in category entry identifies the data block.
Note that this item need not be a number; it can be any unique
identifier.
0
entry_link
Data items in the ENTRY_LINK category record the
relationships between the current data block
identified by attribute id in category entry and other data blocks
within the current file which may be referenced
in the current data block.
Example 1 - example file for the one-dimensional incommensurately
modulated structure of K~2~SeO~4~.
<PDBx:entry_linkCategory>
<PDBx:entry_link entry_id="KSE_TEXT" id="KSE_COM">
<PDBx:details>experimental data common to ref./mod. structures</PDBx:details>
</PDBx:entry_link>
<PDBx:entry_link entry_id="KSE_TEXT" id="KSE_REF">
<PDBx:details>reference structure</PDBx:details>
</PDBx:entry_link>
<PDBx:entry_link entry_id="KSE_TEXT" id="KSE_MOD">
<PDBx:details>modulated structure</PDBx:details>
</PDBx:entry_link>
</PDBx:entry_linkCategory>
0
1
1
1
entry_linkCategory
This property indicates that datablock
has a category holder entry_linkCategory.
entry_linkCategory
This property indicates that entry_linkCategory.
has a category entry_link.
entry_linkItem
Abstract datatype property for entry_link items.
reference_to_entry_link
cross-reference to entry_link.
referenced_by_entry_link
cross-reference from entry_link.
entry_link.details
A description of the relationship between the data blocks
identified by _entry_link.id and _entry_link.entry_id.
entry_link.entry_id
This data item is a pointer to attribute id in category entry in the ENTRY category.
entry_link.id
The value of attribute id in category entry_link identifies a data block
related to the current data block.
0
exptl
Data items in the EXPTL category record details about the
experimental work prior to the intensity measurements and
details about the absorption-correction technique employed.
Example 1 - based on laboratory records for Yb(S-C5H4N)2(THF)4.
<PDBx:exptlCategory>
<PDBx:exptl entry_id="datablock1" method="single-crystal x-ray diffraction">
<PDBx:absorpt_coefficient_mu>1.22</PDBx:absorpt_coefficient_mu>
<PDBx:absorpt_correction_T_max>0.896</PDBx:absorpt_correction_T_max>
<PDBx:absorpt_correction_T_min>0.802</PDBx:absorpt_correction_T_min>
<PDBx:absorpt_correction_type>integration</PDBx:absorpt_correction_type>
<PDBx:absorpt_process_details> Gaussian grid method from SHELX76
Sheldrick, G. M., "SHELX-76: structure determination and
refinement program", Cambridge University, UK, 1976</PDBx:absorpt_process_details>
<PDBx:crystals_number>1</PDBx:crystals_number>
<PDBx:details> Enraf-Nonius LT2 liquid nitrogen variable-temperature
device used</PDBx:details>
<PDBx:method_details> graphite monochromatized Cu K(alpha) fixed tube and
Enraf-Nonius CAD4 diffractometer used</PDBx:method_details>
</PDBx:exptl>
</PDBx:exptlCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
1
exptlCategory
This property indicates that datablock
has a category holder exptlCategory.
exptlCategory
This property indicates that exptlCategory.
has a category exptl.
exptlItem
Abstract datatype property for exptl items.
reference_to_exptl
cross-reference to exptl.
referenced_by_exptl
cross-reference from exptl.
exptl.absorpt_coefficient_mu
The absorption coefficient mu in reciprocal millimetres
calculated from the atomic content of the cell, the density and
the radiation wavelength.
exptl.absorpt_correction_T_max
The maximum transmission factor for the crystal and radiation.
The maximum and minimum transmission factors are also referred
to as the absorption correction
A or 1/A*.
exptl.absorpt_correction_T_min
The minimum transmission factor for the crystal and radiation.
The maximum and minimum transmission factors are also referred
to as the absorption correction
A or 1/A*.
analytical
cylinder
empirical
gaussian
integration
multi-scan
none
numerical
psi-scan
refdelf
sphere
The absorption correction type and method. The value
'empirical' should NOT be used unless more detailed
information is not available.
exptl.absorpt_process_details
Description of the absorption process applied to the
intensities. A literature reference should be supplied for
psi-scan techniques.
Tompa analytical
exptl.crystals_number
The total number of crystals used in the measurement of
intensities.
exptl.details
Any special information about the experimental work prior to the
intensity measurement. See also attribute preparation in category exptl_crystal.
exptl.method_details
A description of special aspects of the experimental method.
29 structures
minimized average structure
exptl.entry_id
This data item is a pointer to attribute id in category entry in the ENTRY category.
X-RAY DIFFRACTION
NEUTRON DIFFRACTION
FIBER DIFFRACTION
ELECTRON CRYSTALLOGRAPHY
ELECTRON MICROSCOPY
SOLUTION NMR
SOLID-STATE NMR
SOLUTION SCATTERING
POWDER DIFFRACTION
INFRARED SPECTROSCOPY
EPR
FLUORESCENCE TRANSFER
THEORETICAL MODEL
The method used in the experiment.
X-RAY DIFFRACTION
NEUTRON DIFFRACTION
FIBER DIFFRACTION
ELECTRON CRYSTALLOGRAPHY
ELECTRON MICROSCOPY
SOLUTION NMR
SOLID-STATE NMR
SOLUTION SCATTERING
POWDER DIFFRACTION
0
exptl_crystal
Data items in the EXPTL_CRYSTAL category record the results of
experimental measurements on the crystal or crystals used,
such as shape, size or density.
Example 1 - based on laboratory records for Yb(S-C5H4N)2(THF)4.
<PDBx:exptl_crystalCategory>
<PDBx:exptl_crystal id="xst2l">
<PDBx:F_000>202</PDBx:F_000>
<PDBx:colour>pale yellow</PDBx:colour>
<PDBx:density_Matthews>1.01</PDBx:density_Matthews>
<PDBx:density_diffrn>1.113</PDBx:density_diffrn>
<PDBx:density_meas>1.11</PDBx:density_meas>
<PDBx:density_meas_temp>294.5</PDBx:density_meas_temp>
<PDBx:density_method>neutral buoyancy</PDBx:density_method>
<PDBx:density_percent_sol>0.15</PDBx:density_percent_sol>
<PDBx:description>hexagonal rod, uncut</PDBx:description>
<PDBx:preparation> hanging drop, crystal soaked in 10% ethylene glycol for
10 h, then placed in nylon loop at data collection time</PDBx:preparation>
<PDBx:size_max>0.30</PDBx:size_max>
<PDBx:size_mid>0.20</PDBx:size_mid>
<PDBx:size_min>0.05</PDBx:size_min>
<PDBx:size_rad>0.025</PDBx:size_rad>
</PDBx:exptl_crystal>
</PDBx:exptl_crystalCategory>
Example 2 - using separate items to define upper and lower
limits for a value.
<PDBx:exptl_crystalCategory>
<PDBx:exptl_crystal id="xst2l">
<PDBx:density_meas_gt>2.5</PDBx:density_meas_gt>
<PDBx:density_meas_lt>5.0</PDBx:density_meas_lt>
</PDBx:exptl_crystal>
</PDBx:exptl_crystalCategory>
Example 3 - here the density was measured at some
unspecified temperature below room temperature.
<PDBx:exptl_crystalCategory>
<PDBx:exptl_crystal id="xst2l">
<PDBx:density_meas_temp_lt>300</PDBx:density_meas_temp_lt>
</PDBx:exptl_crystal>
</PDBx:exptl_crystalCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
exptl_crystalCategory
This property indicates that datablock
has a category holder exptl_crystalCategory.
exptl_crystalCategory
This property indicates that exptl_crystalCategory.
has a category exptl_crystal.
exptl_crystalItem
Abstract datatype property for exptl_crystal items.
reference_to_exptl_crystal
cross-reference to exptl_crystal.
referenced_by_exptl_crystal
cross-reference from exptl_crystal.
exptl_crystal.F_000
The effective number of electrons in the crystal unit cell
contributing to F(000). This may contain dispersion contributions
and is calculated as
F(000) = [ sum (f~r~^2^ + f~i~^2^) ]^1/2^
f~r~ = real part of the scattering factors at theta = 0 degree
f~i~ = imaginary part of the scattering factors at
theta = 0 degree
the sum is taken over each atom in the unit cell
exptl_crystal.colour
The colour of the crystal.
dark green
metallic
dull
clear
The enumeration list of standardized names developed for the
International Centre for Diffraction Data.
The colour of a crystal is given by the combination of
attribute colour_modifier in category exptl_crystal with
attribute colour_primary in category exptl_crystal, as in 'dark-green' or
'bluish-violet', if necessary combined with
attribute colour_lustre in category exptl_crystal, as in 'metallic-green'.
light
dark
whitish
blackish
grayish
brownish
reddish
pinkish
orangish
yellowish
greenish
bluish
The enumeration list of standardized names developed for the
International Centre for Diffraction Data.
The colour of a crystal is given by the combination of
attribute colour_modifier in category exptl_crystal with
attribute colour_primary in category exptl_crystal, as in 'dark-green' or
'bluish-violet', if necessary combined with
attribute colour_lustre in category exptl_crystal, as in 'metallic-green'.
colourless
white
black
gray
brown
red
pink
orange
yellow
green
blue
violet
The enumeration list of standardized names developed for the
International Centre for Diffraction Data.
The colour of a crystal is given by the combination of
attribute colour_modifier in category exptl_crystal with
attribute colour_primary in category exptl_crystal, as in 'dark-green' or
'bluish-violet', if necessary combined with
attribute colour_lustre in category exptl_crystal, as in 'metallic-green'.
exptl_crystal.density_Matthews
The density of the crystal, expressed as the ratio of the
volume of the asymmetric unit to the molecular mass of a
monomer of the structure, in units of angstroms^3^ per dalton.
Ref: Matthews, B. W. (1968). J. Mol. Biol. 33, 491-497.
exptl_crystal.density_diffrn
Density values calculated from the crystal cell and contents. The
units are megagrams per cubic metre (grams per cubic centimetre).
exptl_crystal.density_meas
Density values measured using standard chemical and physical
methods. The units are megagrams per cubic metre (grams per
cubic centimetre).
exptl_crystal.density_meas_esd
The estimated standard deviation of attribute density_meas in category exptl_crystal.
exptl_crystal.density_meas_gt
The value above which the density measured using standard
chemical and physical methods lies. The units are megagrams
per cubic metre (grams per cubic centimetre).
_exptl_crystal.density_meas_gt and _exptl_crystal.density_meas_lt
should not be used to report new experimental work, for which
attribute density_meas in category exptl_crystal should be used. These items are
intended for use in reporting information in existing databases
and archives which would be misleading if reported under
attribute density_meas in category exptl_crystal.
lower limit for the density (only the range
within which the density lies was given in the
original paper)
2.5
exptl_crystal.density_meas_lt
The value below which the density measured using standard
chemical and physical methods lies. The units are megagrams
per cubic metre (grams per cubic centimetre).
_exptl_crystal.density_meas_gt and _exptl_crystal.density_meas_lt
should not be used to report new experimental work, for which
attribute density_meas in category exptl_crystal should be used. These items are
intended for use in reporting information in existing databases
and archives which would be misleading if reported under
attribute density_meas in category exptl_crystal.
specimen floats in water
1.0
upper limit for the density (only the range
within which the density lies was given in the
original paper)
5.0
exptl_crystal.density_meas_temp
Temperature in kelvins at which attribute density_meas
in category exptl_crystal was determined.
exptl_crystal.density_meas_temp_esd
The estimated standard deviation of
attribute density_meas_temp in category exptl_crystal.
exptl_crystal.density_meas_temp_gt
Temperature in kelvins above which attribute density_meas
in category exptl_crystal was determined. attribute density_meas_temp_gt in category exptl_crystal and
attribute density_meas_temp_lt in category exptl_crystal should not be used for
reporting new work, for which the correct temperature of
measurement should be given. These items are intended for
use in reporting information stored in databases or archives
which would be misleading if reported under
attribute density_meas_temp in category exptl_crystal.
exptl_crystal.density_meas_temp_lt
Temperature in kelvins below which attribute density_meas
in category exptl_crystal was determined. attribute density_meas_temp_gt in category exptl_crystal and
attribute density_meas_temp_lt in category exptl_crystal should not be used for
reporting new work, for which the correct temperature of
measurement should be given. These items are intended for
use in reporting information stored in databases or archives
which would be misleading if reported under
attribute density_meas_temp in category exptl_crystal.
The density was measured at some unspecified
temperature below room temperature.
300
exptl_crystal.density_method
The method used to measure attribute density_meas in category exptl_crystal.
exptl_crystal.density_percent_sol
Density value P calculated from the crystal cell and contents,
expressed as per cent solvent.
P = 1 - (1.23 N MMass) / V
N = the number of molecules in the unit cell
MMass = the molecular mass of each molecule (gm/mole)
V = the volume of the unit cell (A^3^)
1.23 = a conversion factor evaluated as:
(0.74 cm^3^/g) (10^24^ A^3^/cm^3^)
--------------------------------------
(6.02*10^23^) molecules/mole
where 0.74 is an assumed value for the partial specific
volume of the molecule
exptl_crystal.description
A description of the quality and habit of the crystal.
The crystal dimensions should not normally be reported here;
use instead the specific items in the EXPTL_CRYSTAL category
relating to size for the gross dimensions of the crystal and
data items in the EXPTL_CRYSTAL_FACE category to describe the
relationship between individual faces.
exptl_crystal.pdbx_crystal_diffrn_lifetime
The measured diffraction limit for this crystal.
exptl_crystal.pdbx_crystal_diffrn_limit
The measured diffraction limit for this crystal.
exptl_crystal.pdbx_crystal_direction_1
The crystal size along the first measured direction in millimeters.
exptl_crystal.pdbx_crystal_direction_2
The crystal size along the second measured direction in millimeters.
exptl_crystal.pdbx_crystal_direction_3
The crystal size along the third measured direction in millimeters.
Y
N
A code to indicate that a crystal image is available
for this crystal.
exptl_crystal.pdbx_crystal_image_format
The image format for the file containing the image of crystal specified
as an RFC2045/RFC2046 mime type.
jpeg
gif
tiff
exptl_crystal.pdbx_crystal_image_url
The URL for an a file containing the image of crystal.
exptl_crystal.pdbx_mosaic_block_size
Isotropic and resolution-independent term representing the average size of
mosaic domains in the crystal specified in Angstroms. Larger size indicates
better ordered crystals.
exptl_crystal.pdbx_mosaic_block_size_esd
The uncertainty in the mosaic block size estimate for the crystal.
exptl_crystal.pdbx_mosaic_method
How parameters derived from the spot shape (such as mosaic block
size and rotation, beam divergence, and crossfire) and their
errors were estimated. See the related items section.
This can be a written description or a citation to a specific
software package that determined these parameters.
Note, these parameters are considered derived terms from the
data, as opposed to measured terms from the instrument (such
as diffrn_radiation.div_x_source, a term similar to
pdbx_crystal_alignment.crossfire_x).
exptl_crystal.pdbx_mosaicity
Isotropic approximation of the distribution of mis-orientation angles
specified in degrees of all the mosaic domain blocks in the crystal,
represented as a standard deviation. Here, a mosaic block is a set of
contiguous unit cells assumed to be perfectly aligned. Lower mosaicity
indicates better ordered crystals. See for example:
Nave, C. (1998). Acta Cryst. D54, 848-853.
Note that many software packages estimate the mosaic rotation distribution
differently and may combine several physical properties of the experiment
into a single mosaic term. This term will help fit the modeled spots
to the observed spots without necessarily being directly related to the
physics of the crystal itself.
exptl_crystal.pdbx_mosaicity_esd
The uncertainty in the mosaicity estimate for the crystal.
Y
N
A code to indicate that an x-ray image is available for
this crystal.
exptl_crystal.pdbx_x-ray_image_type
A description of the type of x-ray image for this crystal.
exptl_crystal.preparation
Details of crystal growth and preparation of the crystal (e.g.
mounting) prior to the intensity measurements.
mounted in an argon-filled quartz capillary
exptl_crystal.size_max
The maximum dimension of the crystal. This item may appear in a
list with attribute id in category exptl_crystal if multiple crystals are used in the
experiment.
exptl_crystal.size_mid
The medial dimension of the crystal. This item may appear in a
list with attribute id in category exptl_crystal if multiple crystals are used in the
experiment.
exptl_crystal.size_min
The minimum dimension of the crystal. This item may appear in a
list with attribute id in category exptl_crystal if multiple crystals are used in the
experiment.
exptl_crystal.size_rad
The radius of the crystal, if the crystal is a sphere or a
cylinder. This item may appear in a list with attribute id
in category exptl_crystal if multiple crystals are used in the experiment.
exptl_crystal.id
The value of attribute id in category exptl_crystal must uniquely identify a record in
the EXPTL_CRYSTAL list.
Note that this item need not be a number; it can be any unique
identifier.
0
exptl_crystal_face
Data items in the EXPTL_CRYSTAL_FACE category record details
of the crystal faces.
Example 1 - based on laboratory records for Yb(S-C5H4N)2(THF)4
for the 100 face of crystal xstl1.
<PDBx:exptl_crystal_faceCategory>
<PDBx:exptl_crystal_face crystal_id="xstl1" index_h="1" index_k="0" index_l="0">
<PDBx:diffr_chi>42.56</PDBx:diffr_chi>
<PDBx:diffr_kappa>30.23</PDBx:diffr_kappa>
<PDBx:diffr_phi>-125.56</PDBx:diffr_phi>
<PDBx:diffr_psi>-0.34</PDBx:diffr_psi>
<PDBx:perp_dist>0.025</PDBx:perp_dist>
</PDBx:exptl_crystal_face>
</PDBx:exptl_crystal_faceCategory>
0
1
0
1
0
1
0
1
0
1
1
1
1
1
exptl_crystal_faceCategory
This property indicates that datablock
has a category holder exptl_crystal_faceCategory.
exptl_crystal_faceCategory
This property indicates that exptl_crystal_faceCategory.
has a category exptl_crystal_face.
exptl_crystal_faceItem
Abstract datatype property for exptl_crystal_face items.
reference_to_exptl_crystal_face
cross-reference to exptl_crystal_face.
referenced_by_exptl_crystal_face
cross-reference from exptl_crystal_face.
exptl_crystal_face.diffr_chi
The chi diffractometer setting angle in degrees for a specific
crystal face associated with attribute perp_dist in category exptl_crystal_face.
exptl_crystal_face.diffr_kappa
The kappa diffractometer setting angle in degrees for a specific
crystal face associated with attribute perp_dist in category exptl_crystal_face.
exptl_crystal_face.diffr_phi
The phi diffractometer setting angle in degrees for a specific
crystal face associated with attribute perp_dist in category exptl_crystal_face.
exptl_crystal_face.diffr_psi
The psi diffractometer setting angle in degrees for a specific
crystal face associated with attribute perp_dist in category exptl_crystal_face.
exptl_crystal_face.perp_dist
The perpendicular distance in millimetres from the face to the
centre of rotation of the crystal.
exptl_crystal_face.crystal_id
This data item is a pointer to attribute id in category exptl_crystal in the
EXPTL_CRYSTAL category.
exptl_crystal_face.index_h
Miller index h of the crystal face associated with the value
attribute perp_dist in category exptl_crystal_face.
exptl_crystal_face.index_k
Miller index k of the crystal face associated with the value
attribute perp_dist in category exptl_crystal_face.
exptl_crystal_face.index_l
Miller index l of the crystal face associated with the value
attribute perp_dist in category exptl_crystal_face.
0
exptl_crystal_grow
Data items in the EXPTL_CRYSTAL_GROW category record details
about the conditions and methods used to grow the crystal.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:exptl_crystal_growCategory>
<PDBx:exptl_crystal_grow crystal_id="1">
<PDBx:apparatus>Linbro plates</PDBx:apparatus>
<PDBx:atmosphere>room air</PDBx:atmosphere>
<PDBx:method>VAPOR DIFFUSION, HANGING DROP</PDBx:method>
<PDBx:pH>4.7</PDBx:pH>
<PDBx:temp>291</PDBx:temp>
<PDBx:time>approximately 2 days</PDBx:time>
</PDBx:exptl_crystal_grow>
</PDBx:exptl_crystal_growCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
exptl_crystal_growCategory
This property indicates that datablock
has a category holder exptl_crystal_growCategory.
exptl_crystal_growCategory
This property indicates that exptl_crystal_growCategory.
has a category exptl_crystal_grow.
exptl_crystal_growItem
Abstract datatype property for exptl_crystal_grow items.
reference_to_exptl_crystal_grow
cross-reference to exptl_crystal_grow.
referenced_by_exptl_crystal_grow
cross-reference from exptl_crystal_grow.
exptl_crystal_grow.apparatus
The physical apparatus in which the crystal was grown.
Linbro plate
sandwich box
ACA plates
exptl_crystal_grow.atmosphere
The nature of the gas or gas mixture in which the crystal was
grown.
room air
nitrogen
argon
exptl_crystal_grow.details
A description of special aspects of the crystal growth.
Solution 2 was prepared as a well solution and
mixed. A droplet containing 2 \ml of solution
1 was delivered onto a cover slip; 2 \ml of
solution 2 was added to the droplet without
mixing.
Crystal plates were originally stored at room
temperature for 1 week but no nucleation
occurred. They were then transferred to 4
degrees C, at which temperature well formed
single crystals grew in 2 days.
The dependence on pH for successful crystal
growth is very sharp. At pH 7.4 only showers
of tiny crystals grew, at pH 7.5 well formed
single crystals grew, at pH 7.6 no
crystallization occurred at all.
exptl_crystal_grow.method
The method used to grow the crystals.
MICROBATCH
VAPOR DIFFUSION, HANGING DROP
exptl_crystal_grow.method_ref
A literature reference that describes the method used to grow
the crystals.
McPherson et al., 1988
exptl_crystal_grow.pH
The pH at which the crystal was grown. If more than one pH was
employed during the crystallization process, the final pH should
be noted here and the protocol involving multiple pH values
should be described in attribute details in category exptl_crystal_grow.
7.4
7.6
4.3
exptl_crystal_grow.pdbx_details
Text description of crystal growth procedure.
PEG 4000, potassium phosphate, magnesium chloride, cacodylate
exptl_crystal_grow.pdbx_pH_range
The range of pH values at which the crystal was grown. Used when
a point estimate of pH is not appropriate.
5.6 - 6.4
exptl_crystal_grow.pressure
The ambient pressure in kilopascals at which the crystal was
grown.
exptl_crystal_grow.pressure_esd
The standard uncertainty (estimated standard deviation)
of attribute pressure in category exptl_crystal_grow.
exptl_crystal_grow.seeding
A description of the protocol used for seeding the crystal
growth.
macroseeding
Microcrystals were introduced from a previous
crystal growth experiment by transfer with a
human hair.
exptl_crystal_grow.seeding_ref
A literature reference that describes the protocol used to seed
the crystal.
Stura et al., 1989
exptl_crystal_grow.temp
The temperature in kelvins at which the crystal was grown.
If more than one temperature was employed during the
crystallization process, the final temperature should be noted
here and the protocol involving multiple temperatures should be
described in attribute details in category exptl_crystal_grow.
exptl_crystal_grow.temp_details
A description of special aspects of temperature control during
crystal growth.
exptl_crystal_grow.temp_esd
The standard uncertainty (estimated standard deviation)
of attribute temp in category exptl_crystal_grow.
exptl_crystal_grow.time
The approximate time that the crystal took to grow to the size
used for data collection.
overnight
2-4 days
6 months
exptl_crystal_grow.crystal_id
This data item is a pointer to attribute id in category exptl_crystal in the
EXPTL_CRYSTAL category.
0
exptl_crystal_grow_comp
Data items in the EXPTL_CRYSTAL_GROW_COMP category record
details about the components of the solutions that were 'mixed'
(by whatever means) to produce the crystal.
In general, solution 1 is the solution that contains the
molecule to be crystallized and solution 2 is the solution
that contains the precipitant. However, the number of solutions
required to describe the crystallization protocol is not limited
to 2.
Details of the crystallization protocol should be given in
attribute details in category exptl_crystal_grow_comp using the solutions
described in EXPTL_CRYSTAL_GROW_COMP.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:exptl_crystal_grow_compCategory>
<PDBx:exptl_crystal_grow_comp crystal_id="1" id="1">
<PDBx:conc>6 mg/ml</PDBx:conc>
<PDBx:details> The protein solution was in a buffer containing 25 mM NaCl,
100 mM NaMES/ MES buffer, pH 7.5, 3 mM NaAzide</PDBx:details>
<PDBx:name>HIV-1 protease</PDBx:name>
<PDBx:sol_id>1</PDBx:sol_id>
<PDBx:volume>0.002 ml</PDBx:volume>
</PDBx:exptl_crystal_grow_comp>
<PDBx:exptl_crystal_grow_comp crystal_id="1" id="2">
<PDBx:conc>4 M</PDBx:conc>
<PDBx:details>in 3 mM NaAzide</PDBx:details>
<PDBx:name>NaCl</PDBx:name>
<PDBx:sol_id>2</PDBx:sol_id>
<PDBx:volume>0.200 ml</PDBx:volume>
</PDBx:exptl_crystal_grow_comp>
<PDBx:exptl_crystal_grow_comp crystal_id="1" id="3">
<PDBx:conc>100 mM</PDBx:conc>
<PDBx:details>in 3 mM NaAzide</PDBx:details>
<PDBx:name>Acetic Acid</PDBx:name>
<PDBx:sol_id>2</PDBx:sol_id>
<PDBx:volume>0.047 ml</PDBx:volume>
</PDBx:exptl_crystal_grow_comp>
<PDBx:exptl_crystal_grow_comp crystal_id="1" id="4">
<PDBx:conc>100 mM</PDBx:conc>
<PDBx:details> in 3 mM NaAzide. Buffer components were mixed to produce a
pH of 4.7 according to a ratio calculated from the pKa. The
actual pH of solution 2 was not measured.</PDBx:details>
<PDBx:name>Na Acetate</PDBx:name>
<PDBx:sol_id>2</PDBx:sol_id>
<PDBx:volume>0.053 ml</PDBx:volume>
</PDBx:exptl_crystal_grow_comp>
<PDBx:exptl_crystal_grow_comp crystal_id="1" id="5">
<PDBx:conc>neat</PDBx:conc>
<PDBx:details>in 3 mM NaAzide</PDBx:details>
<PDBx:name>water</PDBx:name>
<PDBx:sol_id>2</PDBx:sol_id>
<PDBx:volume>0.700 ml</PDBx:volume>
</PDBx:exptl_crystal_grow_comp>
</PDBx:exptl_crystal_grow_compCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
1
exptl_crystal_grow_compCategory
This property indicates that datablock
has a category holder exptl_crystal_grow_compCategory.
exptl_crystal_grow_compCategory
This property indicates that exptl_crystal_grow_compCategory.
has a category exptl_crystal_grow_comp.
exptl_crystal_grow_compItem
Abstract datatype property for exptl_crystal_grow_comp items.
reference_to_exptl_crystal_grow_comp
cross-reference to exptl_crystal_grow_comp.
referenced_by_exptl_crystal_grow_comp
cross-reference from exptl_crystal_grow_comp.
exptl_crystal_grow_comp.conc
The concentration of the solution component.
200 \ml
0.1 ml
exptl_crystal_grow_comp.details
A description of any special aspects of the solution component.
When the solution component is the one that contains the
macromolecule, this could be the specification of the buffer in
which the macromolecule was stored. When the solution component
is a buffer component, this could be the methods (or formula)
used to achieve a desired pH.
in 3 mM NaAzide
The protein solution was in a buffer
containing 25 mM NaCl, 100 mM NaMES/MES
buffer, pH 7.5, 3 mM NaAzide
in 3 mM NaAzide. Buffer components were mixed
to produce a pH of 4.7 according to a ratio
calculated from the pKa. The actual pH of
solution 2 was not measured.
exptl_crystal_grow_comp.name
A common name for the component of the solution.
protein in buffer
acetic acid
exptl_crystal_grow_comp.pdbx_bath
The identification of the cystallization bath.
exptl_crystal_grow_comp.pdbx_conc_final
The concentration of this component in the final
crystallization solution. This data item should
include units of concentration.
exptl_crystal_grow_comp.pdbx_salt
The identification of the crystallization salt.
exptl_crystal_grow_comp.pdbx_soak_salt
The identification of the crystallization soaking salt.
exptl_crystal_grow_comp.pdbx_soak_solv
The identification of the crystallization soaking solvent
exptl_crystal_grow_comp.pdbx_solv
The identification of the crystallization solvent.
exptl_crystal_grow_comp.sol_id
An identifier for the solution to which the given solution
component belongs.
1
well solution
solution A
exptl_crystal_grow_comp.volume
The volume of the solution component.
200 \ml
0.1 ml
exptl_crystal_grow_comp.crystal_id
This data item is a pointer to attribute id in category exptl_crystal in the
EXPTL_CRYSTAL category.
exptl_crystal_grow_comp.id
The value of attribute id in category exptl_crystal_grow_comp must uniquely identify
each item in the EXPTL_CRYSTAL_GROW_COMP list.
Note that this item need not be a number; it can be any unique
identifier.
1
A
protein in buffer
0
geom
Data items in the GEOM and related (GEOM_ANGLE,
GEOM_BOND, GEOM_CONTACT, GEOM_HBOND and GEOM_TORSION)
categories record details about the molecular
geometry as calculated from the contents of the ATOM, CELL
and SYMMETRY data.
Geometry data are therefore redundant, in that they can be
calculated from other more fundamental quantities in the data
block. However, they provide a check on the correctness of
both sets of data and enable the most important geometric data
to be identified for publication by setting the appropriate
publication flag.
0
1
1
geomCategory
This property indicates that datablock
has a category holder geomCategory.
geomCategory
This property indicates that geomCategory.
has a category geom.
geomItem
Abstract datatype property for geom items.
reference_to_geom
cross-reference to geom.
referenced_by_geom
cross-reference from geom.
geom.details
A description of geometry not covered by the
existing data names in the GEOM categories, such as
least-squares planes.
geom.entry_id
This data item is a pointer to attribute id in category entry in the ENTRY category.
0
geom_angle
Data items in the GEOM_ANGLE category record details about the
bond angles as calculated from the contents
of the ATOM, CELL and SYMMETRY data.
Example 1 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
<PDBx:geom_angleCategory>
<PDBx:geom_angle atom_site_id_1="C2" atom_site_id_2="O1" atom_site_id_3="C5" site_symmetry_1="1_555" site_symmetry_2="1_555" site_symmetry_3="1_555">
<PDBx:publ_flag>yes</PDBx:publ_flag>
<PDBx:value>111.6</PDBx:value>
<PDBx:value_esd>0.2</PDBx:value_esd>
</PDBx:geom_angle>
<PDBx:geom_angle atom_site_id_1="O1" atom_site_id_2="C2" atom_site_id_3="C3" site_symmetry_1="1_555" site_symmetry_2="1_555" site_symmetry_3="1_555">
<PDBx:publ_flag>yes</PDBx:publ_flag>
<PDBx:value>110.9</PDBx:value>
<PDBx:value_esd>0.2</PDBx:value_esd>
</PDBx:geom_angle>
<PDBx:geom_angle atom_site_id_1="O1" atom_site_id_2="C2" atom_site_id_3="O21" site_symmetry_1="1_555" site_symmetry_2="1_555" site_symmetry_3="1_555">
<PDBx:publ_flag>yes</PDBx:publ_flag>
<PDBx:value>122.2</PDBx:value>
<PDBx:value_esd>0.3</PDBx:value_esd>
</PDBx:geom_angle>
<PDBx:geom_angle atom_site_id_1="C3" atom_site_id_2="C2" atom_site_id_3="O21" site_symmetry_1="1_555" site_symmetry_2="1_555" site_symmetry_3="1_555">
<PDBx:publ_flag>yes</PDBx:publ_flag>
<PDBx:value>127.0</PDBx:value>
<PDBx:value_esd>0.3</PDBx:value_esd>
</PDBx:geom_angle>
<PDBx:geom_angle atom_site_id_1="C2" atom_site_id_2="C3" atom_site_id_3="N4" site_symmetry_1="1_555" site_symmetry_2="1_555" site_symmetry_3="1_555">
<PDBx:publ_flag>yes</PDBx:publ_flag>
<PDBx:value>101.3</PDBx:value>
<PDBx:value_esd>0.2</PDBx:value_esd>
</PDBx:geom_angle>
<PDBx:geom_angle atom_site_id_1="C2" atom_site_id_2="C3" atom_site_id_3="C31" site_symmetry_1="1_555" site_symmetry_2="1_555" site_symmetry_3="1_555">
<PDBx:publ_flag>yes</PDBx:publ_flag>
<PDBx:value>111.3</PDBx:value>
<PDBx:value_esd>0.2</PDBx:value_esd>
</PDBx:geom_angle>
<PDBx:geom_angle atom_site_id_1="C2" atom_site_id_2="C3" atom_site_id_3="H3" site_symmetry_1="1_555" site_symmetry_2="1_555" site_symmetry_3="1_555">
<PDBx:publ_flag>no</PDBx:publ_flag>
<PDBx:value>107</PDBx:value>
<PDBx:value_esd>1</PDBx:value_esd>
</PDBx:geom_angle>
<PDBx:geom_angle atom_site_id_1="N4" atom_site_id_2="C3" atom_site_id_3="C31" site_symmetry_1="1_555" site_symmetry_2="1_555" site_symmetry_3="1_555">
<PDBx:publ_flag>yes</PDBx:publ_flag>
<PDBx:value>116.7</PDBx:value>
<PDBx:value_esd>0.2</PDBx:value_esd>
</PDBx:geom_angle>
</PDBx:geom_angleCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
1
1
1
1
1
geom_angleCategory
This property indicates that datablock
has a category holder geom_angleCategory.
geom_angleCategory
This property indicates that geom_angleCategory.
has a category geom_angle.
geom_angleItem
Abstract datatype property for geom_angle items.
reference_to_geom_angle
cross-reference to geom_angle.
referenced_by_geom_angle
cross-reference from geom_angle.
geom_angle.atom_site_auth_asym_id_1
An optional identifier of the first of the three atom sites that
define the angle.
This data item is a pointer to attribute auth_asym_id in category atom_site in the
ATOM_SITE category.
geom_angle.atom_site_auth_asym_id_2
An optional identifier of the second of the three atom sites
that define the angle.
This data item is a pointer to attribute auth_asym_id in category atom_site in the
ATOM_SITE category.
geom_angle.atom_site_auth_asym_id_3
An optional identifier of the third of the three atom sites that
define the angle.
This data item is a pointer to attribute auth_asym_id in category atom_site in the
ATOM_SITE category.
geom_angle.atom_site_auth_atom_id_1
An optional identifier of the first of the three atom sites that
define the angle.
This data item is a pointer to attribute auth_atom_id in category atom_site in the
ATOM_SITE category.
geom_angle.atom_site_auth_atom_id_2
An optional identifier of the second of the three atom sites
that define the angle.
This data item is a pointer to attribute auth_atom_id in category atom_site in the
ATOM_SITE category.
geom_angle.atom_site_auth_atom_id_3
An optional identifier of the third of the three atom sites that
define the angle.
This data item is a pointer to attribute auth_atom_id in category atom_site in the
ATOM_SITE category.
geom_angle.atom_site_auth_comp_id_1
An optional identifier of the first of the three atom sites that
define the angle.
This data item is a pointer to attribute auth_comp_id in category atom_site in the
ATOM_SITE category.
geom_angle.atom_site_auth_comp_id_2
An optional identifier of the second of the three atom sites
that define the angle.
This data item is a pointer to attribute auth_comp_id in category atom_site in the
ATOM_SITE category.
geom_angle.atom_site_auth_comp_id_3
An optional identifier of the third of the three atom sites that
define the angle.
This data item is a pointer to attribute auth_comp_id in category atom_site in the
ATOM_SITE category.
geom_angle.atom_site_auth_seq_id_1
An optional identifier of the first of the three atom sites that
define the angle.
This data item is a pointer to attribute auth_seq_id in category atom_site in the
ATOM_SITE category.
geom_angle.atom_site_auth_seq_id_2
An optional identifier of the second of the three atom sites
that define the angle.
This data item is a pointer to attribute auth_seq_id in category atom_site in the
ATOM_SITE category.
geom_angle.atom_site_auth_seq_id_3
An optional identifier of the third of the three atom sites that
define the angle.
This data item is a pointer to attribute auth_seq_id in category atom_site in the
ATOM_SITE category.
geom_angle.atom_site_label_alt_id_1
An optional identifier of the first of the three atom sites that
define the angle.
This data item is a pointer to attribute label_alt_id in category atom_site in the
ATOM_SITE category.
geom_angle.atom_site_label_alt_id_2
An optional identifier of the second of the three atom sites
that define the angle.
This data item is a pointer to attribute label_alt_id in category atom_site in the
ATOM_SITE category.
geom_angle.atom_site_label_alt_id_3
An optional identifier of the third of the three atom sites that
define the angle.
This data item is a pointer to attribute label_alt_id in category atom_site in the
ATOM_SITE category.
geom_angle.atom_site_label_asym_id_1
An optional identifier of the first of the three atom sites that
define the angle.
This data item is a pointer to attribute label_asym_id in category atom_site in the
ATOM_SITE category.
geom_angle.atom_site_label_asym_id_2
An optional identifier of the second of the three atom sites
that define the angle.
This data item is a pointer to attribute label_asym_id in category atom_site in the
ATOM_SITE category.
geom_angle.atom_site_label_asym_id_3
An optional identifier of the third of the three atom sites that
define the angle.
This data item is a pointer to attribute label_asym_id in category atom_site in the
ATOM_SITE category.
geom_angle.atom_site_label_atom_id_1
An optional identifier of the first of the three atom sites that
define the angle.
This data item is a pointer to attribute label_atom_id in category atom_site in the
ATOM_SITE category.
geom_angle.atom_site_label_atom_id_2
An optional identifier of the second of the three atom sites
that define the angle.
This data item is a pointer to attribute label_atom_id in category atom_site in the
ATOM_SITE category.
geom_angle.atom_site_label_atom_id_3
An optional identifier of the third of the three atom sites that
define the angle.
This data item is a pointer to attribute label_atom_id in category atom_site in the
ATOM_SITE category.
geom_angle.atom_site_label_comp_id_1
An optional identifier of the first of the three atom sites that
define the angle.
This data item is a pointer to attribute label_comp_id in category atom_site in the
ATOM_SITE category.
geom_angle.atom_site_label_comp_id_2
An optional identifier of the second of the three atom sites
that define the angle.
This data item is a pointer to attribute label_comp_id in category atom_site in the
ATOM_SITE category.
geom_angle.atom_site_label_comp_id_3
An optional identifier of the third of the three atom sites that
define the angle.
This data item is a pointer to attribute label_comp_id in category atom_site in the
ATOM_SITE category.
geom_angle.atom_site_label_seq_id_1
An optional identifier of the first of the three atom sites that
define the angle.
This data item is a pointer to attribute label_seq_id in category atom_site in the
ATOM_SITE category.
geom_angle.atom_site_label_seq_id_2
An optional identifier of the second of the three atom sites
that define the angle.
This data item is a pointer to attribute label_seq_id in category atom_site in the
ATOM_SITE category.
geom_angle.atom_site_label_seq_id_3
An optional identifier of the third of the three atom sites that
define the angle.
This data item is a pointer to attribute label_seq_id in category atom_site in the
ATOM_SITE category.
geom_angle.pdbx_PDB_model_num
Pointer to attribute pdbx_PDB_model_num in category atom_site
geom_angle.pdbx_atom_site_PDB_ins_code_1
Pointer to attribute pdbx_PDB_ins_code in category atom_site.
geom_angle.pdbx_atom_site_PDB_ins_code_2
Pointer to attribute pdbx_PDB_ins_code in category atom_site.
geom_angle.pdbx_atom_site_PDB_ins_code_3
Pointer to attribute pdbx_PDB_ins_code in category atom_site.
no
n
yes
y
This code signals whether the angle is referred to in a
publication or should be placed in a table of significant angles.
geom_angle.value
Angle in degrees defined by the three sites
_geom_angle.atom_site_id_1, _geom_angle.atom_site_id_2 and
attribute atom_site_id_3 in category geom_angle.
geom_angle.value_esd
The standard uncertainty (estimated standard deviation)
of attribute value in category geom_angle.
geom_angle.atom_site_id_1
The identifier of the first of the three atom sites that define
the angle.
This data item is a pointer to attribute id in category atom_site in the ATOM_SITE
category.
geom_angle.atom_site_id_2
The identifier of the second of the three atom sites that define
the angle. The second atom is taken to be the apex of the angle.
This data item is a pointer to attribute id in category atom_site in the ATOM_SITE
category.
geom_angle.atom_site_id_3
The identifier of the third of the three atom sites that define
the angle.
This data item is a pointer to attribute id in category atom_site in the ATOM_SITE
category.
geom_angle.site_symmetry_1
The symmetry code of the first of the three atom sites that
define the angle.
4th symmetry operation applied
4
7th symm. posn.; +a on x; -b on y
7_645
geom_angle.site_symmetry_2
The symmetry code of the second of the three atom sites that
define the angle.
4th symmetry operation applied
4
7th symm. posn.; +a on x; -b on y
7_645
geom_angle.site_symmetry_3
The symmetry code of the third of the three atom sites that
define the angle.
4th symmetry operation applied
4
7th symm. posn.; +a on x; -b on y
7_645
0
geom_bond
Data items in the GEOM_BOND category record details about
the bond lengths as calculated from the contents
of the ATOM, CELL and SYMMETRY data.
Example 1 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
<PDBx:geom_bondCategory>
<PDBx:geom_bond atom_site_id_1="O1" atom_site_id_2="C2" site_symmetry_1="1_555" site_symmetry_2="1_555">
<PDBx:dist>1.342</PDBx:dist>
<PDBx:dist_esd>0.004</PDBx:dist_esd>
<PDBx:publ_flag>yes</PDBx:publ_flag>
</PDBx:geom_bond>
<PDBx:geom_bond atom_site_id_1="O1" atom_site_id_2="C5" site_symmetry_1="1_555" site_symmetry_2="1_555">
<PDBx:dist>1.439</PDBx:dist>
<PDBx:dist_esd>0.003</PDBx:dist_esd>
<PDBx:publ_flag>yes</PDBx:publ_flag>
</PDBx:geom_bond>
<PDBx:geom_bond atom_site_id_1="C2" atom_site_id_2="C3" site_symmetry_1="1_555" site_symmetry_2="1_555">
<PDBx:dist>1.512</PDBx:dist>
<PDBx:dist_esd>0.004</PDBx:dist_esd>
<PDBx:publ_flag>yes</PDBx:publ_flag>
</PDBx:geom_bond>
<PDBx:geom_bond atom_site_id_1="C2" atom_site_id_2="O21" site_symmetry_1="1_555" site_symmetry_2="1_555">
<PDBx:dist>1.199</PDBx:dist>
<PDBx:dist_esd>0.004</PDBx:dist_esd>
<PDBx:publ_flag>yes</PDBx:publ_flag>
</PDBx:geom_bond>
<PDBx:geom_bond atom_site_id_1="C3" atom_site_id_2="N4" site_symmetry_1="1_555" site_symmetry_2="1_555">
<PDBx:dist>1.465</PDBx:dist>
<PDBx:dist_esd>0.003</PDBx:dist_esd>
<PDBx:publ_flag>yes</PDBx:publ_flag>
</PDBx:geom_bond>
<PDBx:geom_bond atom_site_id_1="C3" atom_site_id_2="C31" site_symmetry_1="1_555" site_symmetry_2="1_555">
<PDBx:dist>1.537</PDBx:dist>
<PDBx:dist_esd>0.004</PDBx:dist_esd>
<PDBx:publ_flag>yes</PDBx:publ_flag>
</PDBx:geom_bond>
<PDBx:geom_bond atom_site_id_1="C3" atom_site_id_2="H3" site_symmetry_1="1_555" site_symmetry_2="1_555">
<PDBx:dist>1.00</PDBx:dist>
<PDBx:dist_esd>0.03</PDBx:dist_esd>
<PDBx:publ_flag>no</PDBx:publ_flag>
</PDBx:geom_bond>
<PDBx:geom_bond atom_site_id_1="N4" atom_site_id_2="C5" site_symmetry_1="1_555" site_symmetry_2="1_555">
<PDBx:dist>1.472</PDBx:dist>
<PDBx:dist_esd>0.003</PDBx:dist_esd>
<PDBx:publ_flag>yes</PDBx:publ_flag>
</PDBx:geom_bond>
</PDBx:geom_bondCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
1
1
1
geom_bondCategory
This property indicates that datablock
has a category holder geom_bondCategory.
geom_bondCategory
This property indicates that geom_bondCategory.
has a category geom_bond.
geom_bondItem
Abstract datatype property for geom_bond items.
reference_to_geom_bond
cross-reference to geom_bond.
referenced_by_geom_bond
cross-reference from geom_bond.
geom_bond.atom_site_auth_asym_id_1
An optional identifier of the first of the two atom sites that
define the bond.
This data item is a pointer to attribute auth_asym_id in category atom_site in the
ATOM_SITE category.
geom_bond.atom_site_auth_asym_id_2
An optional identifier of the second of the two atom sites that
define the bond.
This data item is a pointer to attribute auth_asym_id in category atom_site in the
ATOM_SITE category.
geom_bond.atom_site_auth_atom_id_1
An optional identifier of the first of the two atom sites that
define the bond.
This data item is a pointer to attribute auth_atom_id in category atom_site in the
ATOM_SITE category.
geom_bond.atom_site_auth_atom_id_2
An optional identifier of the second of the two atom sites that
define the bond.
This data item is a pointer to attribute auth_atom_id in category atom_site in the
ATOM_SITE category.
geom_bond.atom_site_auth_comp_id_1
An optional identifier of the first of the two atom sites that
define the bond.
This data item is a pointer to attribute auth_comp_id in category atom_site in the
ATOM_SITE category.
geom_bond.atom_site_auth_comp_id_2
An optional identifier of the second of the two atom sites that
define the bond.
This data item is a pointer to attribute auth_comp_id in category atom_site in the
ATOM_SITE category.
geom_bond.atom_site_auth_seq_id_1
An optional identifier of the first of the two atom sites that
define the bond.
This data item is a pointer to attribute auth_seq_id in category atom_site in the
ATOM_SITE category.
geom_bond.atom_site_auth_seq_id_2
An optional identifier of the second of the two atom sites that
define the bond.
This data item is a pointer to attribute auth_seq_id in category atom_site in the
ATOM_SITE category.
geom_bond.atom_site_label_alt_id_1
An optional identifier of the first of the two atom sites that
define the bond.
This data item is a pointer to attribute label_alt_id in category atom_site in the
ATOM_SITE category.
geom_bond.atom_site_label_alt_id_2
An optional identifier of the second of the two atom sites that
define the bond.
This data item is a pointer to attribute label_alt_id in category atom_site in the
ATOM_SITE category.
geom_bond.atom_site_label_asym_id_1
An optional identifier of the first of the two atom sites that
define the bond.
This data item is a pointer to attribute label_asym_id in category atom_site in the
ATOM_SITE category.
geom_bond.atom_site_label_asym_id_2
An optional identifier of the second of the two atom sites that
define the bond.
This data item is a pointer to attribute label_asym_id in category atom_site in the
ATOM_SITE category.
geom_bond.atom_site_label_atom_id_1
An optional identifier of the first of the two atom sites that
define the bond.
This data item is a pointer to attribute label_atom_id in category atom_site in the
ATOM_SITE category.
geom_bond.atom_site_label_atom_id_2
An optional identifier of the second of the two atom sites that
define the bond.
This data item is a pointer to attribute label_atom_id in category atom_site in the
ATOM_SITE category.
geom_bond.atom_site_label_comp_id_1
An optional identifier of the first of the two atom sites that
define the bond.
This data item is a pointer to attribute label_comp_id in category atom_site in the
ATOM_SITE category.
geom_bond.atom_site_label_comp_id_2
An optional identifier of the second of the two atom sites that
define the bond.
This data item is a pointer to attribute label_comp_id in category atom_site in the
ATOM_SITE category.
geom_bond.atom_site_label_seq_id_1
An optional identifier of the first of the two atom sites that
define the bond.
This data item is a pointer to attribute label_seq_id in category atom_site in the
ATOM_SITE category.
geom_bond.atom_site_label_seq_id_2
An optional identifier of the second of the two atom sites that
define the bond.
This data item is a pointer to attribute label_seq_id in category atom_site in the
ATOM_SITE category.
geom_bond.dist
The intramolecular bond distance in angstroms.
geom_bond.dist_esd
The standard uncertainty (estimated standard deviation)
of attribute dist in category geom_bond.
geom_bond.pdbx_PDB_model_num
Pointer to attribute pdbx_PDB_model_num in category atom_site
geom_bond.pdbx_atom_site_PDB_ins_code_1
Pointer to attribute pdbx_PDB_ins_code in category atom_site.
geom_bond.pdbx_atom_site_PDB_ins_code_2
Pointer to attribute pdbx_PDB_ins_code in category atom_site.
no
n
yes
y
This code signals whether the bond distance is referred to in a
publication or should be placed in a list of significant bond
distances.
geom_bond.valence
The bond valence calculated from attribute dist in category geom_bond.
geom_bond.atom_site_id_1
The identifier of the first of the two atom sites that define the
bond.
This data item is a pointer to attribute id in category atom_site in the ATOM_SITE
category.
geom_bond.atom_site_id_2
The identifier of the second of the two atom sites that define
the bond.
This data item is a pointer to attribute id in category atom_site in the ATOM_SITE
category.
geom_bond.site_symmetry_1
The symmetry code of the first of the two atom sites that
define the bond.
4th symmetry operation applied
4
7th symm. posn.; +a on x; -b on y
7_645
geom_bond.site_symmetry_2
The symmetry code of the second of the two atom sites that
define the bond.
4th symmetry operation applied
4
7th symm. posn.; +a on x; -b on y
7_645
0
geom_contact
Data items in the GEOM_CONTACT category record details about
interatomic contacts as calculated from the contents
of the ATOM, CELL and SYMMETRY data.
Example 1 - based on data set CLPHO6 of Ferguson, Ruhl, McKervey & Browne
[Acta Cryst. (1992), C48, 2262-2264].
<PDBx:geom_contactCategory>
<PDBx:geom_contact atom_site_id_1="O(1)" atom_site_id_2="O(2)" site_symmetry_1="1_555" site_symmetry_2="1_555">
<PDBx:dist>2.735</PDBx:dist>
<PDBx:dist_esd>0.003</PDBx:dist_esd>
<PDBx:publ_flag>yes</PDBx:publ_flag>
</PDBx:geom_contact>
<PDBx:geom_contact atom_site_id_1="H(O1)" atom_site_id_2="O(2)" site_symmetry_1="1_555" site_symmetry_2="1_555">
<PDBx:dist>1.82</PDBx:dist>
<PDBx:dist_esd xsi:nil="true" />
<PDBx:publ_flag>no</PDBx:publ_flag>
</PDBx:geom_contact>
</PDBx:geom_contactCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
1
1
1
geom_contactCategory
This property indicates that datablock
has a category holder geom_contactCategory.
geom_contactCategory
This property indicates that geom_contactCategory.
has a category geom_contact.
geom_contactItem
Abstract datatype property for geom_contact items.
reference_to_geom_contact
cross-reference to geom_contact.
referenced_by_geom_contact
cross-reference from geom_contact.
geom_contact.atom_site_auth_asym_id_1
An optional identifier of the first of the two atom sites that
define the contact.
This data item is a pointer to attribute auth_asym_id in category atom_site in the
ATOM_SITE category.
geom_contact.atom_site_auth_asym_id_2
An optional identifier of the second of the two atom sites that
define the contact.
This data item is a pointer to attribute auth_asym_id in category atom_site in the
ATOM_SITE category.
geom_contact.atom_site_auth_atom_id_1
An optional identifier of the first of the two atom sites that
define the contact.
This data item is a pointer to attribute auth_atom_id in category atom_site in the
ATOM_SITE category.
geom_contact.atom_site_auth_atom_id_2
An optional identifier of the second of the two atom sites that
define the contact.
This data item is a pointer to attribute auth_atom_id in category atom_site in the
ATOM_SITE category.
geom_contact.atom_site_auth_comp_id_1
An optional identifier of the first of the two atom sites that
define the contact.
This data item is a pointer to attribute auth_comp_id in category atom_site in the
ATOM_SITE category.
geom_contact.atom_site_auth_comp_id_2
An optional identifier of the second of the two atom sites that
define the contact.
This data item is a pointer to attribute auth_comp_id in category atom_site in the
ATOM_SITE category.
geom_contact.atom_site_auth_seq_id_1
An optional identifier of the first of the two atom sites that
define the contact.
This data item is a pointer to attribute auth_seq_id in category atom_site in the
ATOM_SITE category.
geom_contact.atom_site_auth_seq_id_2
An optional identifier of the second of the two atom sites that
define the contact.
This data item is a pointer to attribute auth_seq_id in category atom_site in the
ATOM_SITE category.
geom_contact.atom_site_label_alt_id_1
An optional identifier of the first of the two atom sites that
define the contact.
This data item is a pointer to attribute label_alt_id in category atom_site in the
ATOM_SITE category.
geom_contact.atom_site_label_alt_id_2
An optional identifier of the second of the two atom sites that
define the contact.
This data item is a pointer to attribute label_alt_id in category atom_site in the
ATOM_SITE category.
geom_contact.atom_site_label_asym_id_1
An optional identifier of the first of the two atom sites that
define the contact.
This data item is a pointer to attribute label_asym_id in category atom_site in the
ATOM_SITE category.
geom_contact.atom_site_label_asym_id_2
An optional identifier of the second of the two atom sites that
define the contact.
This data item is a pointer to attribute label_asym_id in category atom_site in the
ATOM_SITE category.
geom_contact.atom_site_label_atom_id_1
An optional identifier of the first of the two atom sites that
define the contact.
This data item is a pointer to attribute label_atom_id in category atom_site in the
ATOM_SITE category.
geom_contact.atom_site_label_atom_id_2
An optional identifier of the second of the two atom sites that
define the contact.
This data item is a pointer to attribute label_atom_id in category atom_site in the
ATOM_SITE category.
geom_contact.atom_site_label_comp_id_1
An optional identifier of the first of the two atom sites that
define the contact.
This data item is a pointer to attribute label_comp_id in category atom_site in the
ATOM_SITE category.
geom_contact.atom_site_label_comp_id_2
An optional identifier of the second of the two atom sites that
define the contact.
This data item is a pointer to attribute label_comp_id in category atom_site in the
ATOM_SITE category.
geom_contact.atom_site_label_seq_id_1
An optional identifier of the first of the two atom sites that
define the contact.
This data item is a pointer to attribute label_seq_id in category atom_site in the
ATOM_SITE category.
geom_contact.atom_site_label_seq_id_2
An optional identifier of the second of the two atom sites that
define the contact.
This data item is a pointer to attribute label_seq_id in category atom_site in the
ATOM_SITE category.
geom_contact.dist
The interatomic contact distance in angstroms.
geom_contact.dist_esd
The standard uncertainty (estimated standard deviation)
of attribute dist in category geom_contact.
geom_contact.pdbx_PDB_model_num
Pointer to attribute pdbx_PDB_model_num in category atom_site
geom_contact.pdbx_atom_site_PDB_ins_code_1
Pointer to attribute pdbx_PDB_ins_code in category atom_site.
geom_contact.pdbx_atom_site_PDB_ins_code_2
Pointer to attribute pdbx_PDB_ins_code in category atom_site.
no
n
yes
y
This code signals whether the contact distance is referred to
in a publication or should be placed in a list of significant
contact distances.
geom_contact.atom_site_id_1
The identifier of the first of the two atom sites that define the
contact.
This data item is a pointer to attribute id in category atom_site in the ATOM_SITE
category.
geom_contact.atom_site_id_2
The identifier of the second of the two atom sites that define
the contact.
This data item is a pointer to attribute id in category atom_site in the ATOM_SITE
category.
geom_contact.site_symmetry_1
The symmetry code of the first of the two atom sites that
define the contact.
4th symmetry operation applied
4
7th symm. posn.; +a on x; -b on y
7_645
geom_contact.site_symmetry_2
The symmetry code of the second of the two atom sites that
define the contact.
4th symmetry operation applied
4
7th symm. posn.; +a on x; -b on y
7_645
0
geom_hbond
Data items in the GEOM_HBOND category record details about
hydrogen bonds as calculated from the contents of the ATOM,
CELL and SYMMETRY data.
Example 1 - based on C~14~H~13~ClN~2~O.H~2~O, reported by Palmer,
Puddle & Lisgarten [Acta Cryst. (1993), C49, 1777-1779].
<PDBx:geom_hbondCategory>
<PDBx:geom_hbond atom_site_id_A="OW" atom_site_id_D="N6" atom_site_id_H="HN6">
<PDBx:angle_DHA>169.6</PDBx:angle_DHA>
<PDBx:dist_DA>2.801</PDBx:dist_DA>
<PDBx:dist_DH>0.888</PDBx:dist_DH>
<PDBx:dist_HA>1.921</PDBx:dist_HA>
<PDBx:publ_flag>yes</PDBx:publ_flag>
</PDBx:geom_hbond>
<PDBx:geom_hbond atom_site_id_A="O7" atom_site_id_D="OW" atom_site_id_H="HO2">
<PDBx:angle_DHA>153.5</PDBx:angle_DHA>
<PDBx:dist_DA>2.793</PDBx:dist_DA>
<PDBx:dist_DH>0.917</PDBx:dist_DH>
<PDBx:dist_HA>1.923</PDBx:dist_HA>
<PDBx:publ_flag>yes</PDBx:publ_flag>
</PDBx:geom_hbond>
<PDBx:geom_hbond atom_site_id_A="N10" atom_site_id_D="OW" atom_site_id_H="HO1">
<PDBx:angle_DHA>179.7</PDBx:angle_DHA>
<PDBx:dist_DA>2.842</PDBx:dist_DA>
<PDBx:dist_DH>0.894</PDBx:dist_DH>
<PDBx:dist_HA>1.886</PDBx:dist_HA>
<PDBx:publ_flag>yes</PDBx:publ_flag>
</PDBx:geom_hbond>
</PDBx:geom_hbondCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
1
1
1
1
1
geom_hbondCategory
This property indicates that datablock
has a category holder geom_hbondCategory.
geom_hbondCategory
This property indicates that geom_hbondCategory.
has a category geom_hbond.
geom_hbondItem
Abstract datatype property for geom_hbond items.
reference_to_geom_hbond
cross-reference to geom_hbond.
referenced_by_geom_hbond
cross-reference from geom_hbond.
geom_hbond.angle_DHA
The angle in degrees defined by the donor-, hydrogen- and
acceptor-atom sites in a hydrogen bond.
geom_hbond.angle_DHA_esd
The standard uncertainty (estimated standard deviation)
of attribute angle_DHA in category geom_hbond.
geom_hbond.atom_site_auth_asym_id_A
An optional identifier of the acceptor-atom site that defines
the hydrogen bond.
This data item is a pointer to attribute auth_asym_id in category atom_site in the
ATOM_SITE category.
geom_hbond.atom_site_auth_asym_id_D
An optional identifier of the donor-atom site that defines
the hydrogen bond.
This data item is a pointer to attribute auth_asym_id in category atom_site in the
ATOM_SITE category.
geom_hbond.atom_site_auth_asym_id_H
An optional identifier of the hydrogen-atom site that defines
the hydrogen bond.
This data item is a pointer to attribute auth_asym_id in category atom_site in the
ATOM_SITE category.
geom_hbond.atom_site_auth_atom_id_A
An optional identifier of the acceptor-atom site that defines
the hydrogen bond.
This data item is a pointer to attribute auth_atom_id in category atom_site in the
ATOM_SITE category.
geom_hbond.atom_site_auth_atom_id_D
An optional identifier of the donor-atom site that defines
the hydrogen bond.
This data item is a pointer to attribute auth_atom_id in category atom_site in the
ATOM_SITE category.
geom_hbond.atom_site_auth_atom_id_H
An optional identifier of the hydrogen-atom site that defines
the hydrogen bond.
This data item is a pointer to attribute auth_atom_id in category atom_site in the
ATOM_SITE category.
geom_hbond.atom_site_auth_comp_id_A
An optional identifier of the acceptor-atom site that defines
the hydrogen bond.
This data item is a pointer to attribute auth_comp_id in category atom_site in the
ATOM_SITE category.
geom_hbond.atom_site_auth_comp_id_D
An optional identifier of the donor-atom site that defines
the hydrogen bond.
This data item is a pointer to attribute auth_comp_id in category atom_site in the
ATOM_SITE category.
geom_hbond.atom_site_auth_comp_id_H
An optional identifier of the hydrogen-atom site that defines
the hydrogen bond.
This data item is a pointer to attribute auth_comp_id in category atom_site in the
ATOM_SITE category.
geom_hbond.atom_site_auth_seq_id_A
An optional identifier of the acceptor-atom site that defines
the hydrogen bond.
This data item is a pointer to attribute auth_seq_id in category atom_site in the
ATOM_SITE category.
geom_hbond.atom_site_auth_seq_id_D
An optional identifier of the donor-atom site that defines
the hydrogen bond.
This data item is a pointer to attribute auth_seq_id in category atom_site in the
ATOM_SITE category.
geom_hbond.atom_site_auth_seq_id_H
An optional identifier of the hydrogen-atom site that defines
the hydrogen bond.
This data item is a pointer to attribute auth_seq_id in category atom_site in the
ATOM_SITE category.
geom_hbond.atom_site_label_alt_id_A
An optional identifier of the acceptor-atom site that defines
the hydrogen bond.
This data item is a pointer to attribute label_alt_id in category atom_site in the
ATOM_SITE category.
geom_hbond.atom_site_label_alt_id_D
An optional identifier of the donor-atom site that defines
the hydrogen bond.
This data item is a pointer to attribute label_alt_id in category atom_site in the
ATOM_SITE category.
geom_hbond.atom_site_label_alt_id_H
An optional identifier of the hydrogen-atom site that defines
the hydrogen bond.
This data item is a pointer to attribute label_alt_id in category atom_site in the
ATOM_SITE category.
geom_hbond.atom_site_label_asym_id_A
An optional identifier of the acceptor-atom site that defines
the hydrogen bond.
This data item is a pointer to attribute label_asym_id in category atom_site in the
ATOM_SITE category.
geom_hbond.atom_site_label_asym_id_D
An optional identifier of the donor-atom site that defines
the hydrogen bond.
This data item is a pointer to attribute label_asym_id in category atom_site in the
ATOM_SITE category.
geom_hbond.atom_site_label_asym_id_H
An optional identifier of the hydrogen-atom site that defines
the hydrogen bond.
This data item is a pointer to attribute label_asym_id in category atom_site in the
ATOM_SITE category.
geom_hbond.atom_site_label_atom_id_A
An optional identifier of the acceptor-atom site that defines
the hydrogen bond.
This data item is a pointer to attribute label_atom_id in category atom_site in the
ATOM_SITE category.
geom_hbond.atom_site_label_atom_id_D
An optional identifier of the donor-atom site that defines
the hydrogen bond.
This data item is a pointer to attribute label_atom_id in category atom_site in the
ATOM_SITE category.
geom_hbond.atom_site_label_atom_id_H
An optional identifier of the hydrogen-atom site that defines
the hydrogen bond.
This data item is a pointer to attribute label_atom_id in category atom_site in the
ATOM_SITE category.
geom_hbond.atom_site_label_comp_id_A
An optional identifier of the acceptor-atom site that defines
the hydrogen bond.
This data item is a pointer to attribute label_comp_id in category atom_site in the
ATOM_SITE category.
geom_hbond.atom_site_label_comp_id_D
An optional identifier of the donor-atom site that defines
the hydrogen bond.
This data item is a pointer to attribute label_comp_id in category atom_site in the
ATOM_SITE category.
geom_hbond.atom_site_label_comp_id_H
An optional identifier of the hydrogen-atom site that defines
the hydrogen bond.
This data item is a pointer to attribute label_comp_id in category atom_site in the
ATOM_SITE category.
geom_hbond.atom_site_label_seq_id_A
An optional identifier of the acceptor-atom site that defines
the hydrogen bond.
This data item is a pointer to attribute label_seq_id in category atom_site in the
ATOM_SITE category.
geom_hbond.atom_site_label_seq_id_D
An optional identifier of the donor-atom site that defines
the hydrogen bond.
This data item is a pointer to attribute label_seq_id in category atom_site in the
ATOM_SITE category.
geom_hbond.atom_site_label_seq_id_H
An optional identifier of the hydrogen-atom site that defines
the hydrogen bond.
This data item is a pointer to attribute label_seq_id in category atom_site in the
ATOM_SITE category.
geom_hbond.dist_DA
The distance in angstroms between the donor- and acceptor-atom
sites in a hydrogen bond.
geom_hbond.dist_DA_esd
The standard uncertainty (estimated standard deviation)
in angstroms of attribute dist_DA in category geom_hbond.
geom_hbond.dist_DH
The distance in angstroms between the donor- and hydrogen-atom
sites in a hydrogen bond.
geom_hbond.dist_DH_esd
The standard uncertainty (estimated standard deviation)
in angstroms of attribute dist_DH in category geom_hbond.
geom_hbond.dist_HA
The distance in angstroms between the hydrogen- and acceptor-
atom sites in a hydrogen bond.
geom_hbond.dist_HA_esd
The standard uncertainty (estimated standard deviation)
in angstroms of attribute dist_HA in category geom_hbond.
no
n
yes
y
This code signals whether the hydrogen-bond information is
referred to in a publication or should be placed in a table of
significant hydrogen-bond geometry.
geom_hbond.atom_site_id_A
The identifier of the acceptor-atom site that defines the
hydrogen bond.
This data item is a pointer to attribute id in category atom_site in the ATOM_SITE
category.
geom_hbond.atom_site_id_D
The identifier of the donor-atom site that defines the hydrogen
bond.
This data item is a pointer to attribute id in category atom_site in the ATOM_SITE
category.
geom_hbond.atom_site_id_H
The identifier of the hydrogen-atom site that defines the
hydrogen bond.
This data item is a pointer to attribute id in category atom_site in the ATOM_SITE
category.
geom_hbond.site_symmetry_A
The symmetry code of the acceptor-atom site that defines the
hydrogen bond.
4th symmetry operation applied
4
7th symm. posn.; +a on x; -b on y
7_645
geom_hbond.site_symmetry_D
The symmetry code of the donor-atom site that defines the
hydrogen bond.
4th symmetry operation applied
4
7th symm. posn.; +a on x; -b on y
7_645
geom_hbond.site_symmetry_H
The symmetry code of the hydrogen-atom site that defines the
hydrogen bond.
4th symmetry operation applied
4
7th symm. posn.; +a on x; -b on y
7_645
0
geom_torsion
Data items in the GEOM_TORSION category record details about
torsion angles as calculated from the
contents of the ATOM, CELL and SYMMETRY data.
The vector direction attribute atom_site_id_2 in category geom_torsion to
attribute atom_site_id_3 in category geom_torsion is the viewing direction, and the
torsion angle is the angle of twist required to superimpose the
projection of the vector between site 2 and site 1 onto the
projection of the vector between site 3 and site 4. Clockwise
torsions are positive, anticlockwise torsions are negative.
Ref: Klyne, W. & Prelog, V. (1960). Experientia, 16, 521-523.
Example 1 - based on data set CLPHO6 of Ferguson, Ruhl, McKervey & Browne
[Acta Cryst. (1992), C48, 2262-2264].
<PDBx:geom_torsionCategory>
<PDBx:geom_torsion atom_site_id_1="C(9)" atom_site_id_2="O(2)" atom_site_id_3="C(7)" atom_site_id_4="C(2)" site_symmetry_1="1_555" site_symmetry_2="1_555" site_symmetry_3="1_555" site_symmetry_4="1_555">
<PDBx:publ_flag>yes</PDBx:publ_flag>
<PDBx:value>71.8</PDBx:value>
</PDBx:geom_torsion>
<PDBx:geom_torsion atom_site_id_1="C(7)" atom_site_id_2="O(2)" atom_site_id_3="C(9)" atom_site_id_4="C(10)" site_symmetry_1="1_555" site_symmetry_2="1_555" site_symmetry_3="1_555" site_symmetry_4="2_666">
<PDBx:publ_flag>yes</PDBx:publ_flag>
<PDBx:value>-168.0</PDBx:value>
</PDBx:geom_torsion>
<PDBx:geom_torsion atom_site_id_1="C(10)" atom_site_id_2="O(3)" atom_site_id_3="C(8)" atom_site_id_4="C(6)" site_symmetry_1="1_555" site_symmetry_2="1_555" site_symmetry_3="1_555" site_symmetry_4="1_555">
<PDBx:publ_flag>yes</PDBx:publ_flag>
<PDBx:value>-167.7</PDBx:value>
</PDBx:geom_torsion>
<PDBx:geom_torsion atom_site_id_1="C(8)" atom_site_id_2="O(3)" atom_site_id_3="C(10)" atom_site_id_4="C(9)" site_symmetry_1="1_555" site_symmetry_2="1_555" site_symmetry_3="1_555" site_symmetry_4="2_666">
<PDBx:publ_flag>yes</PDBx:publ_flag>
<PDBx:value>-69.7</PDBx:value>
</PDBx:geom_torsion>
<PDBx:geom_torsion atom_site_id_1="O(1)" atom_site_id_2="C(1)" atom_site_id_3="C(2)" atom_site_id_4="C(3)" site_symmetry_1="1_555" site_symmetry_2="1_555" site_symmetry_3="1_555" site_symmetry_4="1_555">
<PDBx:publ_flag>no</PDBx:publ_flag>
<PDBx:value>-179.5</PDBx:value>
</PDBx:geom_torsion>
<PDBx:geom_torsion atom_site_id_1="O(1)" atom_site_id_2="C(1)" atom_site_id_3="C(2)" atom_site_id_4="C(7)" site_symmetry_1="1_555" site_symmetry_2="1_555" site_symmetry_3="1_555" site_symmetry_4="1_555">
<PDBx:publ_flag>no</PDBx:publ_flag>
<PDBx:value>-0.6</PDBx:value>
</PDBx:geom_torsion>
</PDBx:geom_torsionCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
1
1
1
1
1
1
1
geom_torsionCategory
This property indicates that datablock
has a category holder geom_torsionCategory.
geom_torsionCategory
This property indicates that geom_torsionCategory.
has a category geom_torsion.
geom_torsionItem
Abstract datatype property for geom_torsion items.
reference_to_geom_torsion
cross-reference to geom_torsion.
referenced_by_geom_torsion
cross-reference from geom_torsion.
geom_torsion.atom_site_auth_asym_id_1
An optional identifier of the first of the four atom sites that
define the torsion angle.
This data item is a pointer to attribute auth_asym_id in category atom_site in the
ATOM_SITE category.
geom_torsion.atom_site_auth_asym_id_2
An optional identifier of the second of the four atom sites that
define the torsion angle.
This data item is a pointer to attribute auth_asym_id in category atom_site in the
ATOM_SITE category.
geom_torsion.atom_site_auth_asym_id_3
An optional identifier of the third of the four atom sites that
define the torsion angle.
This data item is a pointer to attribute auth_asym_id in category atom_site in the
ATOM_SITE category.
geom_torsion.atom_site_auth_asym_id_4
An optional identifier of the fourth of the four atom sites that
define the torsion angle.
This data item is a pointer to attribute auth_asym_id in category atom_site in the
ATOM_SITE category.
geom_torsion.atom_site_auth_atom_id_1
An optional identifier of the first of the four atom sites that
define the torsion angle.
This data item is a pointer to attribute auth_atom_id in category atom_site in the
ATOM_SITE category.
geom_torsion.atom_site_auth_atom_id_2
An optional identifier of the second of the four atom sites that
define the torsion angle.
This data item is a pointer to attribute auth_atom_id in category atom_site in the
ATOM_SITE category.
geom_torsion.atom_site_auth_atom_id_3
An optional identifier of the third of the four atom sites that
define the torsion angle.
This data item is a pointer to attribute auth_atom_id in category atom_site in the
ATOM_SITE category.
geom_torsion.atom_site_auth_atom_id_4
An optional identifier of the fourth of the four atom sites that
define the torsion angle.
This data item is a pointer to attribute auth_atom_id in category atom_site in the
ATOM_SITE category.
geom_torsion.atom_site_auth_comp_id_1
An optional identifier of the first of the four atom sites that
define the torsion angle.
This data item is a pointer to attribute auth_comp_id in category atom_site in the
ATOM_SITE category.
geom_torsion.atom_site_auth_comp_id_2
An optional identifier of the second of the four atom sites that
define the torsion angle.
This data item is a pointer to attribute auth_comp_id in category atom_site in the
ATOM_SITE category.
geom_torsion.atom_site_auth_comp_id_3
An optional identifier of the third of the four atom sites that
define the torsion angle.
This data item is a pointer to attribute auth_comp_id in category atom_site in the
ATOM_SITE category.
geom_torsion.atom_site_auth_comp_id_4
An optional identifier of the fourth of the four atom sites that
define the torsion angle.
This data item is a pointer to attribute auth_comp_id in category atom_site in the
ATOM_SITE category.
geom_torsion.atom_site_auth_seq_id_1
An optional identifier of the first of the four atom sites that
define the torsion angle.
This data item is a pointer to attribute auth_seq_id in category atom_site in the
ATOM_SITE category.
geom_torsion.atom_site_auth_seq_id_2
An optional identifier of the second of the four atom sites that
define the torsion angle.
This data item is a pointer to attribute auth_seq_id in category atom_site in the
ATOM_SITE category.
geom_torsion.atom_site_auth_seq_id_3
An optional identifier of the third of the four atom sites that
define the torsion angle.
This data item is a pointer to attribute auth_seq_id in category atom_site in the
ATOM_SITE category.
geom_torsion.atom_site_auth_seq_id_4
An optional identifier of the fourth of the four atom sites that
define the torsion angle.
This data item is a pointer to attribute auth_seq_id in category atom_site in the
ATOM_SITE category.
geom_torsion.atom_site_label_alt_id_1
An optional identifier of the first of the four atom sites that
define the torsion angle.
This data item is a pointer to attribute label_alt_id in category atom_site in the
ATOM_SITE category.
geom_torsion.atom_site_label_alt_id_2
An optional identifier of the second of the four atom sites that
define the torsion angle.
This data item is a pointer to attribute label_alt_id in category atom_site in the
ATOM_SITE category.
geom_torsion.atom_site_label_alt_id_3
An optional identifier of the third of the four atom sites that
define the torsion angle.
This data item is a pointer to attribute label_alt_id in category atom_site in the
ATOM_SITE category.
geom_torsion.atom_site_label_alt_id_4
An optional identifier of the fourth of the four atom sites that
define the torsion angle.
This data item is a pointer to attribute label_alt_id in category atom_site in the
ATOM_SITE category.
geom_torsion.atom_site_label_asym_id_1
An optional identifier of the first of the four atom sites that
define the torsion angle.
This data item is a pointer to attribute label_asym_id in category atom_site in the
ATOM_SITE category.
geom_torsion.atom_site_label_asym_id_2
An optional identifier of the second of the four atom sites that
define the torsion angle.
This data item is a pointer to attribute label_asym_id in category atom_site in the
ATOM_SITE category.
geom_torsion.atom_site_label_asym_id_3
An optional identifier of the third of the four atom sites that
define the torsion angle.
This data item is a pointer to attribute label_asym_id in category atom_site in the
ATOM_SITE category.
geom_torsion.atom_site_label_asym_id_4
An optional identifier of the fourth of the four atom sites that
define the torsion angle.
This data item is a pointer to attribute label_asym_id in category atom_site in the
ATOM_SITE category.
geom_torsion.atom_site_label_atom_id_1
An optional identifier of the first of the four atom sites that
define the torsion angle.
This data item is a pointer to attribute label_atom_id in category atom_site in the
ATOM_SITE category.
geom_torsion.atom_site_label_atom_id_2
An optional identifier of the second of the four atom sites that
define the torsion angle.
This data item is a pointer to attribute label_atom_id in category atom_site in the
ATOM_SITE category.
geom_torsion.atom_site_label_atom_id_3
An optional identifier of the third of the four atom sites that
define the torsion angle.
This data item is a pointer to attribute label_atom_id in category atom_site in the
ATOM_SITE category.
geom_torsion.atom_site_label_atom_id_4
An optional identifier of the fourth of the four atom sites that
define the torsion angle.
This data item is a pointer to attribute label_atom_id in category atom_site in the
ATOM_SITE category.
geom_torsion.atom_site_label_comp_id_1
An optional identifier of the first of the four atom sites that
define the torsion angle.
This data item is a pointer to attribute label_comp_id in category atom_site in the
ATOM_SITE category.
geom_torsion.atom_site_label_comp_id_2
An optional identifier of the second of the four atom sites that
define the torsion angle.
This data item is a pointer to attribute label_comp_id in category atom_site in the
ATOM_SITE category.
geom_torsion.atom_site_label_comp_id_3
An optional identifier of the third of the four atom sites that
define the torsion angle.
This data item is a pointer to attribute label_comp_id in category atom_site in the
ATOM_SITE category.
geom_torsion.atom_site_label_comp_id_4
An optional identifier of the fourth of the four atom sites that
define the torsion angle.
This data item is a pointer to attribute label_comp_id in category atom_site in the
ATOM_SITE category.
geom_torsion.atom_site_label_seq_id_1
An optional identifier of the first of the four atom sites that
define the torsion angle.
This data item is a pointer to attribute label_seq_id in category atom_site in the
ATOM_SITE category.
geom_torsion.atom_site_label_seq_id_2
An optional identifier of the second of the four atom sites that
define the torsion angle.
This data item is a pointer to attribute label_seq_id in category atom_site in the
ATOM_SITE category.
geom_torsion.atom_site_label_seq_id_3
An optional identifier of the third of the four atom sites that
define the torsion angle.
This data item is a pointer to attribute label_seq_id in category atom_site in the
ATOM_SITE category.
geom_torsion.atom_site_label_seq_id_4
An optional identifier of the fourth of the four atom sites that
define the torsion angle.
This data item is a pointer to attribute label_seq_id in category atom_site in the
ATOM_SITE category.
geom_torsion.pdbx_PDB_model_num
Pointer to attribute pdbx_PDB_model_num in category atom_site
geom_torsion.pdbx_atom_site_PDB_ins_code_1
Pointer to attribute pdbx_PDB_ins_code in category atom_site.
geom_torsion.pdbx_atom_site_PDB_ins_code_2
Pointer to attribute pdbx_PDB_ins_code in category atom_site.
geom_torsion.pdbx_atom_site_PDB_ins_code_3
Pointer to attribute pdbx_PDB_ins_code in category atom_site.
geom_torsion.pdbx_atom_site_PDB_ins_code_4
Pointer to attribute pdbx_PDB_ins_code in category atom_site.
no
n
yes
y
This code signals whether the torsion angle is referred to in a
publication or should be placed in a table of significant
torsion angles.
geom_torsion.value
The value of the torsion angle in degrees.
geom_torsion.value_esd
The standard uncertainty (estimated standard deviation)
of attribute value in category geom_torsion.
geom_torsion.atom_site_id_1
The identifier of the first of the four atom sites that define
the torsion angle.
This data item is a pointer to attribute id in category atom_site in the ATOM_SITE
category.
geom_torsion.atom_site_id_2
The identifier of the second of the four atom sites that define
the torsion angle.
This data item is a pointer to attribute id in category atom_site in the ATOM_SITE
category.
geom_torsion.atom_site_id_3
The identifier of the third of the four atom sites that define
the torsion angle.
This data item is a pointer to attribute id in category atom_site in the ATOM_SITE
category.
geom_torsion.atom_site_id_4
The identifier of the fourth of the four atom sites that define
the torsion angle.
This data item is a pointer to attribute id in category atom_site in the ATOM_SITE
category.
geom_torsion.site_symmetry_1
The symmetry code of the first of the four atom sites that
define the torsion angle.
4th symmetry operation applied
4
7th symm. posn.; +a on x; -b on y
7_645
geom_torsion.site_symmetry_2
The symmetry code of the second of the four atom sites that
define the torsion angle.
4th symmetry operation applied
4
7th symm. posn.; +a on x; -b on y
7_645
geom_torsion.site_symmetry_3
The symmetry code of the third of the four atom sites that
define the torsion angle.
4th symmetry operation applied
4
7th symm. posn.; +a on x; -b on y
7_645
geom_torsion.site_symmetry_4
The symmetry code of the fourth of the four atom sites that
define the torsion angle.
4th symmetry operation applied
4
7th symm. posn.; +a on x; -b on y
7_645
0
journal
Data items in the JOURNAL category record details about the
book-keeping by the journal staff when processing
a data block submitted for publication.
The creator of a data block will not normally specify these data.
The data names are not defined in the dictionary because they are
for journal use only.
Example 1 - based on Acta Cryst. file for entry HL0007 [Willis, Beckwith
& Tozer (1991). Acta Cryst. C47, 2276-2277].
<PDBx:journalCategory>
<PDBx:journal entry_id="TOZ">
<PDBx:coden_ASTM>ACSCEE</PDBx:coden_ASTM>
<PDBx:coeditor_code>HL0007</PDBx:coeditor_code>
<PDBx:date_accepted>1991-04-18</PDBx:date_accepted>
<PDBx:date_from_coeditor>1991-04-18</PDBx:date_from_coeditor>
<PDBx:date_printers_first>1991-08-07</PDBx:date_printers_first>
<PDBx:date_proofs_out>1991-08-07</PDBx:date_proofs_out>
<PDBx:date_recd_electronic>1991-04-15</PDBx:date_recd_electronic>
<PDBx:issue>NOV91</PDBx:issue>
<PDBx:name_full>Acta Crystallographica Section C</PDBx:name_full>
<PDBx:page_first>2276</PDBx:page_first>
<PDBx:page_last>2277</PDBx:page_last>
<PDBx:techeditor_code>C910963</PDBx:techeditor_code>
<PDBx:volume>47</PDBx:volume>
<PDBx:year>1991</PDBx:year>
</PDBx:journal>
</PDBx:journalCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
journalCategory
This property indicates that datablock
has a category holder journalCategory.
journalCategory
This property indicates that journalCategory.
has a category journal.
journalItem
Abstract datatype property for journal items.
reference_to_journal
cross-reference to journal.
referenced_by_journal
cross-reference from journal.
journal.coden_ASTM
Journal data items are defined by the journal staff.
journal.coden_Cambridge
Journal data items are defined by the journal staff.
journal.coeditor_address
Journal data items are defined by the journal staff.
journal.coeditor_code
Journal data items are defined by the journal staff.
journal.coeditor_email
Journal data items are defined by the journal staff.
journal.coeditor_fax
Journal data items are defined by the journal staff.
journal.coeditor_name
Journal data items are defined by the journal staff.
journal.coeditor_notes
Journal data items are defined by the journal staff.
journal.coeditor_phone
Journal data items are defined by the journal staff.
journal.data_validation_number
Journal data items are defined by the journal staff.
journal.date_accepted
Journal data items are defined by the journal staff.
journal.date_from_coeditor
Journal data items are defined by the journal staff.
journal.date_printers_final
Journal data items are defined by the journal staff.
journal.date_printers_first
Journal data items are defined by the journal staff.
journal.date_proofs_in
Journal data items are defined by the journal staff.
journal.date_proofs_out
Journal data items are defined by the journal staff.
journal.date_recd_copyright
Journal data items are defined by the journal staff.
journal.date_recd_electronic
Journal data items are defined by the journal staff.
journal.date_recd_hard_copy
Journal data items are defined by the journal staff.
journal.date_to_coeditor
Journal data items are defined by the journal staff.
journal.issue
Journal data items are defined by the journal staff.
journal.language
Journal data items are defined by the journal staff.
journal.name_full
Journal data items are defined by the journal staff.
journal.page_first
Journal data items are defined by the journal staff.
journal.page_last
Journal data items are defined by the journal staff.
journal.paper_category
Journal data items are defined by the journal staff.
journal.suppl_publ_number
Journal data items are defined by the journal staff.
journal.suppl_publ_pages
Journal data items are defined by the journal staff.
journal.techeditor_address
Journal data items are defined by the journal staff.
journal.techeditor_code
Journal data items are defined by the journal staff.
journal.techeditor_email
Journal data items are defined by the journal staff.
journal.techeditor_fax
Journal data items are defined by the journal staff.
journal.techeditor_name
Journal data items are defined by the journal staff.
journal.techeditor_notes
Journal data items are defined by the journal staff.
journal.techeditor_phone
Journal data items are defined by the journal staff.
journal.volume
Journal data items are defined by the journal staff.
journal.year
Journal data items are defined by the journal staff.
journal.entry_id
This data item is a pointer to attribute id in category entry in the ENTRY category.
0
journal_index
Data items in the JOURNAL_INDEX category are used to list terms
used to generate the journal indexes.
The creator of a data block will not normally specify these data
items.
Example 1 - based on a paper by Zhu, Reynolds, Klein & Trudell
[Acta Cryst. (1994), C50, 2067-2069].
<PDBx:journal_indexCategory>
<PDBx:journal_index term="C16H19NO4" type="O">
<PDBx:subterm xsi:nil="true" />
</PDBx:journal_index>
<PDBx:journal_index term="alkaloids" type="S">
<PDBx:subterm>(-)-norcocaine</PDBx:subterm>
</PDBx:journal_index>
<PDBx:journal_index term="(-)-norcocaine" type="S">
<PDBx:subterm xsi:nil="true" />
</PDBx:journal_index>
<PDBx:journal_index term=" [2R,3S-(2\b,3\b)]-methyl 3-(benzoyloxy)-8-azabicyclo[3.2.1]octane-2-carboxylate" type="S">
<PDBx:subterm xsi:nil="true" />
</PDBx:journal_index>
</PDBx:journal_indexCategory>
0
1
1
1
journal_indexCategory
This property indicates that datablock
has a category holder journal_indexCategory.
journal_indexCategory
This property indicates that journal_indexCategory.
has a category journal_index.
journal_indexItem
Abstract datatype property for journal_index items.
reference_to_journal_index
cross-reference to journal_index.
referenced_by_journal_index
cross-reference from journal_index.
journal_index.subterm
Journal index data items are defined by the journal staff.
journal_index.term
Journal index data items are defined by the journal staff.
journal_index.type
Journal index data items are defined by the journal staff.
0
ndb_original_ndb_coordinates
Placeholder category for PDB coordinate data.
1
ndb_original_ndb_coordinatesCategory
This property indicates that datablock
has a category holder ndb_original_ndb_coordinatesCategory.
ndb_original_ndb_coordinatesCategory
This property indicates that ndb_original_ndb_coordinatesCategory.
has a category ndb_original_ndb_coordinates.
ndb_original_ndb_coordinatesItem
Abstract datatype property for ndb_original_ndb_coordinates items.
reference_to_ndb_original_ndb_coordinates
cross-reference to ndb_original_ndb_coordinates.
referenced_by_ndb_original_ndb_coordinates
cross-reference from ndb_original_ndb_coordinates.
ndb_original_ndb_coordinates.coord_section
Placeholder item to hold unparsed coordinate data.
0
ndb_struct_conf_na
Data items in the NDB_STRUCT_CONF_NA category
describes secondary structure features in this entry.
0
1
1
1
ndb_struct_conf_naCategory
This property indicates that datablock
has a category holder ndb_struct_conf_naCategory.
ndb_struct_conf_naCategory
This property indicates that ndb_struct_conf_naCategory.
has a category ndb_struct_conf_na.
ndb_struct_conf_naItem
Abstract datatype property for ndb_struct_conf_na items.
reference_to_ndb_struct_conf_na
cross-reference to ndb_struct_conf_na.
referenced_by_ndb_struct_conf_na
cross-reference from ndb_struct_conf_na.
ndb_struct_conf_na.feature_count
This data item counts the number of occurences of
this feature in this entry.
ndb_struct_conf_na.entry_id
This data item is a pointer to attribute id in category entry in the
ENTRY category.
double helix
a-form double helix
b-form double helix
z-form double helix
other right-handed double helix
triple helix
quadruple helix
parallel strands
internal loop
bulge loop
tetraloop
hairpin loop
two-way junction
three-way junction
four-way junction
mismatched base pair
This data item identifies a secondary structure
feature of this entry.
0
ndb_struct_feature_na
Data items in the NDB_STRUCT_FEATURE_NA category
describes tertiary and other special structural
features in this entry.
0
1
1
1
ndb_struct_feature_naCategory
This property indicates that datablock
has a category holder ndb_struct_feature_naCategory.
ndb_struct_feature_naCategory
This property indicates that ndb_struct_feature_naCategory.
has a category ndb_struct_feature_na.
ndb_struct_feature_naItem
Abstract datatype property for ndb_struct_feature_na items.
reference_to_ndb_struct_feature_na
cross-reference to ndb_struct_feature_na.
referenced_by_ndb_struct_feature_na
cross-reference from ndb_struct_feature_na.
ndb_struct_feature_na.feature_count
This data item counts the number of occurences of
this feature in this entry.
ndb_struct_feature_na.entry_id
This data item is a pointer to attribute id in category entry in the
ENTRY category.
pseudoknot
intercalated base
backbone turn
intramolecular base triplet
ribose zipper
purine platform
bent/kinked double helix
This data item identifies a structural
feature of this entry.
0
ndb_struct_na_base_pair
Data items in the NDB_STRUCT_NA_BASE_PAIR category record details
of base pairing interactions.
<PDBx:ndb_struct_na_base_pairCategory>
<PDBx:ndb_struct_na_base_pair i_label_asym_id="A" i_label_comp_id="G" i_label_seq_id="1" i_symmetry="1_555" j_label_asym_id="A" j_label_comp_id="C" j_label_seq_id="8" j_symmetry="7_555" model_number="1">
<PDBx:buckle>-5.523</PDBx:buckle>
<PDBx:opening>-3.291</PDBx:opening>
<PDBx:propeller>-6.752</PDBx:propeller>
<PDBx:shear>-0.396</PDBx:shear>
<PDBx:stagger>-0.018</PDBx:stagger>
<PDBx:stretch>-0.156</PDBx:stretch>
</PDBx:ndb_struct_na_base_pair>
<PDBx:ndb_struct_na_base_pair i_label_asym_id="A" i_label_comp_id="G" i_label_seq_id="2" i_symmetry="1_555" j_label_asym_id="A" j_label_comp_id="C" j_label_seq_id="7" j_symmetry="7_555" model_number="1">
<PDBx:buckle>-4.727</PDBx:buckle>
<PDBx:opening>2.311</PDBx:opening>
<PDBx:propeller>-9.765</PDBx:propeller>
<PDBx:shear>-0.094</PDBx:shear>
<PDBx:stagger>-0.334</PDBx:stagger>
<PDBx:stretch>-0.220</PDBx:stretch>
</PDBx:ndb_struct_na_base_pair>
<PDBx:ndb_struct_na_base_pair i_label_asym_id="A" i_label_comp_id="G" i_label_seq_id="3" i_symmetry="1_555" j_label_asym_id="A" j_label_comp_id="C" j_label_seq_id="6" j_symmetry="7_555" model_number="1">
<PDBx:buckle>-6.454</PDBx:buckle>
<PDBx:opening>-1.181</PDBx:opening>
<PDBx:propeller>-12.575</PDBx:propeller>
<PDBx:shear>-0.285</PDBx:shear>
<PDBx:stagger>0.008</PDBx:stagger>
<PDBx:stretch>-0.239</PDBx:stretch>
</PDBx:ndb_struct_na_base_pair>
</PDBx:ndb_struct_na_base_pairCategory>
0
1
0
1
0
1
0
1
0
1
1
1
1
1
0
1
1
1
1
1
0
1
1
1
1
1
0
1
0
1
0
1
0
1
1
1
1
1
1
1
1
1
1
ndb_struct_na_base_pairCategory
This property indicates that datablock
has a category holder ndb_struct_na_base_pairCategory.
ndb_struct_na_base_pairCategory
This property indicates that ndb_struct_na_base_pairCategory.
has a category ndb_struct_na_base_pair.
ndb_struct_na_base_pairItem
Abstract datatype property for ndb_struct_na_base_pair items.
reference_to_ndb_struct_na_base_pair
cross-reference to ndb_struct_na_base_pair.
referenced_by_ndb_struct_na_base_pair
cross-reference from ndb_struct_na_base_pair.
ndb_struct_na_base_pair.buckle
The value of the base pair buckle parameter.
ndb_struct_na_base_pair.hbond_type_12
Base pair classification of Westhoff and Leontis.
ndb_struct_na_base_pair.hbond_type_28
Base pair classification of Saenger
cWW
tWW
cWH
cHW
tWH
tHW
cWS
cSW
tWS
tSW
cHH
tHH
cHS
cSH
tHS
tSH
cSS
tSS
Base pair classification of Leontis and Westhof.
The Leontis-Westhof classification system annotates
basepairs according to the interacting edge used by
each base (Watson-Crick, Hoogsteen, or Sugar), and
glycosidic bond orientation (cis, trans). For six of
twelve classes, the correct Leontis-Westhof notation
depends upon the order (i,j) of the identified
nucleotides.
Leontis NB and Westhof E (2001) Geometric nomenclature
and classification of RNA base pairs. RNA 7:499-512.
https://doi.org/10.1017/s1355838201002515
Replacement for category item
attribute hbond_type_12 in category ndb_struct_na_base_pair. The older item
encodes the 12 classes by a numerical index, without
identifying the interacting edges used by each base in
nucleotides i,j.
ndb_struct_na_base_pair.i_PDB_ins_code
Describes the PDB insertion code of the i-th base in the base pair.
This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the
ATOM_SITE category.
ndb_struct_na_base_pair.i_auth_asym_id
Describes the asym id of the i-th base in the base pair.
This data item is a pointer to attribute auth_asym_id in category atom_site in the
ATOM_SITE category.
ndb_struct_na_base_pair.i_auth_seq_id
Describes the sequence number of the i-th base in the base pair.
This data item is a pointer to attribute auth_seq_id in category atom_site in the
ATOM_SITE category.
ndb_struct_na_base_pair.j_PDB_ins_code
Describes the PDB insertion code of the j-th base in the base pair.
This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the
ATOM_SITE category.
ndb_struct_na_base_pair.j_auth_asym_id
Describes the asym id of the j-th base in the base pair.
This data item is a pointer to attribute auth_asym_id in category atom_site in the
ATOM_SITE category.
ndb_struct_na_base_pair.j_auth_seq_id
Describes the sequence number of the j-th base in the base pair.
This data item is a pointer to attribute auth_seq_id in category atom_site in the
ATOM_SITE category.
ndb_struct_na_base_pair.opening
The value of the base pair opening parameter.
ndb_struct_na_base_pair.pair_name
Text label for this base pair.
ndb_struct_na_base_pair.pair_number
Sequential number of pair in the pair sequence.
ndb_struct_na_base_pair.propeller
The value of the base pair propeller parameter.
ndb_struct_na_base_pair.shear
The value of the base pair shear parameter.
ndb_struct_na_base_pair.stagger
The value of the base pair stagger parameter.
ndb_struct_na_base_pair.stretch
The value of the base pair stretch parameter.
ndb_struct_na_base_pair.i_label_asym_id
Describes the asym id of the i-th base in the base pair.
This data item is a pointer to attribute label_asym_id in category atom_site in the
ATOM_SITE category.
ndb_struct_na_base_pair.i_label_comp_id
Describes the component id of the i-th base in the base pair.
This data item is a pointer to attribute label_comp_id in category atom_site in the
ATOM_SITE category.
ndb_struct_na_base_pair.i_label_seq_id
Describes the sequence number of the i-th base in the base pair.
This data item is a pointer to attribute label_seq_id in category atom_site in the
ATOM_SITE category.
ndb_struct_na_base_pair.i_symmetry
Describes the symmetry operation that should be applied to the
coordinates of the i-th base to generate the first partner
in the base pair.
4th symmetry operation applied
4
7th symm. posn.; +a on x; -b on y
7_645
ndb_struct_na_base_pair.j_label_asym_id
Describes the asym id of the j-th base in the base pair.
This data item is a pointer to attribute label_asym_id in category atom_site in the
ATOM_SITE category.
ndb_struct_na_base_pair.j_label_comp_id
Describes the component id of the j-th base in the base pair.
This data item is a pointer to attribute label_comp_id in category atom_site in the
ATOM_SITE category.
ndb_struct_na_base_pair.j_label_seq_id
Describes the sequence number of the j-th base in the base pair.
This data item is a pointer to attribute label_seq_id in category atom_site in the
ATOM_SITE category.
ndb_struct_na_base_pair.j_symmetry
Describes the symmetry operation that should be applied to the
coordinates of the j-th base to generate the second partner
in the base pair.
4th symmetry operation applied
4
7th symm. posn.; +a on x; -b on y
7_645
ndb_struct_na_base_pair.model_number
Describes the model number of the base pair.
This data item is a pointer to attribute pdbx_PDB_model_num in category atom_site in the
ATOM_SITE category.
0
ndb_struct_na_base_pair_step
Data items in the NDB_STRUCT_NA_BASE_PAIR_STEP category record details
of base pair step interactions.
<PDBx:ndb_struct_na_base_pair_stepCategory>
<PDBx:ndb_struct_na_base_pair_step i_label_asym_id_1="A" i_label_asym_id_2="A" i_label_comp_id_1="G" i_label_comp_id_2="G" i_label_seq_id_1="1" i_label_seq_id_2="2" i_symmetry_1="1_555" i_symmetry_2="1_555" j_label_asym_id_1="A" j_label_asym_id_2="A" j_label_comp_id_1="C" j_label_comp_id_2="C" j_label_seq_id_1="8" j_label_seq_id_2="7" j_symmetry_1="7_555" j_symmetry_2="7_555" model_number="1">
<PDBx:rise>3.339</PDBx:rise>
<PDBx:roll>9.755</PDBx:roll>
<PDBx:shift>0.369</PDBx:shift>
<PDBx:slide>-1.414</PDBx:slide>
<PDBx:tilt>3.056</PDBx:tilt>
<PDBx:twist>33.530</PDBx:twist>
</PDBx:ndb_struct_na_base_pair_step>
<PDBx:ndb_struct_na_base_pair_step i_label_asym_id_1="A" i_label_asym_id_2="A" i_label_comp_id_1="G" i_label_comp_id_2="G" i_label_seq_id_1="2" i_label_seq_id_2="3" i_symmetry_1="1_555" i_symmetry_2="1_555" j_label_asym_id_1="A" j_label_asym_id_2="A" j_label_comp_id_1="C" j_label_comp_id_2="C" j_label_seq_id_1="7" j_label_seq_id_2="6" j_symmetry_1="7_555" j_symmetry_2="7_555" model_number="1">
<PDBx:rise>3.371</PDBx:rise>
<PDBx:roll>6.725</PDBx:roll>
<PDBx:shift>0.176</PDBx:shift>
<PDBx:slide>-1.672</PDBx:slide>
<PDBx:tilt>-1.176</PDBx:tilt>
<PDBx:twist>30.004</PDBx:twist>
</PDBx:ndb_struct_na_base_pair_step>
</PDBx:ndb_struct_na_base_pair_stepCategory>
0
1
0
1
0
1
0
1
1
1
1
1
1
1
1
1
0
1
0
1
0
1
1
1
1
1
1
1
1
1
0
1
0
1
0
1
0
1
1
1
1
1
0
1
0
1
0
1
0
1
0
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
ndb_struct_na_base_pair_stepCategory
This property indicates that datablock
has a category holder ndb_struct_na_base_pair_stepCategory.
ndb_struct_na_base_pair_stepCategory
This property indicates that ndb_struct_na_base_pair_stepCategory.
has a category ndb_struct_na_base_pair_step.
ndb_struct_na_base_pair_stepItem
Abstract datatype property for ndb_struct_na_base_pair_step items.
reference_to_ndb_struct_na_base_pair_step
cross-reference to ndb_struct_na_base_pair_step.
referenced_by_ndb_struct_na_base_pair_step
cross-reference from ndb_struct_na_base_pair_step.
ndb_struct_na_base_pair_step.helical_rise
The value of the base pair step helical rise parameter.
ndb_struct_na_base_pair_step.helical_twist
The value of the base pair step helical twist parameter.
ndb_struct_na_base_pair_step.i_PDB_ins_code_1
Describes the PDB insertion code of the i-th base in the
first base pair of the step.
This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in
the ATOM_SITE category.
ndb_struct_na_base_pair_step.i_PDB_ins_code_2
Describes the PDB insertion code of the i-th base in the
second base pair of the step.
This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in
the ATOM_SITE category.
ndb_struct_na_base_pair_step.i_auth_asym_id_1
Describes the author's asym id of the i-th base in the first
base pair of the step.
This data item is a pointer to attribute auth_asym_id in category atom_site in the
ATOM_SITE category.
ndb_struct_na_base_pair_step.i_auth_asym_id_2
Describes the author's asym id of the i-th base in the second
base pair of the step.
This data item is a pointer to attribute auth_asym_id in category atom_site in the
ATOM_SITE category.
ndb_struct_na_base_pair_step.i_auth_seq_id_1
Describes the author's sequence number of the i-th base in the
first base pair of the step.
This data item is a pointer to attribute auth_seq_id in category atom_site in the
ATOM_SITE category.
ndb_struct_na_base_pair_step.i_auth_seq_id_2
Describes the author's sequence number of the i-th base in the
second base pair of the step.
This data item is a pointer to attribute auth_seq_id in category atom_site in the
ATOM_SITE category.
ndb_struct_na_base_pair_step.inclination
The value of the base pair step inclination parameter.
ndb_struct_na_base_pair_step.j_PDB_ins_code_1
Describes the PDB insertion code of the j-th base in the
first base pair of the step.
This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in
the ATOM_SITE category.
ndb_struct_na_base_pair_step.j_PDB_ins_code_2
Describes the PDB insertion code of the j-th base in the
second base pair of the step.
This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in
the ATOM_SITE category.
ndb_struct_na_base_pair_step.j_auth_asym_id_1
Describes the author's asym id of the j-th base in the first
base pair of the step.
This data item is a pointer to attribute auth_asym_id in category atom_site in the
ATOM_SITE category.
ndb_struct_na_base_pair_step.j_auth_asym_id_2
Describes the author's asym id of the j-th base in the second
base pair of the step.
This data item is a pointer to attribute auth_asym_id in category atom_site in the
ATOM_SITE category.
ndb_struct_na_base_pair_step.j_auth_seq_id_1
Describes the author's sequence number of the j-th base in the
first base pair of the step.
This data item is a pointer to attribute auth_seq_id in category atom_site in the
ATOM_SITE category.
ndb_struct_na_base_pair_step.j_auth_seq_id_2
Describes the author's sequence number of the j-th base in the
second base pair of the step.
This data item is a pointer to attribute auth_seq_id in category atom_site in the
ATOM_SITE category.
ndb_struct_na_base_pair_step.rise
The value of the base pair step rise parameter.
ndb_struct_na_base_pair_step.roll
The value of the base pair step roll parameter.
ndb_struct_na_base_pair_step.shift
The value of the base pair step shift parameter.
ndb_struct_na_base_pair_step.slide
The value of the base pair step slide parameter.
ndb_struct_na_base_pair_step.step_name
The text name of this step.
ndb_struct_na_base_pair_step.step_number
The sequence number of this step in the step sequence.
ndb_struct_na_base_pair_step.tilt
The value of the base pair step tilt parameter.
ndb_struct_na_base_pair_step.tip
The value of the base pair step twist parameter.
ndb_struct_na_base_pair_step.twist
The value of the base pair step twist parameter.
ndb_struct_na_base_pair_step.x_displacement
The value of the base pair step X displacement parameter.
ndb_struct_na_base_pair_step.y_displacement
The value of the base pair step Y displacement parameter.
ndb_struct_na_base_pair_step.i_label_asym_id_1
Describes the asym id of the i-th base in the first base pair
of the step.
This data item is a pointer to attribute label_asym_id in category atom_site in the
ATOM_SITE category.
ndb_struct_na_base_pair_step.i_label_asym_id_2
Describes the asym id of the i-th base in the second base pair
of the step.
This data item is a pointer to attribute label_asym_id in category atom_site in the
ATOM_SITE category.
ndb_struct_na_base_pair_step.i_label_comp_id_1
Describes the component id of the i-th base in the first base pair
of the step.
This data item is a pointer to attribute label_comp_id in category atom_site in the
ATOM_SITE category.
ndb_struct_na_base_pair_step.i_label_comp_id_2
Describes the component id of the i-th base in the second base pair
of the step.
This data item is a pointer to attribute label_comp_id in category atom_site in the
ATOM_SITE category.
ndb_struct_na_base_pair_step.i_label_seq_id_1
Describes the sequence number of the i-th base in the first base pair
of the step.
This data item is a pointer to attribute label_seq_id in category atom_site in the
ATOM_SITE category.
ndb_struct_na_base_pair_step.i_label_seq_id_2
Describes the sequence number of the i-th base in the second base pair
of the step.
This data item is a pointer to attribute label_seq_id in category atom_site in the
ATOM_SITE category.
ndb_struct_na_base_pair_step.i_symmetry_1
Describes the symmetry operation that should be applied to the
coordinates of the i-th base to generate the first partner
in the first base pair of the step.
4th symmetry operation applied
4
7th symm. posn.; +a on x; -b on y
7_645
ndb_struct_na_base_pair_step.i_symmetry_2
Describes the symmetry operation that should be applied to the
coordinates of the i-th base to generate the first partner
in the second base pair of the step.
4th symmetry operation applied
4
7th symm. posn.; +a on x; -b on y
7_645
ndb_struct_na_base_pair_step.j_label_asym_id_1
Describes the asym id of the j-th base in the first base pair
of the step.
This data item is a pointer to attribute label_asym_id in category atom_site in the
ATOM_SITE category.
ndb_struct_na_base_pair_step.j_label_asym_id_2
Describes the asym id of the j-th base in the second base pair
of the step.
This data item is a pointer to attribute label_asym_id in category atom_site in the
ATOM_SITE category.
ndb_struct_na_base_pair_step.j_label_comp_id_1
Describes the component id of the j-th base in the first base pair
of the step.
This data item is a pointer to attribute label_comp_id in category atom_site in the
ATOM_SITE category.
ndb_struct_na_base_pair_step.j_label_comp_id_2
Describes the component id of the j-th base in the second base pair
of the step.
This data item is a pointer to attribute label_comp_id in category atom_site in the
ATOM_SITE category.
ndb_struct_na_base_pair_step.j_label_seq_id_1
Describes the sequence number of the j-th base in the first base pair
of the step.
This data item is a pointer to attribute label_seq_id in category atom_site in the
ATOM_SITE category.
ndb_struct_na_base_pair_step.j_label_seq_id_2
Describes the sequence number of the j-th base in the second base pair
of the step.
This data item is a pointer to attribute label_seq_id in category atom_site in the
ATOM_SITE category.
ndb_struct_na_base_pair_step.j_symmetry_1
Describes the symmetry operation that should be applied to the
coordinates of the j-th base to generate the second partner
in the first base pair of the step.
4th symmetry operation applied
4
7th symm. posn.; +a on x; -b on y
7_645
ndb_struct_na_base_pair_step.j_symmetry_2
Describes the symmetry operation that should be applied to the
coordinates of the j-th base to generate the second partner
in the second base pair of the step.
4th symmetry operation applied
4
7th symm. posn.; +a on x; -b on y
7_645
ndb_struct_na_base_pair_step.model_number
Describes the model number of the base pair step.
This data item is a pointer to attribute pdbx_PDB_model_num in category atom_site in the
ATOM_SITE category.
0
pdbx_SG_project
Data items in the PDBX_CONTACT_AUTHOR category record details
about the Structural Genomics Project and name and initials
for each Center.
Example 1 -
<PDBx:pdbx_SG_projectCategory>
<PDBx:pdbx_SG_project id="1">
<PDBx:full_name_of_center>Berkeley Structural Genomics Center</PDBx:full_name_of_center>
<PDBx:initial_of_center>BSGC</PDBx:initial_of_center>
<PDBx:project_name>PSI, Protein Structure Initiative</PDBx:project_name>
</PDBx:pdbx_SG_project>
</PDBx:pdbx_SG_projectCategory>
0
1
0
1
0
1
1
pdbx_SG_projectCategory
This property indicates that datablock
has a category holder pdbx_SG_projectCategory.
pdbx_SG_projectCategory
This property indicates that pdbx_SG_projectCategory.
has a category pdbx_SG_project.
pdbx_SG_projectItem
Abstract datatype property for pdbx_SG_project items.
reference_to_pdbx_SG_project
cross-reference to pdbx_SG_project.
referenced_by_pdbx_SG_project
cross-reference from pdbx_SG_project.
Accelerated Technologies Center for Gene to 3D Structure
Bacterial targets at IGS-CNRS, France
Berkeley Structural Genomics Center
Montreal-Kingston Bacterial Structural Genomics Initiative
Chaperone-Enabled Studies of Epigenetic Regulation Enzymes
Assembly, Dynamics and Evolution of Cell-Cell and Cell-Matrix Adhesions
Center for Eukaryotic Structural Genomics
Structure, Dynamics and Activation Mechanisms of Chemokine Receptors
Center for High-Throughput Structural Biology
Center for Structural Biology of Infectious Diseases
Center for Structural Genomics of Infectious Diseases
Center for Structures of Membrane Proteins
GPCR Network
Atoms-to-Animals: The Immune Function Network
Integrated Center for Structure and Function Innovation
Israel Structural Proteomics Center
Joint Center for Structural Genomics
Midwest Center for Macromolecular Research
Midwest Center for Structural Genomics
Center for Membrane Proteins of Infectious Diseases
Mitochondrial Protein Partnership
Membrane Protein Structural Biology Consortium
Membrane Protein Structures by Solution NMR
Marseilles Structural Genomics Program @ AFMB
Medical Structural Genomics of Pathogenic Protozoa
Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors
Enzyme Discovery for Natural Product Biosynthesis
Nucleocytoplasmic Transport: a Target for Cellular Control
New York Consortium on Membrane Protein Structure
New York Structural Genomics Research Consortium
New York SGX Research Center for Structural Genomics
New York Structural GenomiX Research Consortium
Northeast Structural Genomics Consortium
Partnership for Nuclear Receptor Signaling Code Biology
Ontario Centre for Structural Proteomics
Oxford Protein Production Facility
Program for the Characterization of Secreted Effector Proteins
Protein Structure Factory
RIKEN Structural Genomics/Proteomics Initiative
Structure 2 Function Project
South Africa Structural Targets Annotation Database
Southeast Collaboratory for Structural Genomics
Structural Genomics Consortium
Structural Genomics Consortium for Research on Gene Expression
Structural Genomics of Pathogenic Protozoa Consortium
Structural Proteomics in Europe
Structural Proteomics in Europe 2
Seattle Structural Genomics Center for Infectious Disease
Scottish Structural Proteomics Facility
Partnership for Stem Cell Biology
TB Structural Genomics Consortium
Partnership for T-Cell Biology
Transcontinental EM Initiative for Membrane Protein Structure
Structure-Function Studies of Tight Junction Membrane Proteins
Transmembrane Protein Center
Center for the X-ray Structure Determination of Human Transporters
Structure-Function Analysis of Polymorphic CDI Toxin-Immunity Protein Complexes
Mycobacterium Tuberculosis Structural Proteomics Project
Paris-Sud Yeast Structural Genomics
The value identifies the full name of center.
Midwest Center for Structural Genomics
ATCG3D
BIGS
BSGC
BSGI
CEBS
CELLMAT
CESG
CHSAM
CHTSB
CSBID
CSGID
CSMP
GPCR
IFN
ISFI
ISPC
JCSG
MCMR
MCSG
MPID
MPP
MPSBC
MPSbyNMR
MSGP
MSGPP
MTBI
NatPro
NHRs
NPCXstals
NYCOMPS
NYSGRC
NYSGXRC
NESG
OCSP
OPPF
PCSEP
PSF
RSGI
S2F
SASTAD
SECSG
SGC
SGCGES
SGPP
SPINE
SPINE-2
SSGCID
SSPF
STEMCELL
TBSGC
TCELL
TEMIMPS
TJMP
TMPC
TransportPDB
UC4CDI
XMTB
YSG
The value identifies the full name of center.
JCSG
PSI:Biology
PSI, Protein Structure Initiative
NIAID, National Institute of Allergy and Infectious Diseases
NPPSFA, National Project on Protein Structural and Functional Analyses
Enzyme Function Initiative
The value identifies the Structural Genomics project.
PSI, Protein Structure Initiative
1
2
3
4
5
6
7
8
9
10
A unique integer identifier for this center
1 2 3
0
pdbx_atlas
Gives information about the organization of the
NDB Structural Atlas.
1
1
1
1
pdbx_atlasCategory
This property indicates that datablock
has a category holder pdbx_atlasCategory.
pdbx_atlasCategory
This property indicates that pdbx_atlasCategory.
has a category pdbx_atlas.
pdbx_atlasItem
Abstract datatype property for pdbx_atlas items.
reference_to_pdbx_atlas
cross-reference to pdbx_atlas.
referenced_by_pdbx_atlas
cross-reference from pdbx_atlas.
pdbx_atlas.page_name
Text of the Atlas index entry.
pdbx_atlas.entry_id
Entry ID.
pdbx_atlas.page_id
A unique identifier for a NDB ATLAS index page.
0
pdbx_atom_site_aniso_tls
Data items in the PDBX_ATOM_SITE_ANISO_TLS category record details
about the TLS contribution to anisotropic displacement parameters.
Example 1
<PDBx:pdbx_atom_site_aniso_tlsCategory>
<PDBx:pdbx_atom_site_aniso_tls id="1" tls_group_id="1">
<PDBx:U_tls11>2541</PDBx:U_tls11>
<PDBx:U_tls12>676</PDBx:U_tls12>
<PDBx:U_tls13>-827</PDBx:U_tls13>
<PDBx:U_tls22>2835</PDBx:U_tls22>
<PDBx:U_tls23>341</PDBx:U_tls23>
<PDBx:U_tls33>3175</PDBx:U_tls33>
<PDBx:auth_asym_id>A</PDBx:auth_asym_id>
<PDBx:auth_atom_id>CB</PDBx:auth_atom_id>
<PDBx:auth_comp_id>SER</PDBx:auth_comp_id>
<PDBx:auth_seq_id>8</PDBx:auth_seq_id>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:pdbx_atom_site_aniso_tls>
<PDBx:pdbx_atom_site_aniso_tls id="2" tls_group_id="1">
<PDBx:U_tls11>3708</PDBx:U_tls11>
<PDBx:U_tls12>633</PDBx:U_tls12>
<PDBx:U_tls13>-724</PDBx:U_tls13>
<PDBx:U_tls22>3876</PDBx:U_tls22>
<PDBx:U_tls23>342</PDBx:U_tls23>
<PDBx:U_tls33>4181</PDBx:U_tls33>
<PDBx:auth_asym_id>A</PDBx:auth_asym_id>
<PDBx:auth_atom_id>OG</PDBx:auth_atom_id>
<PDBx:auth_comp_id>SER</PDBx:auth_comp_id>
<PDBx:auth_seq_id>8</PDBx:auth_seq_id>
<PDBx:type_symbol>O</PDBx:type_symbol>
</PDBx:pdbx_atom_site_aniso_tls>
<PDBx:pdbx_atom_site_aniso_tls id="3" tls_group_id="1">
<PDBx:U_tls11>7054</PDBx:U_tls11>
<PDBx:U_tls12>619</PDBx:U_tls12>
<PDBx:U_tls13>-966</PDBx:U_tls13>
<PDBx:U_tls22>7457</PDBx:U_tls22>
<PDBx:U_tls23>344</PDBx:U_tls23>
<PDBx:U_tls33>7553</PDBx:U_tls33>
<PDBx:auth_asym_id>A</PDBx:auth_asym_id>
<PDBx:auth_atom_id>C</PDBx:auth_atom_id>
<PDBx:auth_comp_id>SER</PDBx:auth_comp_id>
<PDBx:auth_seq_id>8</PDBx:auth_seq_id>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:pdbx_atom_site_aniso_tls>
<PDBx:pdbx_atom_site_aniso_tls id="4" tls_group_id="1">
<PDBx:U_tls11>6837</PDBx:U_tls11>
<PDBx:U_tls12>567</PDBx:U_tls12>
<PDBx:U_tls13>-974</PDBx:U_tls13>
<PDBx:U_tls22>7210</PDBx:U_tls22>
<PDBx:U_tls23>341</PDBx:U_tls23>
<PDBx:U_tls33>7184</PDBx:U_tls33>
<PDBx:auth_asym_id>A</PDBx:auth_asym_id>
<PDBx:auth_atom_id>O</PDBx:auth_atom_id>
<PDBx:auth_comp_id>SER</PDBx:auth_comp_id>
<PDBx:auth_seq_id>8</PDBx:auth_seq_id>
<PDBx:type_symbol>O</PDBx:type_symbol>
</PDBx:pdbx_atom_site_aniso_tls>
<PDBx:pdbx_atom_site_aniso_tls id="5" tls_group_id="1">
<PDBx:U_tls11>5792</PDBx:U_tls11>
<PDBx:U_tls12>538</PDBx:U_tls12>
<PDBx:U_tls13>-778</PDBx:U_tls13>
<PDBx:U_tls22>6180</PDBx:U_tls22>
<PDBx:U_tls23>290</PDBx:U_tls23>
<PDBx:U_tls33>6271</PDBx:U_tls33>
<PDBx:auth_asym_id>A</PDBx:auth_asym_id>
<PDBx:auth_atom_id>N</PDBx:auth_atom_id>
<PDBx:auth_comp_id>SER</PDBx:auth_comp_id>
<PDBx:auth_seq_id>8</PDBx:auth_seq_id>
<PDBx:type_symbol>N</PDBx:type_symbol>
</PDBx:pdbx_atom_site_aniso_tls>
<PDBx:pdbx_atom_site_aniso_tls id="6" tls_group_id="1">
<PDBx:U_tls11>8440</PDBx:U_tls11>
<PDBx:U_tls12>616</PDBx:U_tls12>
<PDBx:U_tls13>-861</PDBx:U_tls13>
<PDBx:U_tls22>8771</PDBx:U_tls22>
<PDBx:U_tls23>331</PDBx:U_tls23>
<PDBx:U_tls33>8935</PDBx:U_tls33>
<PDBx:auth_asym_id>A</PDBx:auth_asym_id>
<PDBx:auth_atom_id>CA</PDBx:auth_atom_id>
<PDBx:auth_comp_id>SER</PDBx:auth_comp_id>
<PDBx:auth_seq_id>8</PDBx:auth_seq_id>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:pdbx_atom_site_aniso_tls>
</PDBx:pdbx_atom_site_aniso_tlsCategory>
0
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
0
1
0
1
0
1
0
1
1
1
1
1
pdbx_atom_site_aniso_tlsCategory
This property indicates that datablock
has a category holder pdbx_atom_site_aniso_tlsCategory.
pdbx_atom_site_aniso_tlsCategory
This property indicates that pdbx_atom_site_aniso_tlsCategory.
has a category pdbx_atom_site_aniso_tls.
pdbx_atom_site_aniso_tlsItem
Abstract datatype property for pdbx_atom_site_aniso_tls items.
reference_to_pdbx_atom_site_aniso_tls
cross-reference to pdbx_atom_site_aniso_tls.
referenced_by_pdbx_atom_site_aniso_tls
cross-reference from pdbx_atom_site_aniso_tls.
pdbx_atom_site_aniso_tls.PDB_ins_code
This data item is a pointer to attribute pdbx_ins_code in category atom_site in the
ATOM_SITE category.
pdbx_atom_site_aniso_tls.U_tls11
The [1][1] element of the TLS contribution to the atomic
displacement matrix U.
The unique elements of the real symmetric matrix are
entered by row.
pdbx_atom_site_aniso_tls.U_tls12
The [1][2] element of the TLS contribution to the atomic
displacement matrix U.
The unique elements of the real symmetric matrix are
entered by row.
pdbx_atom_site_aniso_tls.U_tls13
The [1][3] element of the TLS contribution to the atomic
displacement matrix U.
The unique elements of the real symmetric matrix are
entered by row.
pdbx_atom_site_aniso_tls.U_tls22
The [2][2] element of the TLS contribution to the atomic
displacement matrix U.
The unique elements of the real symmetric matrix are
entered by row.
pdbx_atom_site_aniso_tls.U_tls23
The [2][3] element of the TLS contribution to the atomic
displacement matrix U.
The unique elements of the real symmetric matrix are
entered by row.
pdbx_atom_site_aniso_tls.U_tls33
The [3][3] element of the TLS contribution to the atomic
displacement matrix U.
The unique elements of the real symmetric matrix are
entered by row.
pdbx_atom_site_aniso_tls.auth_asym_id
This data item is a pointer to attribute auth_asym_id in category atom_site in the
ATOM_SITE category.
pdbx_atom_site_aniso_tls.auth_atom_id
This data item is a pointer to attribute auth_atom_id in category atom_site in the
ATOM_SITE category.
pdbx_atom_site_aniso_tls.auth_comp_id
This data item is a pointer to attribute auth_comp_id in category atom_site in the
ATOM_SITE category.
pdbx_atom_site_aniso_tls.auth_seq_id
This data item is a pointer to attribute auth_seq_id in category atom_site in the
ATOM_SITE category.
pdbx_atom_site_aniso_tls.label_alt_id
This data item is a pointer to attribute id in category atom_sites_alt in the
ATOM_SITE category.
pdbx_atom_site_aniso_tls.label_asym_id
This data item is a pointer to attribute label_asym_id in category atom_site in the
ATOM_SITE category.
pdbx_atom_site_aniso_tls.label_atom_id
This data item is a pointer to attribute label_atom_id in category atom_site in the
ATOM_SITE category.
pdbx_atom_site_aniso_tls.label_comp_id
This data item is a pointer to attribute label_comp_id in category atom_site in the
ATOM_SITE category.
pdbx_atom_site_aniso_tls.label_seq_id
This data item is a pointer to attribute label_seq_id in category atom_site in the
ATOM_SITE category.
pdbx_atom_site_aniso_tls.type_symbol
This data item is a pointer to attribute symbol in category atom_type in the
ATOM_TYPE category.
pdbx_atom_site_aniso_tls.id
This data item is a pointer to attribute id in category atom_site in the ATOM_SITE
category.
pdbx_atom_site_aniso_tls.tls_group_id
This data item identifies the TLS group membership for
this atom.
0
pdbx_audit
The PDBX_AUDIT holds current version information.
1
1
1
pdbx_auditCategory
This property indicates that datablock
has a category holder pdbx_auditCategory.
pdbx_auditCategory
This property indicates that pdbx_auditCategory.
has a category pdbx_audit.
pdbx_auditItem
Abstract datatype property for pdbx_audit items.
reference_to_pdbx_audit
cross-reference to pdbx_audit.
referenced_by_pdbx_audit
cross-reference from pdbx_audit.
pdbx_audit.current_version
The value of attribute entry_id in category pdbx_audit identifies the data block.
1
pdbx_audit.entry_id
The value of attribute entry_id in category pdbx_audit identifies the data block.
BDL001
0
pdbx_audit_author
Data items in the PDBX_AUDIT_AUTHOR category record details about
the author(s) of the data block.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
<PDBx:pdbx_audit_authorCategory>
<PDBx:pdbx_audit_author ordinal="1">
<PDBx:address> Department of Biophysical Chemistry
Merck Research Laboratories
P. O. Box 2000, Ry80M203
Rahway, New Jersey 07065
USA</PDBx:address>
<PDBx:name>Fitzgerald, Paula M.D.</PDBx:name>
</PDBx:pdbx_audit_author>
<PDBx:pdbx_audit_author ordinal="2">
<PDBx:address> Department of Biophysical Chemistry
Merck Research Laboratories
P. O. Box 2000, Ry80M203
Rahway, New Jersey 07065
USA</PDBx:address>
<PDBx:name>McKeever, Brian M.</PDBx:name>
</PDBx:pdbx_audit_author>
<PDBx:pdbx_audit_author ordinal="3">
<PDBx:address> Department of Biophysical Chemistry
Merck Research Laboratories
P. O. Box 2000, Ry80M203
Rahway, New Jersey 07065
USA</PDBx:address>
<PDBx:name>Van Middlesworth, J.F.</PDBx:name>
</PDBx:pdbx_audit_author>
<PDBx:pdbx_audit_author ordinal="4">
<PDBx:address> Department of Biophysical Chemistry
Merck Research Laboratories
P. O. Box 2000, Ry80M203
Rahway, New Jersey 07065
USA</PDBx:address>
<PDBx:name>Springer, James P.</PDBx:name>
</PDBx:pdbx_audit_author>
</PDBx:pdbx_audit_authorCategory>
0
1
1
1
1
pdbx_audit_authorCategory
This property indicates that datablock
has a category holder pdbx_audit_authorCategory.
pdbx_audit_authorCategory
This property indicates that pdbx_audit_authorCategory.
has a category pdbx_audit_author.
pdbx_audit_authorItem
Abstract datatype property for pdbx_audit_author items.
reference_to_pdbx_audit_author
cross-reference to pdbx_audit_author.
referenced_by_pdbx_audit_author
cross-reference from pdbx_audit_author.
pdbx_audit_author.address
The address of an author of this data block. If there are
multiple authors, attribute address in category pdbx_audit_author is looped with
attribute name in category pdbx_audit_author.
Department
Institute
Street
City and postcode
COUNTRY
pdbx_audit_author.name
The name of an author of this data block. If there are multiple
authors, _pdbx_audit_author.name is looped with _pdbx_audit_author.address.
The family name(s), followed by a comma and including any
dynastic compoents, precedes the first name(s) or initial(s).
Bleary, Percival R.
O'Neil, F.K.
Van den Bossche, G.
Yang, D.-L.
Simonov, Yu.A
pdbx_audit_author.ordinal
A unique sequential integer identifier for each author.
1
2
3
0
pdbx_audit_conform
Data items in the PDBX_AUDIT_CONFORM category describe the
dictionary versions against which the data names appearing in
the current data block are conformant.
Example 1 - Data file conforming to the current PDBx/mmCIF dictionary.
<PDBx:pdbx_audit_conformCategory>
<PDBx:pdbx_audit_conform dict_name="mmcif_pdbx.dic" dict_version="5.339">
<PDBx:dict_location>https://mmcif.wwpdb.org/dictionaries/ascii/mmcif_pdbx_v50.dic</PDBx:dict_location>
</PDBx:pdbx_audit_conform>
</PDBx:pdbx_audit_conformCategory>
0
1
1
1
pdbx_audit_conformCategory
This property indicates that datablock
has a category holder pdbx_audit_conformCategory.
pdbx_audit_conformCategory
This property indicates that pdbx_audit_conformCategory.
has a category pdbx_audit_conform.
pdbx_audit_conformItem
Abstract datatype property for pdbx_audit_conform items.
reference_to_pdbx_audit_conform
cross-reference to pdbx_audit_conform.
referenced_by_pdbx_audit_conform
cross-reference from pdbx_audit_conform.
pdbx_audit_conform.dict_location
A file name or uniform resource locator (URL) for the
dictionary to which the current data block conforms.
pdbx_audit_conform.dict_name
The dictionary name defining data names used in this file.
pdbx_audit_conform.dict_version
The version number of the dictionary to which the current
data block conforms.
0
pdbx_audit_conform_extension
Data items in the PDBX_AUDIT_CONFORM_EXTENSION category describe
extension dictionary versions against which the data names appearing
the current data block are conformant.
Example 1 - Conforming to EMD V 1.0 extension dictionary.
<PDBx:pdbx_audit_conform_extensionCategory>
<PDBx:pdbx_audit_conform_extension extension_dict_name="EMD" extension_dict_version="1.0">
<PDBx:extension_dict_location>http://mmcif.wwpdb.org/dictionaries/ascii/mmcif_pdbx_v5_next.dic</PDBx:extension_dict_location>
</PDBx:pdbx_audit_conform_extension>
</PDBx:pdbx_audit_conform_extensionCategory>
0
1
1
1
pdbx_audit_conform_extensionCategory
This property indicates that datablock
has a category holder pdbx_audit_conform_extensionCategory.
pdbx_audit_conform_extensionCategory
This property indicates that pdbx_audit_conform_extensionCategory.
has a category pdbx_audit_conform_extension.
pdbx_audit_conform_extensionItem
Abstract datatype property for pdbx_audit_conform_extension items.
reference_to_pdbx_audit_conform_extension
cross-reference to pdbx_audit_conform_extension.
referenced_by_pdbx_audit_conform_extension
cross-reference from pdbx_audit_conform_extension.
pdbx_audit_conform_extension.extension_dict_location
A file name or uniform resource locator (URL) for the
file containing the extension dictionary.
EMD
An identifier for the extension dictionary to which the current data block conforms.
pdbx_audit_conform_extension.extension_dict_version
The version number of the extension dictionary to which the currrent data block conforms.
0
pdbx_audit_revision_category
Data items in the PDBX_AUDIT_REVISION_CATEGORY category
report the data categories associated with a PDBX_AUDIT_REVISION_HISTORY record.
Example 1
<PDBx:pdbx_audit_revision_categoryCategory>
<PDBx:pdbx_audit_revision_category data_content_type="Structure model" ordinal="1" revision_ordinal="1">
<PDBx:category>audit_author</PDBx:category>
</PDBx:pdbx_audit_revision_category>
<PDBx:pdbx_audit_revision_category data_content_type="Structure model" ordinal="2" revision_ordinal="1">
<PDBx:category>citation</PDBx:category>
</PDBx:pdbx_audit_revision_category>
<PDBx:pdbx_audit_revision_category data_content_type="Structure model" ordinal="3" revision_ordinal="1">
<PDBx:category>citation_author</PDBx:category>
</PDBx:pdbx_audit_revision_category>
<PDBx:pdbx_audit_revision_category data_content_type="Structure model" ordinal="4" revision_ordinal="2">
<PDBx:category>citation</PDBx:category>
</PDBx:pdbx_audit_revision_category>
</PDBx:pdbx_audit_revision_categoryCategory>
1
1
1
1
1
pdbx_audit_revision_categoryCategory
This property indicates that datablock
has a category holder pdbx_audit_revision_categoryCategory.
pdbx_audit_revision_categoryCategory
This property indicates that pdbx_audit_revision_categoryCategory.
has a category pdbx_audit_revision_category.
pdbx_audit_revision_categoryItem
Abstract datatype property for pdbx_audit_revision_category items.
reference_to_pdbx_audit_revision_category
cross-reference to pdbx_audit_revision_category.
referenced_by_pdbx_audit_revision_category
cross-reference from pdbx_audit_revision_category.
pdbx_audit_revision_category.category
The category updated in the pdbx_audit_revision_category record.
audit_author
citation
Structure model
NMR restraints
NMR shifts
Structure factors
Chemical component
The type of file that the pdbx_audit_revision_history record refers to.
Structure model
pdbx_audit_revision_category.ordinal
A unique identifier for the pdbx_audit_revision_category record.
1
pdbx_audit_revision_category.revision_ordinal
A pointer to attribute ordinal in category pdbx_audit_revision_history
1
0
pdbx_audit_revision_details
Data items in the PDBX_audit_revision_details category
record descriptions of changes associated with
PDBX_AUDIT_REVISION_HISTORY records.
Example 1
<PDBx:pdbx_audit_revision_detailsCategory>
<PDBx:pdbx_audit_revision_details data_content_type="Structure model" ordinal="1" revision_ordinal="1">
<PDBx:provider>repository</PDBx:provider>
<PDBx:type>Initial release</PDBx:type>
</PDBx:pdbx_audit_revision_details>
<PDBx:pdbx_audit_revision_details data_content_type="Structure model" ordinal="2" revision_ordinal="7">
<PDBx:description>Remodeling of inhibitor</PDBx:description>
<PDBx:provider>author</PDBx:provider>
<PDBx:type>Coordinate replacement</PDBx:type>
</PDBx:pdbx_audit_revision_details>
</PDBx:pdbx_audit_revision_detailsCategory>
0
1
0
1
0
1
0
1
1
1
1
pdbx_audit_revision_detailsCategory
This property indicates that datablock
has a category holder pdbx_audit_revision_detailsCategory.
pdbx_audit_revision_detailsCategory
This property indicates that pdbx_audit_revision_detailsCategory.
has a category pdbx_audit_revision_details.
pdbx_audit_revision_detailsItem
Abstract datatype property for pdbx_audit_revision_details items.
reference_to_pdbx_audit_revision_details
cross-reference to pdbx_audit_revision_details.
referenced_by_pdbx_audit_revision_details
cross-reference from pdbx_audit_revision_details.
pdbx_audit_revision_details.description
Additional details describing the revision.
pdbx_audit_revision_details.details
Further details describing the revision.
repository
author
The provider of the revision.
repository
Initial release
Coordinate replacement
Obsolete
Remediation
A type classification of the revision
Initial release
Structure model
NMR restraints
NMR shifts
Structure factors
Chemical component
The type of file that the pdbx_audit_revision_history record refers to.
Structure model
pdbx_audit_revision_details.ordinal
A unique identifier for the pdbx_audit_revision_details record.
1
pdbx_audit_revision_details.revision_ordinal
A pointer to attribute ordinal in category pdbx_audit_revision_history
1
0
pdbx_audit_revision_group
Data items in the PDBX_AUDIT_revision_group category
report the content groups associated with a PDBX_AUDIT_REVISION_HISTORY
record.
Example 1
<PDBx:pdbx_audit_revision_groupCategory>
<PDBx:pdbx_audit_revision_group data_content_type="Structure model" ordinal="1" revision_ordinal="2">
<PDBx:group>citation</PDBx:group>
</PDBx:pdbx_audit_revision_group>
<PDBx:pdbx_audit_revision_group data_content_type="Structure model" ordinal="2" revision_ordinal="3">
<PDBx:group>sample</PDBx:group>
</PDBx:pdbx_audit_revision_group>
</PDBx:pdbx_audit_revision_groupCategory>
1
1
1
1
1
pdbx_audit_revision_groupCategory
This property indicates that datablock
has a category holder pdbx_audit_revision_groupCategory.
pdbx_audit_revision_groupCategory
This property indicates that pdbx_audit_revision_groupCategory.
has a category pdbx_audit_revision_group.
pdbx_audit_revision_groupItem
Abstract datatype property for pdbx_audit_revision_group items.
reference_to_pdbx_audit_revision_group
cross-reference to pdbx_audit_revision_group.
referenced_by_pdbx_audit_revision_group
cross-reference from pdbx_audit_revision_group.
Advisory
Atomic model
Author supporting evidence
Data collection
Data processing
Database references
Derived calculations
Experimental data
Experimental preparation
Initial release
Non-polymer description
Other
Polymer sequence
Refinement description
Structure summary
Source and taxonomy
Version format compliance
The collection of categories updated with this revision.
citation
Structure model
NMR restraints
NMR shifts
Structure factors
Chemical component
The type of file that the pdbx_audit_revision_history record refers to.
Structure model
pdbx_audit_revision_group.ordinal
A unique identifier for the pdbx_audit_revision_group record.
1
pdbx_audit_revision_group.revision_ordinal
A pointer to attribute ordinal in category pdbx_audit_revision_history
1
0
pdbx_audit_revision_history
Data items in the PDBX_AUDIT_REVISION_HISTORY category record
the revision history for a data entry.
Example 1
<PDBx:pdbx_audit_revision_historyCategory>
<PDBx:pdbx_audit_revision_history data_content_type="Structure model" ordinal="1">
<PDBx:internal_deposition_id>D_123456789</PDBx:internal_deposition_id>
<PDBx:internal_version>4</PDBx:internal_version>
<PDBx:major_revision>1</PDBx:major_revision>
<PDBx:minor_revision>0</PDBx:minor_revision>
<PDBx:revision_date>2017-03-01</PDBx:revision_date>
</PDBx:pdbx_audit_revision_history>
<PDBx:pdbx_audit_revision_history data_content_type="Structure model" ordinal="2">
<PDBx:internal_deposition_id>D_123456789</PDBx:internal_deposition_id>
<PDBx:internal_version>6</PDBx:internal_version>
<PDBx:major_revision>1</PDBx:major_revision>
<PDBx:minor_revision>1</PDBx:minor_revision>
<PDBx:revision_date>2017-03-08</PDBx:revision_date>
</PDBx:pdbx_audit_revision_history>
</PDBx:pdbx_audit_revision_historyCategory>
0
1
0
1
1
1
1
1
1
1
1
1
pdbx_audit_revision_historyCategory
This property indicates that datablock
has a category holder pdbx_audit_revision_historyCategory.
pdbx_audit_revision_historyCategory
This property indicates that pdbx_audit_revision_historyCategory.
has a category pdbx_audit_revision_history.
pdbx_audit_revision_historyItem
Abstract datatype property for pdbx_audit_revision_history items.
reference_to_pdbx_audit_revision_history
cross-reference to pdbx_audit_revision_history.
referenced_by_pdbx_audit_revision_history
cross-reference from pdbx_audit_revision_history.
pdbx_audit_revision_history.internal_deposition_id
The deposition id that corresponds to this millestone file
D_123456789
pdbx_audit_revision_history.internal_version
An internal version number corresponding to millestone file
13
pdbx_audit_revision_history.major_revision
The major version number of deposition release.
1
pdbx_audit_revision_history.minor_revision
The minor version number of deposition release.
1
pdbx_audit_revision_history.revision_date
The release date of the revision
2017-03-08
Structure model
NMR restraints
NMR shifts
Structure factors
Chemical component
The type of file that the pdbx_audit_revision_history record refers to.
Structure model
pdbx_audit_revision_history.ordinal
A unique identifier for the pdbx_audit_revision_history record.
1
0
pdbx_audit_revision_item
Data items in the PDBX_AUDIT_REVISION_ITEM category
report the data items associated with a PDBX_AUDIT_REVISION_HISTORY record.
Example 1
<PDBx:pdbx_audit_revision_itemCategory>
<PDBx:pdbx_audit_revision_item data_content_type="Structure model" ordinal="1" revision_ordinal="1">
<PDBx:item>_atom_site.type_symbol</PDBx:item>
</PDBx:pdbx_audit_revision_item>
</PDBx:pdbx_audit_revision_itemCategory>
1
1
1
1
1
pdbx_audit_revision_itemCategory
This property indicates that datablock
has a category holder pdbx_audit_revision_itemCategory.
pdbx_audit_revision_itemCategory
This property indicates that pdbx_audit_revision_itemCategory.
has a category pdbx_audit_revision_item.
pdbx_audit_revision_itemItem
Abstract datatype property for pdbx_audit_revision_item items.
reference_to_pdbx_audit_revision_item
cross-reference to pdbx_audit_revision_item.
referenced_by_pdbx_audit_revision_item
cross-reference from pdbx_audit_revision_item.
pdbx_audit_revision_item.item
A high level explanation the author has provided for submitting a revision.
_atom_site.type_symbol
Structure model
NMR restraints
NMR shifts
Structure factors
Chemical component
The type of file that the pdbx_audit_revision_history record refers to.
Structure model
pdbx_audit_revision_item.ordinal
A unique identifier for the pdbx_audit_revision_item record.
1
pdbx_audit_revision_item.revision_ordinal
A pointer to attribute ordinal in category pdbx_audit_revision_history
1
0
pdbx_audit_support
Data items in the PDBX_AUDIT_SUPPORT category record details about
funding support for the entry.
Example 1 -
<PDBx:pdbx_audit_supportCategory>
<PDBx:pdbx_audit_support ordinal="1">
<PDBx:country>United States</PDBx:country>
<PDBx:funding_organization>National Institutes of Health/National Institute of General Medical Sciences</PDBx:funding_organization>
<PDBx:grant_number>1R01GM072999-01</PDBx:grant_number>
</PDBx:pdbx_audit_support>
</PDBx:pdbx_audit_supportCategory>
0
1
0
1
0
1
0
1
1
pdbx_audit_supportCategory
This property indicates that datablock
has a category holder pdbx_audit_supportCategory.
pdbx_audit_supportCategory
This property indicates that pdbx_audit_supportCategory.
has a category pdbx_audit_support.
pdbx_audit_supportItem
Abstract datatype property for pdbx_audit_support items.
reference_to_pdbx_audit_support
cross-reference to pdbx_audit_support.
referenced_by_pdbx_audit_support
cross-reference from pdbx_audit_support.
pdbx_audit_support.country
The country/region providing the funding support for the entry.
pdbx_audit_support.details
Additional details regarding the funding of this entry
pdbx_audit_support.funding_organization
The name of the organization providing funding support for the
entry.
National Institutes of Health
Wellcome Trust
National Institutes of Health/National Institute of General Medical Sciences
pdbx_audit_support.grant_number
The grant number associated with this source of support.
pdbx_audit_support.ordinal
A unique sequential integer identifier for each source of support for this entry.
1
2
3
0
pdbx_bond_distance_limits
This category provides a table of upper and lower distance
limits used as criteria in determining covalent bonds.
The table is organized by atom type pairs.
Example 1 - Abbreviated bond distance limit table
<PDBx:pdbx_bond_distance_limitsCategory>
<PDBx:pdbx_bond_distance_limits atom_type_1="N" atom_type_2="Ag">
<PDBx:lower_limit>1.85</PDBx:lower_limit>
<PDBx:upper_limit>2.70</PDBx:upper_limit>
</PDBx:pdbx_bond_distance_limits>
<PDBx:pdbx_bond_distance_limits atom_type_1="O" atom_type_2="Ag">
<PDBx:lower_limit>1.85</PDBx:lower_limit>
<PDBx:upper_limit>2.70</PDBx:upper_limit>
</PDBx:pdbx_bond_distance_limits>
<PDBx:pdbx_bond_distance_limits atom_type_1="S" atom_type_2="Ag">
<PDBx:lower_limit>2.00</PDBx:lower_limit>
<PDBx:upper_limit>3.00</PDBx:upper_limit>
</PDBx:pdbx_bond_distance_limits>
<PDBx:pdbx_bond_distance_limits atom_type_1="Al" atom_type_2="H">
<PDBx:lower_limit>1.35</PDBx:lower_limit>
<PDBx:upper_limit>1.65</PDBx:upper_limit>
</PDBx:pdbx_bond_distance_limits>
<PDBx:pdbx_bond_distance_limits atom_type_1="As" atom_type_2="H">
<PDBx:lower_limit>1.20</PDBx:lower_limit>
<PDBx:upper_limit>1.60</PDBx:upper_limit>
</PDBx:pdbx_bond_distance_limits>
<PDBx:pdbx_bond_distance_limits atom_type_1="N" atom_type_2="Au">
<PDBx:lower_limit>1.80</PDBx:lower_limit>
<PDBx:upper_limit>2.80</PDBx:upper_limit>
</PDBx:pdbx_bond_distance_limits>
<PDBx:pdbx_bond_distance_limits atom_type_1="O" atom_type_2="Au">
<PDBx:lower_limit>1.80</PDBx:lower_limit>
<PDBx:upper_limit>2.80</PDBx:upper_limit>
</PDBx:pdbx_bond_distance_limits>
<PDBx:pdbx_bond_distance_limits atom_type_1="S" atom_type_2="Au">
<PDBx:lower_limit>1.80</PDBx:lower_limit>
<PDBx:upper_limit>3.00</PDBx:upper_limit>
</PDBx:pdbx_bond_distance_limits>
<PDBx:pdbx_bond_distance_limits atom_type_1="B" atom_type_2="B">
<PDBx:lower_limit>1.45</PDBx:lower_limit>
<PDBx:upper_limit>1.95</PDBx:upper_limit>
</PDBx:pdbx_bond_distance_limits>
<PDBx:pdbx_bond_distance_limits atom_type_1="C" atom_type_2="B">
<PDBx:lower_limit>1.20</PDBx:lower_limit>
<PDBx:upper_limit>1.85</PDBx:upper_limit>
</PDBx:pdbx_bond_distance_limits>
<PDBx:pdbx_bond_distance_limits atom_type_1="F" atom_type_2="B">
<PDBx:lower_limit>1.20</PDBx:lower_limit>
<PDBx:upper_limit>1.75</PDBx:upper_limit>
</PDBx:pdbx_bond_distance_limits>
</PDBx:pdbx_bond_distance_limitsCategory>
1
1
1
1
1
1
pdbx_bond_distance_limitsCategory
This property indicates that datablock
has a category holder pdbx_bond_distance_limitsCategory.
pdbx_bond_distance_limitsCategory
This property indicates that pdbx_bond_distance_limitsCategory.
has a category pdbx_bond_distance_limits.
pdbx_bond_distance_limitsItem
Abstract datatype property for pdbx_bond_distance_limits items.
reference_to_pdbx_bond_distance_limits
cross-reference to pdbx_bond_distance_limits.
referenced_by_pdbx_bond_distance_limits
cross-reference from pdbx_bond_distance_limits.
pdbx_bond_distance_limits.lower_limit
The lower bond distance limit.
pdbx_bond_distance_limits.upper_limit
The upper bond distance limit.
pdbx_bond_distance_limits.atom_type_1
The first atom type defining the bond
C
N
P
pdbx_bond_distance_limits.atom_type_2
The first atom type defining the bond
C
N
P
0
pdbx_branch_scheme
The PDBX_BRANCH_SCHEME category provides residue level nomenclature
mapping for branch chain entities.
Example 1 -
<PDBx:pdbx_branch_schemeCategory>
<PDBx:pdbx_branch_scheme asym_id="B" entity_id="2" mon_id="NAG" num="1">
<PDBx:auth_asym_id>A</PDBx:auth_asym_id>
<PDBx:auth_mon_id>NAG</PDBx:auth_mon_id>
<PDBx:auth_seq_num>1592</PDBx:auth_seq_num>
<PDBx:hetero>n</PDBx:hetero>
<PDBx:pdb_asym_id>B</PDBx:pdb_asym_id>
<PDBx:pdb_mon_id>NAG</PDBx:pdb_mon_id>
<PDBx:pdb_seq_num>1</PDBx:pdb_seq_num>
</PDBx:pdbx_branch_scheme>
<PDBx:pdbx_branch_scheme asym_id="B" entity_id="2" mon_id="GAL" num="2">
<PDBx:auth_asym_id>A</PDBx:auth_asym_id>
<PDBx:auth_mon_id>GAL</PDBx:auth_mon_id>
<PDBx:auth_seq_num>1591</PDBx:auth_seq_num>
<PDBx:hetero>n</PDBx:hetero>
<PDBx:pdb_asym_id>B</PDBx:pdb_asym_id>
<PDBx:pdb_mon_id>GAL</PDBx:pdb_mon_id>
<PDBx:pdb_seq_num>2</PDBx:pdb_seq_num>
</PDBx:pdbx_branch_scheme>
<PDBx:pdbx_branch_scheme asym_id="B" entity_id="2" mon_id="FUC" num="3">
<PDBx:auth_asym_id>A</PDBx:auth_asym_id>
<PDBx:auth_mon_id>FUC</PDBx:auth_mon_id>
<PDBx:auth_seq_num>1590</PDBx:auth_seq_num>
<PDBx:hetero>n</PDBx:hetero>
<PDBx:pdb_asym_id>B</PDBx:pdb_asym_id>
<PDBx:pdb_mon_id>FUC</PDBx:pdb_mon_id>
<PDBx:pdb_seq_num>3</PDBx:pdb_seq_num>
</PDBx:pdbx_branch_scheme>
<PDBx:pdbx_branch_scheme asym_id="B" entity_id="2" mon_id="FUC" num="4">
<PDBx:auth_asym_id>A</PDBx:auth_asym_id>
<PDBx:auth_mon_id>FUC</PDBx:auth_mon_id>
<PDBx:auth_seq_num>1593</PDBx:auth_seq_num>
<PDBx:hetero>n</PDBx:hetero>
<PDBx:pdb_asym_id>B</PDBx:pdb_asym_id>
<PDBx:pdb_mon_id>FUC</PDBx:pdb_mon_id>
<PDBx:pdb_seq_num>4</PDBx:pdb_seq_num>
</PDBx:pdbx_branch_scheme>
</PDBx:pdbx_branch_schemeCategory>
0
1
0
1
0
1
0
1
1
1
0
1
1
1
1
1
1
1
1
1
pdbx_branch_schemeCategory
This property indicates that datablock
has a category holder pdbx_branch_schemeCategory.
pdbx_branch_schemeCategory
This property indicates that pdbx_branch_schemeCategory.
has a category pdbx_branch_scheme.
pdbx_branch_schemeItem
Abstract datatype property for pdbx_branch_scheme items.
reference_to_pdbx_branch_scheme
cross-reference to pdbx_branch_scheme.
referenced_by_pdbx_branch_scheme
cross-reference from pdbx_branch_scheme.
pdbx_branch_scheme.auth_asym_id
This data item is a pointer to attribute pdbx_auth_asym_id in category atom_site in the
ATOM_SITE category.
pdbx_branch_scheme.auth_mon_id
This data item is a pointer to attribute pdbx_auth_comp_id in category atom_site in the
ATOM_SITE category.
pdbx_branch_scheme.auth_seq_num
This data item is a pointer to attribute pdbx_auth_seq_id in category atom_site in the
ATOM_SITE category.
no
n
yes
y
A flag to indicate whether this monomer in the entity is
heterogeneous in sequence.
pdbx_branch_scheme.pdb_asym_id
This data item is a pointer to attribute auth_asym_id in category atom_site in the
ATOM_SITE category.
pdbx_branch_scheme.pdb_ins_code
This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the
ATOM_SITE category.
pdbx_branch_scheme.pdb_mon_id
This data item is a pointer to attribute auth_comp_id in category atom_site in the
ATOM_SITE category.
pdbx_branch_scheme.pdb_seq_num
This data item is a pointer to attribute auth_seq_id in category atom_site in the
ATOM_SITE category.
pdbx_branch_scheme.asym_id
Pointer to attribute label_asym_id in category atom_site.
1
A
2B3
pdbx_branch_scheme.entity_id
This data item is a pointer to attribute id in category entity in the ENTITY category.
pdbx_branch_scheme.mon_id
This data item is a pointer to attribute label_comp_id in category atom_site in the
PDBX_ENTITY_BRANCH_LIST category.
pdbx_branch_scheme.num
This data item is a pointer to attribute num in category pdbx_entity_branch_list in the
PDBX_ENTITY_BRANCH_LIST category.
0
pdbx_buffer
Data items in the PDBX_BUFFER category
record details of the sample buffer.
0
1
0
1
1
pdbx_bufferCategory
This property indicates that datablock
has a category holder pdbx_bufferCategory.
pdbx_bufferCategory
This property indicates that pdbx_bufferCategory.
has a category pdbx_buffer.
pdbx_bufferItem
Abstract datatype property for pdbx_buffer items.
reference_to_pdbx_buffer
cross-reference to pdbx_buffer.
referenced_by_pdbx_buffer
cross-reference from pdbx_buffer.
pdbx_buffer.details
Any additional details to do with buffer.
aerated
pdbx_buffer.name
The name of each buffer.
Acetic acid
pdbx_buffer.id
The value of attribute id in category pdbx_buffer must
uniquely identify the sample buffer.
0
pdbx_buffer_components
Constituents of buffer in sample
Example 1 - based on PDB entry 1DYL and laboratory records for the
structure corresponding to PDB entry 1DYL
<PDBx:pdbx_buffer_componentsCategory>
<PDBx:pdbx_buffer_components buffer_id="1" id="1">
<PDBx:conc>4 </PDBx:conc>
<PDBx:details xsi:nil="true" />
<PDBx:name>NaCl</PDBx:name>
<PDBx:volume>0.200 </PDBx:volume>
</PDBx:pdbx_buffer_components>
<PDBx:pdbx_buffer_components buffer_id="1" id="2">
<PDBx:conc>100</PDBx:conc>
<PDBx:details xsi:nil="true" />
<PDBx:name>Acetic Acid</PDBx:name>
<PDBx:volume>0.047 </PDBx:volume>
</PDBx:pdbx_buffer_components>
<PDBx:pdbx_buffer_components buffer_id="1" id="3">
<PDBx:conc>neat</PDBx:conc>
<PDBx:details xsi:nil="true" />
<PDBx:name>water</PDBx:name>
<PDBx:volume>0.700 </PDBx:volume>
</PDBx:pdbx_buffer_components>
</PDBx:pdbx_buffer_componentsCategory>
0
1
0
1
0
1
0
1
0
1
0
1
1
1
pdbx_buffer_componentsCategory
This property indicates that datablock
has a category holder pdbx_buffer_componentsCategory.
pdbx_buffer_componentsCategory
This property indicates that pdbx_buffer_componentsCategory.
has a category pdbx_buffer_components.
pdbx_buffer_componentsItem
Abstract datatype property for pdbx_buffer_components items.
reference_to_pdbx_buffer_components
cross-reference to pdbx_buffer_components.
referenced_by_pdbx_buffer_components
cross-reference from pdbx_buffer_components.
pdbx_buffer_components.conc
The millimolar concentration of buffer component.
200
%
mM
mg/mL
M
g/L
The concentration units of the component.
mg/mL for mg per milliliter
mM for millimolar
% for percent by volume
pdbx_buffer_components.details
Any additional details to do with buffer composition.
pH adjusted with NaOH
pdbx_buffer_components.isotopic_labeling
The isotopic composition of each component, including
the % labeling level, if known. For example:
1. Uniform (random) labeling with 15N: U-15N
2. Uniform (random) labeling with 13C, 15N at known labeling
levels: U-95% 13C;U-98% 15N
3. Residue selective labeling: U-95% 15N-Thymine
4. Site specific labeling: 95% 13C-Ala18,
5. Natural abundance labeling in an otherwise uniformly labled
biomolecule is designated by NA: U-13C; NA-K,H
U-15N
U-13C
U-15N,13C
U-2H
other
pdbx_buffer_components.name
The name of each buffer component.
Acetic acid
pdbx_buffer_components.volume
The volume of buffer component.
0.200
pdbx_buffer_components.buffer_id
This data item is a pointer to attribute id in category pdbx_buffer in the BUFFER category.
pdbx_buffer_components.id
The value of attribute id in category pdbx_buffer_components must
uniquely identify a component of the buffer.
0
pdbx_chain_remapping
When producing a biological assembly model file, data items in the pdbx_chain_remapping provide a mapping
from the entity in original model file to this data file.
Example 1 - 6vjo
<PDBx:pdbx_chain_remappingCategory>
<PDBx:pdbx_chain_remapping entity_id="1" label_asym_id="A">
<PDBx:applied_operations>1</PDBx:applied_operations>
<PDBx:auth_asym_id>A</PDBx:auth_asym_id>
<PDBx:orig_auth_asym_id>A</PDBx:orig_auth_asym_id>
<PDBx:orig_label_asym_id>A</PDBx:orig_label_asym_id>
</PDBx:pdbx_chain_remapping>
<PDBx:pdbx_chain_remapping entity_id="2" label_asym_id="B">
<PDBx:applied_operations>1</PDBx:applied_operations>
<PDBx:auth_asym_id>B</PDBx:auth_asym_id>
<PDBx:orig_auth_asym_id>B</PDBx:orig_auth_asym_id>
<PDBx:orig_label_asym_id>B</PDBx:orig_label_asym_id>
</PDBx:pdbx_chain_remapping>
<PDBx:pdbx_chain_remapping entity_id="1" label_asym_id="A_2">
<PDBx:applied_operations>2</PDBx:applied_operations>
<PDBx:auth_asym_id>A_2</PDBx:auth_asym_id>
<PDBx:orig_auth_asym_id>A</PDBx:orig_auth_asym_id>
<PDBx:orig_label_asym_id>A</PDBx:orig_label_asym_id>
</PDBx:pdbx_chain_remapping>
<PDBx:pdbx_chain_remapping entity_id="2" label_asym_id="B_2">
<PDBx:applied_operations>2</PDBx:applied_operations>
<PDBx:auth_asym_id>B_2</PDBx:auth_asym_id>
<PDBx:orig_auth_asym_id>B</PDBx:orig_auth_asym_id>
<PDBx:orig_label_asym_id>B</PDBx:orig_label_asym_id>
</PDBx:pdbx_chain_remapping>
<PDBx:pdbx_chain_remapping entity_id="1" label_asym_id="A_3">
<PDBx:applied_operations>3</PDBx:applied_operations>
<PDBx:auth_asym_id>A_3</PDBx:auth_asym_id>
<PDBx:orig_auth_asym_id>A</PDBx:orig_auth_asym_id>
<PDBx:orig_label_asym_id>A</PDBx:orig_label_asym_id>
</PDBx:pdbx_chain_remapping>
<PDBx:pdbx_chain_remapping entity_id="2" label_asym_id="B_3">
<PDBx:applied_operations>3</PDBx:applied_operations>
<PDBx:auth_asym_id>B_3</PDBx:auth_asym_id>
<PDBx:orig_auth_asym_id>B</PDBx:orig_auth_asym_id>
<PDBx:orig_label_asym_id>B</PDBx:orig_label_asym_id>
</PDBx:pdbx_chain_remapping>
<PDBx:pdbx_chain_remapping entity_id="3" label_asym_id="C">
<PDBx:applied_operations>1</PDBx:applied_operations>
<PDBx:auth_asym_id>A</PDBx:auth_asym_id>
<PDBx:orig_auth_asym_id>A</PDBx:orig_auth_asym_id>
<PDBx:orig_label_asym_id>C</PDBx:orig_label_asym_id>
</PDBx:pdbx_chain_remapping>
<PDBx:pdbx_chain_remapping entity_id="3" label_asym_id="D">
<PDBx:applied_operations>1</PDBx:applied_operations>
<PDBx:auth_asym_id>B</PDBx:auth_asym_id>
<PDBx:orig_auth_asym_id>B</PDBx:orig_auth_asym_id>
<PDBx:orig_label_asym_id>D</PDBx:orig_label_asym_id>
</PDBx:pdbx_chain_remapping>
<PDBx:pdbx_chain_remapping entity_id="3" label_asym_id="C_2">
<PDBx:applied_operations>2</PDBx:applied_operations>
<PDBx:auth_asym_id>A_2</PDBx:auth_asym_id>
<PDBx:orig_auth_asym_id>A</PDBx:orig_auth_asym_id>
<PDBx:orig_label_asym_id>C</PDBx:orig_label_asym_id>
</PDBx:pdbx_chain_remapping>
<PDBx:pdbx_chain_remapping entity_id="3" label_asym_id="D_2">
<PDBx:applied_operations>2</PDBx:applied_operations>
<PDBx:auth_asym_id>B_2</PDBx:auth_asym_id>
<PDBx:orig_auth_asym_id>B</PDBx:orig_auth_asym_id>
<PDBx:orig_label_asym_id>D</PDBx:orig_label_asym_id>
</PDBx:pdbx_chain_remapping>
<PDBx:pdbx_chain_remapping entity_id="3" label_asym_id="C_3">
<PDBx:applied_operations>3</PDBx:applied_operations>
<PDBx:auth_asym_id>A_3</PDBx:auth_asym_id>
<PDBx:orig_auth_asym_id>A</PDBx:orig_auth_asym_id>
<PDBx:orig_label_asym_id>C</PDBx:orig_label_asym_id>
</PDBx:pdbx_chain_remapping>
<PDBx:pdbx_chain_remapping entity_id="3" label_asym_id="D_3">
<PDBx:applied_operations>3</PDBx:applied_operations>
<PDBx:auth_asym_id>B_3</PDBx:auth_asym_id>
<PDBx:orig_auth_asym_id>B</PDBx:orig_auth_asym_id>
<PDBx:orig_label_asym_id>D</PDBx:orig_label_asym_id>
</PDBx:pdbx_chain_remapping>
</PDBx:pdbx_chain_remappingCategory>
1
1
1
1
1
1
1
1
1
1
pdbx_chain_remappingCategory
This property indicates that datablock
has a category holder pdbx_chain_remappingCategory.
pdbx_chain_remappingCategory
This property indicates that pdbx_chain_remappingCategory.
has a category pdbx_chain_remapping.
pdbx_chain_remappingItem
Abstract datatype property for pdbx_chain_remapping items.
reference_to_pdbx_chain_remapping
cross-reference to pdbx_chain_remapping.
referenced_by_pdbx_chain_remapping
cross-reference from pdbx_chain_remapping.
pdbx_chain_remapping.applied_operations
The set of operations identified pdbx_struct_oper_list.id
that were applied to original atom_site coordinates to produce
the coordinates in atom_site in this data block.
pdbx_chain_remapping.auth_asym_id
An alternative identifier for attribute label_asym_id in category atom_site. Frequently the
chain id.
pdbx_chain_remapping.orig_auth_asym_id
An alternative identifier for attribute label_asym_id in category atom_site in the original
model file. Frequently the author's chain id.
pdbx_chain_remapping.orig_label_asym_id
This data item is a pointer to attribute id in category struct_asym in the
STRUCT_ASYM category in the original model file.
pdbx_chain_remapping.entity_id
Identifies an attribute id in category entity in this data block.
pdbx_chain_remapping.label_asym_id
This data item is a pointer to attribute label_asym_id in category atom_site in the
ATOM_SITE category.
0
pdbx_chem_comp_atom_edit
Data items in the PDBX_CHEM_COMP_ATOM_EDIT category provide
atom level editing instructions to be applied to imported
chemical components.
Example 1 -
<PDBx:pdbx_chem_comp_atom_editCategory>
<PDBx:pdbx_chem_comp_atom_edit ordinal="1">
<PDBx:atom_id>HN2</PDBx:atom_id>
<PDBx:comp_id>LYS</PDBx:comp_id>
<PDBx:edit_op>DELETE</PDBx:edit_op>
</PDBx:pdbx_chem_comp_atom_edit>
</PDBx:pdbx_chem_comp_atom_editCategory>
1
1
1
1
1
1
0
1
1
1
1
pdbx_chem_comp_atom_editCategory
This property indicates that datablock
has a category holder pdbx_chem_comp_atom_editCategory.
pdbx_chem_comp_atom_editCategory
This property indicates that pdbx_chem_comp_atom_editCategory.
has a category pdbx_chem_comp_atom_edit.
pdbx_chem_comp_atom_editItem
Abstract datatype property for pdbx_chem_comp_atom_edit items.
reference_to_pdbx_chem_comp_atom_edit
cross-reference to pdbx_chem_comp_atom_edit.
referenced_by_pdbx_chem_comp_atom_edit
cross-reference from pdbx_chem_comp_atom_edit.
pdbx_chem_comp_atom_edit.atom_id
The identifier for the target atom in imported component to be edited.
pdbx_chem_comp_atom_edit.comp_id
This data item is a pointer to attribute comp_id in category pdbx_chem_comp_import in the CHEM_COMP
category.
pdbx_chem_comp_atom_edit.edit_atom_id
The identifier for the edited atom in the generated component.
pdbx_chem_comp_atom_edit.edit_atom_value
The value for the edited atomic property value in the generated component.
RENAME
DELETE
ADD
CHARGE
PARTIAL_CHARGE
MODEL_CARTN_X
MODEL_CARTN_Y
MODEL_CARTN_Z
STEREO_CONFIG
AROMATIC_FLAG
The operation applied to the named imported component.
pdbx_chem_comp_atom_edit.ordinal
This data item uniquely identifies and orders each atom edit instruction.
0
pdbx_chem_comp_atom_feature
Data items in the PDBX_CHEM_COMP_ATOM_FEATURE category provide
a selected list of atom level features for the chemical component.
Example 1 -
<PDBx:pdbx_chem_comp_atom_featureCategory>
<PDBx:pdbx_chem_comp_atom_feature atom_id="N" comp_id="LYS" feature_type="NT"></PDBx:pdbx_chem_comp_atom_feature>
<PDBx:pdbx_chem_comp_atom_feature atom_id="C" comp_id="LYS" feature_type="CT"></PDBx:pdbx_chem_comp_atom_feature>
<PDBx:pdbx_chem_comp_atom_feature atom_id="CA" comp_id="LYS" feature_type="CPA"></PDBx:pdbx_chem_comp_atom_feature>
</PDBx:pdbx_chem_comp_atom_featureCategory>
1
1
1
pdbx_chem_comp_atom_featureCategory
This property indicates that datablock
has a category holder pdbx_chem_comp_atom_featureCategory.
pdbx_chem_comp_atom_featureCategory
This property indicates that pdbx_chem_comp_atom_featureCategory.
has a category pdbx_chem_comp_atom_feature.
pdbx_chem_comp_atom_featureItem
Abstract datatype property for pdbx_chem_comp_atom_feature items.
reference_to_pdbx_chem_comp_atom_feature
cross-reference to pdbx_chem_comp_atom_feature.
referenced_by_pdbx_chem_comp_atom_feature
cross-reference from pdbx_chem_comp_atom_feature.
pdbx_chem_comp_atom_feature.atom_id
The identifier for the target atom to which the feature is assigned.
pdbx_chem_comp_atom_feature.comp_id
This data item is a pointer to attribute comp_id in category pdbx_chem_comp_import in the CHEM_COMP
category.
CT
NT
5PT
3PT
CPA
CNA
The feature assigned to this atom.
0
pdbx_chem_comp_atom_related
PDBX_CHEM_COMP_ATOM_RELATED provides atom level nomenclature mapping between two related chemical components.
Example 1 -
<PDBx:pdbx_chem_comp_atom_relatedCategory>
<PDBx:pdbx_chem_comp_atom_related comp_id="SGN" ordinal="1" related_comp_id="GLC">
<PDBx:atom_id>C1</PDBx:atom_id>
<PDBx:related_atom_id>C1</PDBx:related_atom_id>
<PDBx:related_type>Carbohydrate core</PDBx:related_type>
</PDBx:pdbx_chem_comp_atom_related>
<PDBx:pdbx_chem_comp_atom_related comp_id="SGN" ordinal="2" related_comp_id="GLC">
<PDBx:atom_id>C2</PDBx:atom_id>
<PDBx:related_atom_id>C2</PDBx:related_atom_id>
<PDBx:related_type>Carbohydrate core</PDBx:related_type>
</PDBx:pdbx_chem_comp_atom_related>
<PDBx:pdbx_chem_comp_atom_related comp_id="SGN" ordinal="3" related_comp_id="GLC">
<PDBx:atom_id>C3</PDBx:atom_id>
<PDBx:related_atom_id>C3</PDBx:related_atom_id>
<PDBx:related_type>Carbohydrate core</PDBx:related_type>
</PDBx:pdbx_chem_comp_atom_related>
<PDBx:pdbx_chem_comp_atom_related comp_id="SGN" ordinal="4" related_comp_id="GLC">
<PDBx:atom_id>C4</PDBx:atom_id>
<PDBx:related_atom_id>C4</PDBx:related_atom_id>
<PDBx:related_type>Carbohydrate core</PDBx:related_type>
</PDBx:pdbx_chem_comp_atom_related>
<PDBx:pdbx_chem_comp_atom_related comp_id="SGN" ordinal="5" related_comp_id="GLC">
<PDBx:atom_id>C5</PDBx:atom_id>
<PDBx:related_atom_id>C5</PDBx:related_atom_id>
<PDBx:related_type>Carbohydrate core</PDBx:related_type>
</PDBx:pdbx_chem_comp_atom_related>
<PDBx:pdbx_chem_comp_atom_related comp_id="SGN" ordinal="6" related_comp_id="GLC">
<PDBx:atom_id>C6</PDBx:atom_id>
<PDBx:related_atom_id>C6</PDBx:related_atom_id>
<PDBx:related_type>Carbohydrate core</PDBx:related_type>
</PDBx:pdbx_chem_comp_atom_related>
<PDBx:pdbx_chem_comp_atom_related comp_id="SGN" ordinal="7" related_comp_id="GLC">
<PDBx:atom_id>N</PDBx:atom_id>
<PDBx:related_type>Carbohydrate core</PDBx:related_type>
</PDBx:pdbx_chem_comp_atom_related>
<PDBx:pdbx_chem_comp_atom_related comp_id="SGN" ordinal="8" related_comp_id="GLC">
<PDBx:atom_id>O1</PDBx:atom_id>
<PDBx:related_atom_id>O1</PDBx:related_atom_id>
<PDBx:related_type>Carbohydrate core</PDBx:related_type>
</PDBx:pdbx_chem_comp_atom_related>
<PDBx:pdbx_chem_comp_atom_related comp_id="SGN" ordinal="9" related_comp_id="GLC">
<PDBx:atom_id>O3</PDBx:atom_id>
<PDBx:related_atom_id>O3</PDBx:related_atom_id>
<PDBx:related_type>Carbohydrate core</PDBx:related_type>
</PDBx:pdbx_chem_comp_atom_related>
<PDBx:pdbx_chem_comp_atom_related comp_id="SGN" ordinal="10" related_comp_id="GLC">
<PDBx:atom_id>O4</PDBx:atom_id>
<PDBx:related_atom_id>O4</PDBx:related_atom_id>
<PDBx:related_type>Carbohydrate core</PDBx:related_type>
</PDBx:pdbx_chem_comp_atom_related>
<PDBx:pdbx_chem_comp_atom_related comp_id="SGN" ordinal="11" related_comp_id="GLC">
<PDBx:atom_id>O5</PDBx:atom_id>
<PDBx:related_atom_id>O5</PDBx:related_atom_id>
<PDBx:related_type>Carbohydrate core</PDBx:related_type>
</PDBx:pdbx_chem_comp_atom_related>
<PDBx:pdbx_chem_comp_atom_related comp_id="SGN" ordinal="12" related_comp_id="GLC">
<PDBx:atom_id>O6</PDBx:atom_id>
<PDBx:related_atom_id>O6</PDBx:related_atom_id>
<PDBx:related_type>Carbohydrate core</PDBx:related_type>
</PDBx:pdbx_chem_comp_atom_related>
<PDBx:pdbx_chem_comp_atom_related comp_id="SGN" ordinal="13" related_comp_id="GLC">
<PDBx:atom_id>S1</PDBx:atom_id>
<PDBx:related_type>Carbohydrate core</PDBx:related_type>
</PDBx:pdbx_chem_comp_atom_related>
<PDBx:pdbx_chem_comp_atom_related comp_id="SGN" ordinal="14" related_comp_id="GLC">
<PDBx:atom_id>O1S</PDBx:atom_id>
<PDBx:related_type>Carbohydrate core</PDBx:related_type>
</PDBx:pdbx_chem_comp_atom_related>
<PDBx:pdbx_chem_comp_atom_related comp_id="SGN" ordinal="15" related_comp_id="GLC">
<PDBx:atom_id>O2S</PDBx:atom_id>
<PDBx:related_type>Carbohydrate core</PDBx:related_type>
</PDBx:pdbx_chem_comp_atom_related>
<PDBx:pdbx_chem_comp_atom_related comp_id="SGN" ordinal="16" related_comp_id="GLC">
<PDBx:atom_id>O3S</PDBx:atom_id>
<PDBx:related_type>Carbohydrate core</PDBx:related_type>
</PDBx:pdbx_chem_comp_atom_related>
<PDBx:pdbx_chem_comp_atom_related comp_id="SGN" ordinal="17" related_comp_id="GLC">
<PDBx:atom_id>S2</PDBx:atom_id>
<PDBx:related_type>Carbohydrate core</PDBx:related_type>
</PDBx:pdbx_chem_comp_atom_related>
<PDBx:pdbx_chem_comp_atom_related comp_id="SGN" ordinal="18" related_comp_id="GLC">
<PDBx:atom_id>O4S</PDBx:atom_id>
<PDBx:related_type>Carbohydrate core</PDBx:related_type>
</PDBx:pdbx_chem_comp_atom_related>
<PDBx:pdbx_chem_comp_atom_related comp_id="SGN" ordinal="19" related_comp_id="GLC">
<PDBx:atom_id>O5S</PDBx:atom_id>
<PDBx:related_type>Carbohydrate core</PDBx:related_type>
</PDBx:pdbx_chem_comp_atom_related>
<PDBx:pdbx_chem_comp_atom_related comp_id="SGN" ordinal="20" related_comp_id="GLC">
<PDBx:atom_id>O6S</PDBx:atom_id>
<PDBx:related_type>Carbohydrate core</PDBx:related_type>
</PDBx:pdbx_chem_comp_atom_related>
<PDBx:pdbx_chem_comp_atom_related comp_id="SGN" ordinal="21" related_comp_id="GLC">
<PDBx:atom_id>H1</PDBx:atom_id>
<PDBx:related_atom_id>H1</PDBx:related_atom_id>
<PDBx:related_type>Carbohydrate core</PDBx:related_type>
</PDBx:pdbx_chem_comp_atom_related>
<PDBx:pdbx_chem_comp_atom_related comp_id="SGN" ordinal="22" related_comp_id="GLC">
<PDBx:atom_id>H2</PDBx:atom_id>
<PDBx:related_atom_id>H2</PDBx:related_atom_id>
<PDBx:related_type>Carbohydrate core</PDBx:related_type>
</PDBx:pdbx_chem_comp_atom_related>
<PDBx:pdbx_chem_comp_atom_related comp_id="SGN" ordinal="23" related_comp_id="GLC">
<PDBx:atom_id>H3</PDBx:atom_id>
<PDBx:related_atom_id>H3</PDBx:related_atom_id>
<PDBx:related_type>Carbohydrate core</PDBx:related_type>
</PDBx:pdbx_chem_comp_atom_related>
<PDBx:pdbx_chem_comp_atom_related comp_id="SGN" ordinal="24" related_comp_id="GLC">
<PDBx:atom_id>H4</PDBx:atom_id>
<PDBx:related_atom_id>H4</PDBx:related_atom_id>
<PDBx:related_type>Carbohydrate core</PDBx:related_type>
</PDBx:pdbx_chem_comp_atom_related>
<PDBx:pdbx_chem_comp_atom_related comp_id="SGN" ordinal="25" related_comp_id="GLC">
<PDBx:atom_id>H5</PDBx:atom_id>
<PDBx:related_atom_id>H5</PDBx:related_atom_id>
<PDBx:related_type>Carbohydrate core</PDBx:related_type>
</PDBx:pdbx_chem_comp_atom_related>
<PDBx:pdbx_chem_comp_atom_related comp_id="SGN" ordinal="26" related_comp_id="GLC">
<PDBx:atom_id>H61</PDBx:atom_id>
<PDBx:related_atom_id>H61</PDBx:related_atom_id>
<PDBx:related_type>Carbohydrate core</PDBx:related_type>
</PDBx:pdbx_chem_comp_atom_related>
<PDBx:pdbx_chem_comp_atom_related comp_id="SGN" ordinal="27" related_comp_id="GLC">
<PDBx:atom_id>H62</PDBx:atom_id>
<PDBx:related_atom_id>H62</PDBx:related_atom_id>
<PDBx:related_type>Carbohydrate core</PDBx:related_type>
</PDBx:pdbx_chem_comp_atom_related>
<PDBx:pdbx_chem_comp_atom_related comp_id="SGN" ordinal="28" related_comp_id="GLC">
<PDBx:atom_id>HN</PDBx:atom_id>
<PDBx:related_type>Carbohydrate core</PDBx:related_type>
</PDBx:pdbx_chem_comp_atom_related>
<PDBx:pdbx_chem_comp_atom_related comp_id="SGN" ordinal="29" related_comp_id="GLC">
<PDBx:atom_id>HO1</PDBx:atom_id>
<PDBx:related_atom_id>HO1</PDBx:related_atom_id>
<PDBx:related_type>Carbohydrate core</PDBx:related_type>
</PDBx:pdbx_chem_comp_atom_related>
<PDBx:pdbx_chem_comp_atom_related comp_id="SGN" ordinal="30" related_comp_id="GLC">
<PDBx:atom_id>HO3</PDBx:atom_id>
<PDBx:related_atom_id>HO3</PDBx:related_atom_id>
<PDBx:related_type>Carbohydrate core</PDBx:related_type>
</PDBx:pdbx_chem_comp_atom_related>
<PDBx:pdbx_chem_comp_atom_related comp_id="SGN" ordinal="31" related_comp_id="GLC">
<PDBx:atom_id>HO4</PDBx:atom_id>
<PDBx:related_atom_id>HO4</PDBx:related_atom_id>
<PDBx:related_type>Carbohydrate core</PDBx:related_type>
</PDBx:pdbx_chem_comp_atom_related>
<PDBx:pdbx_chem_comp_atom_related comp_id="SGN" ordinal="32" related_comp_id="GLC">
<PDBx:atom_id>HOS3</PDBx:atom_id>
<PDBx:related_type>Carbohydrate core</PDBx:related_type>
</PDBx:pdbx_chem_comp_atom_related>
<PDBx:pdbx_chem_comp_atom_related comp_id="SGN" ordinal="33" related_comp_id="GLC">
<PDBx:atom_id>HOS6</PDBx:atom_id>
<PDBx:related_type>Carbohydrate core</PDBx:related_type>
</PDBx:pdbx_chem_comp_atom_related>
</PDBx:pdbx_chem_comp_atom_relatedCategory>
1
1
0
1
1
1
1
1
1
pdbx_chem_comp_atom_relatedCategory
This property indicates that datablock
has a category holder pdbx_chem_comp_atom_relatedCategory.
pdbx_chem_comp_atom_relatedCategory
This property indicates that pdbx_chem_comp_atom_relatedCategory.
has a category pdbx_chem_comp_atom_related.
pdbx_chem_comp_atom_relatedItem
Abstract datatype property for pdbx_chem_comp_atom_related items.
reference_to_pdbx_chem_comp_atom_related
cross-reference to pdbx_chem_comp_atom_related.
referenced_by_pdbx_chem_comp_atom_related
cross-reference from pdbx_chem_comp_atom_related.
pdbx_chem_comp_atom_related.atom_id
The atom identifier/name for the atom mapping
pdbx_chem_comp_atom_related.related_atom_id
The atom identifier/name for the atom mapping in the related chemical component
Carbohydrate core
Precursor
Describes the type of relationship
pdbx_chem_comp_atom_related.comp_id
The chemical component for which this relationship applies.
pdbx_chem_comp_atom_related.ordinal
An ordinal index for this category
1
2
pdbx_chem_comp_atom_related.related_comp_id
The related chemical component for which this chemical component is based.
0
pdbx_chem_comp_audit
Data items in the PDBX_CHEM_COMP_AUDIT category records
the status and tracking information for this component.
Example 1 -
<PDBx:pdbx_chem_comp_auditCategory>
<PDBx:pdbx_chem_comp_audit action_type="Create componenet" comp_id="ATP" date="2007-12-01">
<PDBx:annotator>JY</PDBx:annotator>
<PDBx:processing_site>RCSB</PDBx:processing_site>
</PDBx:pdbx_chem_comp_audit>
<PDBx:pdbx_chem_comp_audit action_type="Modify leaving atom flag" comp_id="ATP" date="2008-10-03">
<PDBx:annotator>CS</PDBx:annotator>
<PDBx:processing_site>RCSB</PDBx:processing_site>
</PDBx:pdbx_chem_comp_audit>
<PDBx:pdbx_chem_comp_audit action_type="Modify synonyms" comp_id="ATP" date="2009-07-03">
<PDBx:annotator>MZ</PDBx:annotator>
<PDBx:processing_site>RCSB</PDBx:processing_site>
</PDBx:pdbx_chem_comp_audit>
</PDBx:pdbx_chem_comp_auditCategory>
0
1
0
1
0
1
1
1
1
pdbx_chem_comp_auditCategory
This property indicates that datablock
has a category holder pdbx_chem_comp_auditCategory.
pdbx_chem_comp_auditCategory
This property indicates that pdbx_chem_comp_auditCategory.
has a category pdbx_chem_comp_audit.
pdbx_chem_comp_auditItem
Abstract datatype property for pdbx_chem_comp_audit items.
reference_to_pdbx_chem_comp_audit
cross-reference to pdbx_chem_comp_audit.
referenced_by_pdbx_chem_comp_audit
cross-reference from pdbx_chem_comp_audit.
pdbx_chem_comp_audit.annotator
The initials of the annotator creating of modifying the component.
JO
SJ
KB
pdbx_chem_comp_audit.details
Additional details decribing this change.
Added C14 as a leaving atom.
pdbx_chem_comp_audit.processing_site
An identifier for the wwPDB site creating or modifying the component.
RCSB
PDBE
PDBJ
BMRB
PDBC
Create component
Modify name
Modify formula
Modify synonyms
Modify linking type
Modify internal type
Modify parent residue
Modify processing site
Modify subcomponent list
Modify one letter code
Modify model coordinates code
Modify formal charge
Modify atom id
Modify charge
Modify aromatic_flag
Modify leaving atom flag
Modify component atom id
Modify component comp_id
Modify value order
Modify descriptor
Modify identifier
Modify coordinates
Modify backbone
Other modification
Obsolete component
Initial release
The action associated with this audit record.
pdbx_chem_comp_audit.comp_id
This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP
category.
pdbx_chem_comp_audit.date
The date associated with this audit record.
0
pdbx_chem_comp_bond_edit
Data items in the PDBX_CHEM_COMP_BOND_EDIT category provide
bond level editing instructions to be applied to imported
chemical components.
Example 1 -
<PDBx:pdbx_chem_comp_bond_editCategory>
<PDBx:pdbx_chem_comp_bond_edit atom_id_1="OXT" atom_id_2="HXT" comp_id="LYS" edit_op="DELETE">
<PDBx:ordinal>1</PDBx:ordinal>
</PDBx:pdbx_chem_comp_bond_edit>
</PDBx:pdbx_chem_comp_bond_editCategory>
0
1
1
1
1
1
1
1
pdbx_chem_comp_bond_editCategory
This property indicates that datablock
has a category holder pdbx_chem_comp_bond_editCategory.
pdbx_chem_comp_bond_editCategory
This property indicates that pdbx_chem_comp_bond_editCategory.
has a category pdbx_chem_comp_bond_edit.
pdbx_chem_comp_bond_editItem
Abstract datatype property for pdbx_chem_comp_bond_edit items.
reference_to_pdbx_chem_comp_bond_edit
cross-reference to pdbx_chem_comp_bond_edit.
referenced_by_pdbx_chem_comp_bond_edit
cross-reference from pdbx_chem_comp_bond_edit.
pdbx_chem_comp_bond_edit.edit_bond_value
The value for the edited bond property value in the generated component.
pdbx_chem_comp_bond_edit.ordinal
This data item uniquely identifies and orders each bond edit instruction.
pdbx_chem_comp_bond_edit.atom_id_1
The identifier for the first atom in the target bond
in imported component.
pdbx_chem_comp_bond_edit.atom_id_2
The identifier for the second atom in the target bond
in imported component.
pdbx_chem_comp_bond_edit.comp_id
This data item is a pointer to attribute comp_id in category pdbx_chem_comp_import in the CHEM_COMP
category.
DELETE
ADD
VALUE_ORDER
VALUE_DIST
STEREO_CONFIG
AROMATIC_FLAG
The operation or assignment applied to the named imported component.
0
pdbx_chem_comp_depositor_info
Data items in the PDBX_CHEM_COMP_DEPOSITOR_INFO category record additional
details provided by depositors about deposited chemical components.
Example 1 -
<PDBx:pdbx_chem_comp_depositor_infoCategory>
<PDBx:pdbx_chem_comp_depositor_info ordinal="1">
<PDBx:alt_comp_id xsi:nil="true" />
<PDBx:comp_id>GNC</PDBx:comp_id>
<PDBx:descriptor>CC(=O)N[C@H]1[C@H](O)O[C@H](CO)[C@@H](O)[C@@H]1O</PDBx:descriptor>
<PDBx:descriptor_type>SMILES</PDBx:descriptor_type>
<PDBx:formula>C8 H15 N O6</PDBx:formula>
<PDBx:name>N-acetyl-beta-D-glucosamine</PDBx:name>
</PDBx:pdbx_chem_comp_depositor_info>
</PDBx:pdbx_chem_comp_depositor_infoCategory>
0
1
1
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
pdbx_chem_comp_depositor_infoCategory
This property indicates that datablock
has a category holder pdbx_chem_comp_depositor_infoCategory.
pdbx_chem_comp_depositor_infoCategory
This property indicates that pdbx_chem_comp_depositor_infoCategory.
has a category pdbx_chem_comp_depositor_info.
pdbx_chem_comp_depositor_infoItem
Abstract datatype property for pdbx_chem_comp_depositor_info items.
reference_to_pdbx_chem_comp_depositor_info
cross-reference to pdbx_chem_comp_depositor_info.
referenced_by_pdbx_chem_comp_depositor_info
cross-reference from pdbx_chem_comp_depositor_info.
pdbx_chem_comp_depositor_info.alt_comp_id
The alternate chemical component identifier matching the deposited chemical component.
pdbx_chem_comp_depositor_info.comp_id
The chemical component identifier used by the depositor to represent this component.
pdbx_chem_comp_depositor_info.descriptor
This data item contains the descriptor value for this
component.
SMILES
InChI
InChIKey
This data item contains the descriptor type.
pdbx_chem_comp_depositor_info.details
This data item contains additional details about this
component.
pdbx_chem_comp_depositor_info.formula
The formula for the chemical component. Formulae are written
according to the following rules:
(1) Only recognized element symbols may be used.
(2) Each element symbol is followed by a 'count' number. A count
of '1' may be omitted.
(3) A space or parenthesis must separate each cluster of
(element symbol + count), but in general parentheses are
not used.
(4) The order of elements depends on whether carbon is
present or not. If carbon is present, the order should be:
C, then H, then the other elements in alphabetical order
of their symbol. If carbon is not present, the elements
are listed purely in alphabetic order of their symbol. This
is the 'Hill' system used by Chemical Abstracts.
C18 H19 N7 O8 S
Y
N
A flag to indicate if the chemical component is defined in the chemical component dictionary.
pdbx_chem_comp_depositor_info.name
The chemical name of the component.
alanine
valine
adenine
cytosine
D-peptide linking
L-peptide linking
DNA linking
RNA linking
L-RNA linking
L-DNA linking
saccharide
non-polymer
peptide linking
peptide-like
other
This data item contains the chemical component type.
pdbx_chem_comp_depositor_info.upload_file_name
The filename of an uploaded description of a component
component.
pdbx_chem_comp_depositor_info.upload_file_type
The type of an uploaded description of a component
component.
pdbx_chem_comp_depositor_info.ordinal
Ordinal index for this category.
0
pdbx_chem_comp_descriptor
Data items in the CHEM_COMP_DESCRIPTOR category provide
string descriptors of component chemical structure.
Example 1 -
<PDBx:pdbx_chem_comp_descriptorCategory>
<PDBx:pdbx_chem_comp_descriptor comp_id="ATP" program="OPENEYE" program_version="1.5.0" type="SMILES">
<PDBx:descriptor>c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N</PDBx:descriptor>
</PDBx:pdbx_chem_comp_descriptor>
</PDBx:pdbx_chem_comp_descriptorCategory>
1
1
0
1
1
1
1
1
pdbx_chem_comp_descriptorCategory
This property indicates that datablock
has a category holder pdbx_chem_comp_descriptorCategory.
pdbx_chem_comp_descriptorCategory
This property indicates that pdbx_chem_comp_descriptorCategory.
has a category pdbx_chem_comp_descriptor.
pdbx_chem_comp_descriptorItem
Abstract datatype property for pdbx_chem_comp_descriptor items.
reference_to_pdbx_chem_comp_descriptor
cross-reference to pdbx_chem_comp_descriptor.
referenced_by_pdbx_chem_comp_descriptor
cross-reference from pdbx_chem_comp_descriptor.
pdbx_chem_comp_descriptor.descriptor
This data item contains the descriptor value for this
component.
pdbx_chem_comp_descriptor.ordinal
Ordinal index for this category.
pdbx_chem_comp_descriptor.comp_id
This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP
category.
pdbx_chem_comp_descriptor.program
This data item contains the name of the program
or library used to compute the descriptor.
OpenEye OECHEM library
OPENEYE
CACTVS program library
CACTVS
Daylight program library
DAYLIGHT
Other program or library
OTHER
pdbx_chem_comp_descriptor.program_version
This data item contains the version of the program
or library used to compute the descriptor.
SMILES_CANNONICAL
SMILES_CANONICAL
SMILES
InChI
InChI_MAIN
InChI_MAIN_FORMULA
InChI_MAIN_CONNECT
InChI_MAIN_HATOM
InChI_CHARGE
InChI_STEREO
InChI_ISOTOPE
InChI_FIXEDH
InChI_RECONNECT
InChIKey
This data item contains the descriptor type.
0
pdbx_chem_comp_feature
Additional features associated with the chemical component.
Example 1 -
<PDBx:pdbx_chem_comp_featureCategory>
<PDBx:pdbx_chem_comp_feature comp_id="00X" source="PDB" type="ENZYME INHIBITED" value="ASPARTIC PROTEINASE"></PDBx:pdbx_chem_comp_feature>
<PDBx:pdbx_chem_comp_feature comp_id="00X" source="PDB" type="FUNCTION" value="Transistion-state analogue inhibitor"></PDBx:pdbx_chem_comp_feature>
<PDBx:pdbx_chem_comp_feature comp_id="00X" source="IUCR" type="STRUCTURE IMAGE URL" value="http://journals.iucr.org/00X.jpg"></PDBx:pdbx_chem_comp_feature>
</PDBx:pdbx_chem_comp_featureCategory>
0
1
1
1
1
1
pdbx_chem_comp_featureCategory
This property indicates that datablock
has a category holder pdbx_chem_comp_featureCategory.
pdbx_chem_comp_featureCategory
This property indicates that pdbx_chem_comp_featureCategory.
has a category pdbx_chem_comp_feature.
pdbx_chem_comp_featureItem
Abstract datatype property for pdbx_chem_comp_feature items.
reference_to_pdbx_chem_comp_feature
cross-reference to pdbx_chem_comp_feature.
referenced_by_pdbx_chem_comp_feature
cross-reference from pdbx_chem_comp_feature.
pdbx_chem_comp_feature.support
The supporting evidence for this feature.
Biological assay
Data obtained from PNAS August 17, 1999 vol. 96 no. 17 9586-9590
pdbx_chem_comp_feature.comp_id
The component identifier for this feature.
ABC
ATP
pdbx_chem_comp_feature.source
The information source for the component feature.
PDB
CHEBI
DRUGBANK
PUBCHEM
CARBOHYDRATE ANOMER
CARBOHYDRATE ISOMER
CARBOHYDRATE RING
CARBOHYDRATE PRIMARY CARBONYL GROUP
The component feature type.
CARBOHYDRATE ANOMER
CARBOHYDRATE ISOMER
CARBOHYDRATE RING
pdbx_chem_comp_feature.value
The component feature value.
0
pdbx_chem_comp_identifier
Data items in the CHEM_COMP_IDENTIFIER category provide
identifiers for chemical components.
Example 1 -
<PDBx:pdbx_chem_comp_identifierCategory>
<PDBx:pdbx_chem_comp_identifier comp_id="ATP" program="ACDLabs" program_version="10.04" type="SYSTEMATIC NAME">
<PDBx:identifier>adenosine 5'-(tetrahydrogen triphosphate)</PDBx:identifier>
</PDBx:pdbx_chem_comp_identifier>
</PDBx:pdbx_chem_comp_identifierCategory>
1
1
0
1
1
1
1
1
pdbx_chem_comp_identifierCategory
This property indicates that datablock
has a category holder pdbx_chem_comp_identifierCategory.
pdbx_chem_comp_identifierCategory
This property indicates that pdbx_chem_comp_identifierCategory.
has a category pdbx_chem_comp_identifier.
pdbx_chem_comp_identifierItem
Abstract datatype property for pdbx_chem_comp_identifier items.
reference_to_pdbx_chem_comp_identifier
cross-reference to pdbx_chem_comp_identifier.
referenced_by_pdbx_chem_comp_identifier
cross-reference from pdbx_chem_comp_identifier.
pdbx_chem_comp_identifier.identifier
This data item contains the identifier value for this
component.
pdbx_chem_comp_identifier.ordinal
Ordinal index for this category.
pdbx_chem_comp_identifier.comp_id
This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP
category.
pdbx_chem_comp_identifier.program
This data item contains the name of the program
or library used to compute the identifier.
OpenEye OECHEM program
OPENEYE
Daylight program library
DAYLIGHT
Advanced Chemistry Development Naming Program
ACD
Belstein AutoNom Naming Program
AUTONOM
Compound identifier
PUBCHEM_CID
Substance identifier
PUBCHEM_SID
Other program or library
OTHER
Non-programmatic identifier
NONE
pdbx_chem_comp_identifier.program_version
This data item contains the version of the program
or library used to compute the identifier.
COMMON NAME
SYSTEMATIC NAME
CAS REGISTRY NUMBER
PUBCHEM Identifier
MDL Identifier
SYNONYM
CONDENSED IUPAC CARB SYMBOL
IUPAC CARB SYMBOL
SNFG CARB SYMBOL
CONDENSED IUPAC CARBOHYDRATE SYMBOL
IUPAC CARBOHYDRATE SYMBOL
SNFG CARBOHYDRATE SYMBOL
This data item contains the identifier type.
0
pdbx_chem_comp_import
Data items in the PDBX_CHEM_COMP_IMPORT category identify
existing chemical components to be imported into the
current component definition. Components in this list
can be edited by instructions in categories
pdbx_chem_comp_atom_edit and pdbx_chem_comp_bond_edit.
Example 1 -
<PDBx:pdbx_chem_comp_importCategory>
<PDBx:pdbx_chem_comp_import comp_id="ATP"></PDBx:pdbx_chem_comp_import>
</PDBx:pdbx_chem_comp_importCategory>
1
pdbx_chem_comp_importCategory
This property indicates that datablock
has a category holder pdbx_chem_comp_importCategory.
pdbx_chem_comp_importCategory
This property indicates that pdbx_chem_comp_importCategory.
has a category pdbx_chem_comp_import.
pdbx_chem_comp_importItem
Abstract datatype property for pdbx_chem_comp_import items.
reference_to_pdbx_chem_comp_import
cross-reference to pdbx_chem_comp_import.
referenced_by_pdbx_chem_comp_import
cross-reference from pdbx_chem_comp_import.
pdbx_chem_comp_import.comp_id
This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP
category.
0
pdbx_chem_comp_instance_depositor_info
Data items in the PDBX_CHEM_COMP_INSTANCE_DEPOSITOR_INFO category records
depositor provided information about the chemical context of component instances.
Example -
<PDBx:pdbx_chem_comp_instance_depositor_infoCategory>
<PDBx:pdbx_chem_comp_instance_depositor_info ordinal="1">
<PDBx:PDB_ins_code xsi:nil="true" />
<PDBx:auth_asym_id>W</PDBx:auth_asym_id>
<PDBx:auth_seq_id>102</PDBx:auth_seq_id>
<PDBx:author_provided_flag>Y</PDBx:author_provided_flag>
<PDBx:comp_id>X78</PDBx:comp_id>
<PDBx:in_polymer_flag>N</PDBx:in_polymer_flag>
<PDBx:label_alt_id xsi:nil="true" />
</PDBx:pdbx_chem_comp_instance_depositor_info>
</PDBx:pdbx_chem_comp_instance_depositor_infoCategory>
0
1
1
1
1
1
0
1
1
1
0
1
0
1
0
1
1
pdbx_chem_comp_instance_depositor_infoCategory
This property indicates that datablock
has a category holder pdbx_chem_comp_instance_depositor_infoCategory.
pdbx_chem_comp_instance_depositor_infoCategory
This property indicates that pdbx_chem_comp_instance_depositor_infoCategory.
has a category pdbx_chem_comp_instance_depositor_info.
pdbx_chem_comp_instance_depositor_infoItem
Abstract datatype property for pdbx_chem_comp_instance_depositor_info items.
reference_to_pdbx_chem_comp_instance_depositor_info
cross-reference to pdbx_chem_comp_instance_depositor_info.
referenced_by_pdbx_chem_comp_instance_depositor_info
cross-reference from pdbx_chem_comp_instance_depositor_info.
pdbx_chem_comp_instance_depositor_info.PDB_ins_code
Optional element of the chemical component instance identifier.
This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the
ATOM_SITE category.
pdbx_chem_comp_instance_depositor_info.auth_asym_id
An element of the chemical component instance identifier.
This data item corresponds to attribute auth_asym_id in category atom_site in the
ATOM_SITE category.
pdbx_chem_comp_instance_depositor_info.auth_seq_id
An element of the chemical component instance identifier.
This data item corresponds to attribute auth_seq_id in category atom_site in the
ATOM_SITE category.
Y
N
A flag to indicate if details about this chemical component instance have been provided by the depositor.
pdbx_chem_comp_instance_depositor_info.comp_id
An element of the chemical component instance identifier.
This data item is a pointer to attribute label_comp_id in category atom_site in the
ATOM_SITE category.
pdbx_chem_comp_instance_depositor_info.formula
The observed formula for the chemical component in the deposited coordinates.
Formulae are written according to the following rules:
(1) Only recognized element symbols may be used.
(2) Each element symbol is followed by a 'count' number. A count
of '1' may be omitted.
(3) A space or parenthesis must separate each cluster of
(element symbol + count), but in general parentheses are
not used.
(4) The order of elements depends on whether carbon is
present or not. If carbon is present, the order should be:
C, then H, then the other elements in alphabetical order
of their symbol. If carbon is not present, the elements
are listed purely in alphabetic order of their symbol. This
is the 'Hill' system used by Chemical Abstracts.
C18 H19 N7 O8 S
Y
N
A flag to indicate if the chemical component instance is a part of a polymer molecule.
pdbx_chem_comp_instance_depositor_info.label_alt_id
An element of the chemical component instance identifier.
This data item is a pointer to attribute label_alt_id in category atom_site in the
ATOM_SITE category.
pdbx_chem_comp_instance_depositor_info.ordinal
The value of pdbx_chem_comp_instance_depositor_info.ordinal must uniquely identify a record in
the PDBX_CHEM_COMP_INSTANCE_DEPOSITOR_INFO list.
0
pdbx_chem_comp_model
Data items in the PDBX_CHEM_COMP_MODEL category give details about each
of the chemical component model instances.
Example 1 -
<PDBx:pdbx_chem_comp_modelCategory>
<PDBx:pdbx_chem_comp_model id="M_ZZV_00001">
<PDBx:comp_id>ZZV</PDBx:comp_id>
</PDBx:pdbx_chem_comp_model>
</PDBx:pdbx_chem_comp_modelCategory>
1
1
1
pdbx_chem_comp_modelCategory
This property indicates that datablock
has a category holder pdbx_chem_comp_modelCategory.
pdbx_chem_comp_modelCategory
This property indicates that pdbx_chem_comp_modelCategory.
has a category pdbx_chem_comp_model.
pdbx_chem_comp_modelItem
Abstract datatype property for pdbx_chem_comp_model items.
reference_to_pdbx_chem_comp_model
cross-reference to pdbx_chem_comp_model.
referenced_by_pdbx_chem_comp_model
cross-reference from pdbx_chem_comp_model.
pdbx_chem_comp_model.comp_id
An identifier for chemical component definition.
ABC
pdbx_chem_comp_model.id
The value of attribute id in category pdbx_chem_comp_model must uniquely identify each
model instance the PDBX_CHEM_COMP_MODEL list.
M_ABC_00001
0
pdbx_chem_comp_model_atom
Data items in the PDBX_CHEM_COMP_MODEL_ATOM category record coordinates
for the chemical component model instance.
Example 1 -
<PDBx:pdbx_chem_comp_model_atomCategory>
<PDBx:pdbx_chem_comp_model_atom atom_id="CAA" model_id="M_ZZV_00001">
<PDBx:charge>0</PDBx:charge>
<PDBx:model_Cartn_x>2.180</PDBx:model_Cartn_x>
<PDBx:model_Cartn_y>6.561</PDBx:model_Cartn_y>
<PDBx:model_Cartn_z>8.402</PDBx:model_Cartn_z>
<PDBx:ordinal_id>1</PDBx:ordinal_id>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:pdbx_chem_comp_model_atom>
<PDBx:pdbx_chem_comp_model_atom atom_id="CAB" model_id="M_ZZV_00001">
<PDBx:charge>0</PDBx:charge>
<PDBx:model_Cartn_x>5.709</PDBx:model_Cartn_x>
<PDBx:model_Cartn_y>6.659</PDBx:model_Cartn_y>
<PDBx:model_Cartn_z>8.211</PDBx:model_Cartn_z>
<PDBx:ordinal_id>2</PDBx:ordinal_id>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:pdbx_chem_comp_model_atom>
<PDBx:pdbx_chem_comp_model_atom atom_id="OAC" model_id="M_ZZV_00001">
<PDBx:charge>0</PDBx:charge>
<PDBx:model_Cartn_x>1.912</PDBx:model_Cartn_x>
<PDBx:model_Cartn_y>12.185</PDBx:model_Cartn_y>
<PDBx:model_Cartn_z>12.303</PDBx:model_Cartn_z>
<PDBx:ordinal_id>3</PDBx:ordinal_id>
<PDBx:type_symbol>O</PDBx:type_symbol>
</PDBx:pdbx_chem_comp_model_atom>
<PDBx:pdbx_chem_comp_model_atom atom_id="OAD" model_id="M_ZZV_00001">
<PDBx:charge>0</PDBx:charge>
<PDBx:model_Cartn_x>4.002</PDBx:model_Cartn_x>
<PDBx:model_Cartn_y>7.560</PDBx:model_Cartn_y>
<PDBx:model_Cartn_z>6.491</PDBx:model_Cartn_z>
<PDBx:ordinal_id>4</PDBx:ordinal_id>
<PDBx:type_symbol>O</PDBx:type_symbol>
</PDBx:pdbx_chem_comp_model_atom>
<PDBx:pdbx_chem_comp_model_atom atom_id="OAE" model_id="M_ZZV_00001">
<PDBx:charge>0</PDBx:charge>
<PDBx:model_Cartn_x>4.992</PDBx:model_Cartn_x>
<PDBx:model_Cartn_y>9.134</PDBx:model_Cartn_y>
<PDBx:model_Cartn_z>8.117</PDBx:model_Cartn_z>
<PDBx:ordinal_id>5</PDBx:ordinal_id>
<PDBx:type_symbol>O</PDBx:type_symbol>
</PDBx:pdbx_chem_comp_model_atom>
<PDBx:pdbx_chem_comp_model_atom atom_id="OAF" model_id="M_ZZV_00001">
<PDBx:charge>0</PDBx:charge>
<PDBx:model_Cartn_x>2.970</PDBx:model_Cartn_x>
<PDBx:model_Cartn_y>10.013</PDBx:model_Cartn_y>
<PDBx:model_Cartn_z>13.854</PDBx:model_Cartn_z>
<PDBx:ordinal_id>6</PDBx:ordinal_id>
<PDBx:type_symbol>O</PDBx:type_symbol>
</PDBx:pdbx_chem_comp_model_atom>
<PDBx:pdbx_chem_comp_model_atom atom_id="FAG" model_id="M_ZZV_00001">
<PDBx:charge>0</PDBx:charge>
<PDBx:model_Cartn_x>-3.392</PDBx:model_Cartn_x>
<PDBx:model_Cartn_y>12.249</PDBx:model_Cartn_y>
<PDBx:model_Cartn_z>6.995</PDBx:model_Cartn_z>
<PDBx:ordinal_id>7</PDBx:ordinal_id>
<PDBx:type_symbol>F</PDBx:type_symbol>
</PDBx:pdbx_chem_comp_model_atom>
<PDBx:pdbx_chem_comp_model_atom atom_id="CAH" model_id="M_ZZV_00001">
<PDBx:charge>0</PDBx:charge>
<PDBx:model_Cartn_x>4.361</PDBx:model_Cartn_x>
<PDBx:model_Cartn_y>5.472</PDBx:model_Cartn_y>
<PDBx:model_Cartn_z>12.379</PDBx:model_Cartn_z>
<PDBx:ordinal_id>8</PDBx:ordinal_id>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:pdbx_chem_comp_model_atom>
<PDBx:pdbx_chem_comp_model_atom atom_id="CAI" model_id="M_ZZV_00001">
<PDBx:charge>0</PDBx:charge>
<PDBx:model_Cartn_x>4.277</PDBx:model_Cartn_x>
<PDBx:model_Cartn_y>6.182</PDBx:model_Cartn_y>
<PDBx:model_Cartn_z>13.595</PDBx:model_Cartn_z>
<PDBx:ordinal_id>9</PDBx:ordinal_id>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:pdbx_chem_comp_model_atom>
<PDBx:pdbx_chem_comp_model_atom atom_id="CAJ" model_id="M_ZZV_00001">
<PDBx:charge>0</PDBx:charge>
<PDBx:model_Cartn_x>-2.132</PDBx:model_Cartn_x>
<PDBx:model_Cartn_y>12.408</PDBx:model_Cartn_y>
<PDBx:model_Cartn_z>8.958</PDBx:model_Cartn_z>
<PDBx:ordinal_id>10</PDBx:ordinal_id>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:pdbx_chem_comp_model_atom>
<PDBx:pdbx_chem_comp_model_atom atom_id="CAK" model_id="M_ZZV_00001">
<PDBx:charge>0</PDBx:charge>
<PDBx:model_Cartn_x>-1.112</PDBx:model_Cartn_x>
<PDBx:model_Cartn_y>12.651</PDBx:model_Cartn_y>
<PDBx:model_Cartn_z>6.807</PDBx:model_Cartn_z>
<PDBx:ordinal_id>11</PDBx:ordinal_id>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:pdbx_chem_comp_model_atom>
<PDBx:pdbx_chem_comp_model_atom atom_id="CAL" model_id="M_ZZV_00001">
<PDBx:charge>0</PDBx:charge>
<PDBx:model_Cartn_x>-0.902</PDBx:model_Cartn_x>
<PDBx:model_Cartn_y>12.579</PDBx:model_Cartn_y>
<PDBx:model_Cartn_z>9.557</PDBx:model_Cartn_z>
<PDBx:ordinal_id>12</PDBx:ordinal_id>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:pdbx_chem_comp_model_atom>
<PDBx:pdbx_chem_comp_model_atom atom_id="CAM" model_id="M_ZZV_00001">
<PDBx:charge>0</PDBx:charge>
<PDBx:model_Cartn_x>0.139</PDBx:model_Cartn_x>
<PDBx:model_Cartn_y>12.801</PDBx:model_Cartn_y>
<PDBx:model_Cartn_z>7.421</PDBx:model_Cartn_z>
<PDBx:ordinal_id>13</PDBx:ordinal_id>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:pdbx_chem_comp_model_atom>
<PDBx:pdbx_chem_comp_model_atom atom_id="CAN" model_id="M_ZZV_00001">
<PDBx:charge>0</PDBx:charge>
<PDBx:model_Cartn_x>4.004</PDBx:model_Cartn_x>
<PDBx:model_Cartn_y>6.101</PDBx:model_Cartn_y>
<PDBx:model_Cartn_z>11.237</PDBx:model_Cartn_z>
<PDBx:ordinal_id>14</PDBx:ordinal_id>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:pdbx_chem_comp_model_atom>
</PDBx:pdbx_chem_comp_model_atomCategory>
0
1
0
1
0
1
0
1
1
1
1
1
1
1
pdbx_chem_comp_model_atomCategory
This property indicates that datablock
has a category holder pdbx_chem_comp_model_atomCategory.
pdbx_chem_comp_model_atomCategory
This property indicates that pdbx_chem_comp_model_atomCategory.
has a category pdbx_chem_comp_model_atom.
pdbx_chem_comp_model_atomItem
Abstract datatype property for pdbx_chem_comp_model_atom items.
reference_to_pdbx_chem_comp_model_atom
cross-reference to pdbx_chem_comp_model_atom.
referenced_by_pdbx_chem_comp_model_atom
cross-reference from pdbx_chem_comp_model_atom.
pdbx_chem_comp_model_atom.charge
The net integer charge assigned to this atom. This is the
formal charge assignment normally found in chemical diagrams.
for an ammonium nitrogen
1
for a chloride ion
-1
pdbx_chem_comp_model_atom.model_Cartn_x
The x component of the coordinates for this atom in this
component model specified as orthogonal angstroms.
pdbx_chem_comp_model_atom.model_Cartn_y
The y component of the coordinates for this atom in this
component model specified as orthogonal angstroms.
pdbx_chem_comp_model_atom.model_Cartn_z
The z component of the coordinates for this atom in this
component model specified as orthogonal angstroms.
pdbx_chem_comp_model_atom.ordinal_id
The value of attribute ordinal_id in category pdbx_chem_comp_model_atom is an
ordinal identifer for each atom in the PDBX_CHEM_COMP_MODEL_ATOM list.
pdbx_chem_comp_model_atom.type_symbol
The code used to identify the atom species representing
this atom type. Normally this code is the element
symbol.
C
N
O
pdbx_chem_comp_model_atom.atom_id
The value of attribute atom_id in category pdbx_chem_comp_model_atom uniquely identifies
each atom in the PDBX_CHEM_COMP_MODEL_ATOM list.
pdbx_chem_comp_model_atom.model_id
This data item is a pointer to attribute id in category pdbx_chem_comp_model in the PDBX_CHEM_COMP_MODEL
category.
0
pdbx_chem_comp_model_audit
Data items in the PDBX_CHEM_COMP_MODEL_AUDIT category records
the status and tracking information for this component model instance.
Example 1 -
<PDBx:pdbx_chem_comp_model_auditCategory>
<PDBx:pdbx_chem_comp_model_audit action_type="Create component model" date="2014-11-30" model_id="M_ZZV_00001">
<PDBx:annotator>JDW</PDBx:annotator>
<PDBx:processing_site>RCSB</PDBx:processing_site>
</PDBx:pdbx_chem_comp_model_audit>
</PDBx:pdbx_chem_comp_model_auditCategory>
0
1
0
1
0
1
1
1
1
pdbx_chem_comp_model_auditCategory
This property indicates that datablock
has a category holder pdbx_chem_comp_model_auditCategory.
pdbx_chem_comp_model_auditCategory
This property indicates that pdbx_chem_comp_model_auditCategory.
has a category pdbx_chem_comp_model_audit.
pdbx_chem_comp_model_auditItem
Abstract datatype property for pdbx_chem_comp_model_audit items.
reference_to_pdbx_chem_comp_model_audit
cross-reference to pdbx_chem_comp_model_audit.
referenced_by_pdbx_chem_comp_model_audit
cross-reference from pdbx_chem_comp_model_audit.
pdbx_chem_comp_model_audit.annotator
The initials of the annotator creating of modifying the component.
JO
SJ
KB
pdbx_chem_comp_model_audit.details
Additional details decribing this change.
Added C14 as a leaving atom.
pdbx_chem_comp_model_audit.processing_site
An identifier for the wwPDB site creating or modifying the component.
RCSB
PDBE
PDBJ
BMRB
PDBC
Create component
Modify formal charge
Modify atom id
Modify charge
Modify component atom id
Modify component comp_id
Modify value order
Modify descriptor
Modify identifier
Modify coordinates
Other modification
Obsolete model
Initial release
The action associated with this audit record.
pdbx_chem_comp_model_audit.date
The date associated with this audit record.
pdbx_chem_comp_model_audit.model_id
This data item is a pointer to attribute id in category pdbx_chem_comp_model in the PDBX_CHEM_COMP_MODEL
category.
0
pdbx_chem_comp_model_bond
Data items in the PDBX_CHEM_COMP_MODEL_BOND category record details about
the bonds between atoms in a chemical component model instance.
Example 1 -
<PDBx:pdbx_chem_comp_model_bondCategory>
<PDBx:pdbx_chem_comp_model_bond atom_id_1="CAA" atom_id_2="NBA" model_id="M_ZZV_00001">
<PDBx:ordinal_id>1</PDBx:ordinal_id>
<PDBx:value_order>SING</PDBx:value_order>
</PDBx:pdbx_chem_comp_model_bond>
<PDBx:pdbx_chem_comp_model_bond atom_id_1="CAA" atom_id_2="HAA" model_id="M_ZZV_00001">
<PDBx:ordinal_id>2</PDBx:ordinal_id>
<PDBx:value_order>SING</PDBx:value_order>
</PDBx:pdbx_chem_comp_model_bond>
<PDBx:pdbx_chem_comp_model_bond atom_id_1="CAA" atom_id_2="HAAA" model_id="M_ZZV_00001">
<PDBx:ordinal_id>3</PDBx:ordinal_id>
<PDBx:value_order>SING</PDBx:value_order>
</PDBx:pdbx_chem_comp_model_bond>
<PDBx:pdbx_chem_comp_model_bond atom_id_1="CAA" atom_id_2="HAAB" model_id="M_ZZV_00001">
<PDBx:ordinal_id>4</PDBx:ordinal_id>
<PDBx:value_order>SING</PDBx:value_order>
</PDBx:pdbx_chem_comp_model_bond>
<PDBx:pdbx_chem_comp_model_bond atom_id_1="CAB" atom_id_2="SBC" model_id="M_ZZV_00001">
<PDBx:ordinal_id>5</PDBx:ordinal_id>
<PDBx:value_order>SING</PDBx:value_order>
</PDBx:pdbx_chem_comp_model_bond>
<PDBx:pdbx_chem_comp_model_bond atom_id_1="CAB" atom_id_2="HAB" model_id="M_ZZV_00001">
<PDBx:ordinal_id>6</PDBx:ordinal_id>
<PDBx:value_order>SING</PDBx:value_order>
</PDBx:pdbx_chem_comp_model_bond>
<PDBx:pdbx_chem_comp_model_bond atom_id_1="CAB" atom_id_2="HABA" model_id="M_ZZV_00001">
<PDBx:ordinal_id>7</PDBx:ordinal_id>
<PDBx:value_order>SING</PDBx:value_order>
</PDBx:pdbx_chem_comp_model_bond>
<PDBx:pdbx_chem_comp_model_bond atom_id_1="CAB" atom_id_2="HABB" model_id="M_ZZV_00001">
<PDBx:ordinal_id>8</PDBx:ordinal_id>
<PDBx:value_order>SING</PDBx:value_order>
</PDBx:pdbx_chem_comp_model_bond>
<PDBx:pdbx_chem_comp_model_bond atom_id_1="OAC" atom_id_2="CAR" model_id="M_ZZV_00001">
<PDBx:ordinal_id>9</PDBx:ordinal_id>
<PDBx:value_order>DOUB</PDBx:value_order>
</PDBx:pdbx_chem_comp_model_bond>
<PDBx:pdbx_chem_comp_model_bond atom_id_1="OAD" atom_id_2="SBC" model_id="M_ZZV_00001">
<PDBx:ordinal_id>10</PDBx:ordinal_id>
<PDBx:value_order>DOUB</PDBx:value_order>
</PDBx:pdbx_chem_comp_model_bond>
<PDBx:pdbx_chem_comp_model_bond atom_id_1="OAE" atom_id_2="SBC" model_id="M_ZZV_00001">
<PDBx:ordinal_id>11</PDBx:ordinal_id>
<PDBx:value_order>DOUB</PDBx:value_order>
</PDBx:pdbx_chem_comp_model_bond>
<PDBx:pdbx_chem_comp_model_bond atom_id_1="OAF" atom_id_2="CAU" model_id="M_ZZV_00001">
<PDBx:ordinal_id>12</PDBx:ordinal_id>
<PDBx:value_order>SING</PDBx:value_order>
</PDBx:pdbx_chem_comp_model_bond>
<PDBx:pdbx_chem_comp_model_bond atom_id_1="OAF" atom_id_2="HOAF" model_id="M_ZZV_00001">
<PDBx:ordinal_id>13</PDBx:ordinal_id>
<PDBx:value_order>SING</PDBx:value_order>
</PDBx:pdbx_chem_comp_model_bond>
<PDBx:pdbx_chem_comp_model_bond atom_id_1="FAG" atom_id_2="CAS" model_id="M_ZZV_00001">
<PDBx:ordinal_id>14</PDBx:ordinal_id>
<PDBx:value_order>SING</PDBx:value_order>
</PDBx:pdbx_chem_comp_model_bond>
<PDBx:pdbx_chem_comp_model_bond atom_id_1="CAH" atom_id_2="CAI" model_id="M_ZZV_00001">
<PDBx:ordinal_id>15</PDBx:ordinal_id>
<PDBx:value_order>DOUB</PDBx:value_order>
</PDBx:pdbx_chem_comp_model_bond>
<PDBx:pdbx_chem_comp_model_bond atom_id_1="CAH" atom_id_2="CAN" model_id="M_ZZV_00001">
<PDBx:ordinal_id>16</PDBx:ordinal_id>
<PDBx:value_order>SING</PDBx:value_order>
</PDBx:pdbx_chem_comp_model_bond>
<PDBx:pdbx_chem_comp_model_bond atom_id_1="CAH" atom_id_2="HAH" model_id="M_ZZV_00001">
<PDBx:ordinal_id>17</PDBx:ordinal_id>
<PDBx:value_order>SING</PDBx:value_order>
</PDBx:pdbx_chem_comp_model_bond>
<PDBx:pdbx_chem_comp_model_bond atom_id_1="CAI" atom_id_2="NAQ" model_id="M_ZZV_00001">
<PDBx:ordinal_id>18</PDBx:ordinal_id>
<PDBx:value_order>SING</PDBx:value_order>
</PDBx:pdbx_chem_comp_model_bond>
<PDBx:pdbx_chem_comp_model_bond atom_id_1="CAI" atom_id_2="HAI" model_id="M_ZZV_00001">
<PDBx:ordinal_id>19</PDBx:ordinal_id>
<PDBx:value_order>SING</PDBx:value_order>
</PDBx:pdbx_chem_comp_model_bond>
</PDBx:pdbx_chem_comp_model_bondCategory>
1
1
0
1
1
1
1
pdbx_chem_comp_model_bondCategory
This property indicates that datablock
has a category holder pdbx_chem_comp_model_bondCategory.
pdbx_chem_comp_model_bondCategory
This property indicates that pdbx_chem_comp_model_bondCategory.
has a category pdbx_chem_comp_model_bond.
pdbx_chem_comp_model_bondItem
Abstract datatype property for pdbx_chem_comp_model_bond items.
reference_to_pdbx_chem_comp_model_bond
cross-reference to pdbx_chem_comp_model_bond.
referenced_by_pdbx_chem_comp_model_bond
cross-reference from pdbx_chem_comp_model_bond.
pdbx_chem_comp_model_bond.ordinal_id
The value of attribute ordinal_id in category pdbx_chem_comp_model_bond is an
ordinal identifer for each atom in the PDBX_CHEM_COMP_MODEL_BOND list.
SING
DOUB
TRIP
QUAD
AROM
POLY
DELO
PI
The value that should be taken as the target for the chemical
bond associated with the specified atoms, expressed as a bond
order.
pdbx_chem_comp_model_bond.atom_id_1
The ID of the first of the two atoms that define the bond.
This data item is a pointer to attribute atom_id in category pdbx_chem_comp_model_atom in the
PDBX_CHEM_COMP_MODEL_ATOM category.
pdbx_chem_comp_model_bond.atom_id_2
The ID of the second of the two atoms that define the bond.
This data item is a pointer to attribute atom_id in category pdbx_chem_comp_model_atom in the
PDBX_CHEM_COMP_MODEL_ATOM category.
pdbx_chem_comp_model_bond.model_id
This data item is a pointer to attribute id in category pdbx_chem_comp_model in the PDBX_CHEM_COMP_MODEL
category.
0
pdbx_chem_comp_model_descriptor
Data items in the CHEM_COMP_MODEL_DESCRIPTOR category provide
string descriptors for component model structures.
Example 1 -
<PDBx:pdbx_chem_comp_model_descriptorCategory>
<PDBx:pdbx_chem_comp_model_descriptor model_id="M_ZZV_00001" type="SMILES">
<PDBx:descriptor>CN(c1c2cccnc2c(c3c1CN(C3=O)Cc4ccc(cc4)F)O)S(=O)(=O)C</PDBx:descriptor>
</PDBx:pdbx_chem_comp_model_descriptor>
<PDBx:pdbx_chem_comp_model_descriptor model_id="M_ZZV_00001" type="SMILES_CANNONICAL">
<PDBx:descriptor>CN(c1c2cccnc2c(c3c1CN(C3=O)Cc4ccc(cc4)F)O)S(=O)(=O)C</PDBx:descriptor>
</PDBx:pdbx_chem_comp_model_descriptor>
</PDBx:pdbx_chem_comp_model_descriptorCategory>
1
1
1
1
pdbx_chem_comp_model_descriptorCategory
This property indicates that datablock
has a category holder pdbx_chem_comp_model_descriptorCategory.
pdbx_chem_comp_model_descriptorCategory
This property indicates that pdbx_chem_comp_model_descriptorCategory.
has a category pdbx_chem_comp_model_descriptor.
pdbx_chem_comp_model_descriptorItem
Abstract datatype property for pdbx_chem_comp_model_descriptor items.
reference_to_pdbx_chem_comp_model_descriptor
cross-reference to pdbx_chem_comp_model_descriptor.
referenced_by_pdbx_chem_comp_model_descriptor
cross-reference from pdbx_chem_comp_model_descriptor.
pdbx_chem_comp_model_descriptor.descriptor
This data item contains the descriptor value for this
component.
pdbx_chem_comp_model_descriptor.model_id
This data item is a pointer to attribute id in category pdbx_chem_comp_model in the PDBX_CHEM_COMP_MODEL
category.
SMILES_CANONICAL
SMILES
InChI
InChIKey
This data item contains the descriptor type.
0
pdbx_chem_comp_model_feature
Additional features associated with the chemical component.
Example 1 -
<PDBx:pdbx_chem_comp_model_featureCategory>
<PDBx:pdbx_chem_comp_model_feature feature_name="experiment_temperature" model_id="M_ZZV_00001">
<PDBx:feature_value>218.0</PDBx:feature_value>
</PDBx:pdbx_chem_comp_model_feature>
<PDBx:pdbx_chem_comp_model_feature feature_name="publication_doi" model_id="M_ZZV_00001">
<PDBx:feature_value>10.1016/j.bmcl.2008.01.018</PDBx:feature_value>
</PDBx:pdbx_chem_comp_model_feature>
<PDBx:pdbx_chem_comp_model_feature feature_name="r_factor" model_id="M_ZZV_00001">
<PDBx:feature_value>6.92</PDBx:feature_value>
</PDBx:pdbx_chem_comp_model_feature>
<PDBx:pdbx_chem_comp_model_feature feature_name="all_atoms_have_sites" model_id="M_ZZV_00001">
<PDBx:feature_value>Y</PDBx:feature_value>
</PDBx:pdbx_chem_comp_model_feature>
<PDBx:pdbx_chem_comp_model_feature feature_name="has_disorder" model_id="M_ZZV_00001">
<PDBx:feature_value>Y</PDBx:feature_value>
</PDBx:pdbx_chem_comp_model_feature>
</PDBx:pdbx_chem_comp_model_featureCategory>
1
1
1
1
pdbx_chem_comp_model_featureCategory
This property indicates that datablock
has a category holder pdbx_chem_comp_model_featureCategory.
pdbx_chem_comp_model_featureCategory
This property indicates that pdbx_chem_comp_model_featureCategory.
has a category pdbx_chem_comp_model_feature.
pdbx_chem_comp_model_featureItem
Abstract datatype property for pdbx_chem_comp_model_feature items.
reference_to_pdbx_chem_comp_model_feature
cross-reference to pdbx_chem_comp_model_feature.
referenced_by_pdbx_chem_comp_model_feature
cross-reference from pdbx_chem_comp_model_feature.
pdbx_chem_comp_model_feature.feature_value
The component feature value.
pdbx_chem_comp_model_feature.feature_name
The component model feature type.
experiment_temperature
publication_doi
r_factor
all_atoms_have_sites
has_disorder
pdbx_chem_comp_model_feature.model_id
The component model identifier for this feature.
M_ABC_00001
M_ATP_00001
0
pdbx_chem_comp_model_reference
Additional features associated with the chemical component.
Example 1 -
<PDBx:pdbx_chem_comp_model_referenceCategory>
<PDBx:pdbx_chem_comp_model_reference db_code="PIWVIB" db_name="CSD" model_id="M_ZZV_00001"></PDBx:pdbx_chem_comp_model_reference>
</PDBx:pdbx_chem_comp_model_referenceCategory>
1
1
1
pdbx_chem_comp_model_referenceCategory
This property indicates that datablock
has a category holder pdbx_chem_comp_model_referenceCategory.
pdbx_chem_comp_model_referenceCategory
This property indicates that pdbx_chem_comp_model_referenceCategory.
has a category pdbx_chem_comp_model_reference.
pdbx_chem_comp_model_referenceItem
Abstract datatype property for pdbx_chem_comp_model_reference items.
reference_to_pdbx_chem_comp_model_reference
cross-reference to pdbx_chem_comp_model_reference.
referenced_by_pdbx_chem_comp_model_reference
cross-reference from pdbx_chem_comp_model_reference.
pdbx_chem_comp_model_reference.db_code
The component feature value.
pdbx_chem_comp_model_reference.db_name
The component model feature type.
CSD
pdbx_chem_comp_model_reference.model_id
The component model identifier for this feature.
M_ABC_00001
M_ATP_00001
0
pdbx_chem_comp_nonstandard
Data items in the PDBX_CHEM_COMP_NONSTANDARD category describes
common nucleotide modifications and nonstandard features.
1
1
pdbx_chem_comp_nonstandardCategory
This property indicates that datablock
has a category holder pdbx_chem_comp_nonstandardCategory.
pdbx_chem_comp_nonstandardCategory
This property indicates that pdbx_chem_comp_nonstandardCategory.
has a category pdbx_chem_comp_nonstandard.
pdbx_chem_comp_nonstandardItem
Abstract datatype property for pdbx_chem_comp_nonstandard items.
reference_to_pdbx_chem_comp_nonstandard
cross-reference to pdbx_chem_comp_nonstandard.
referenced_by_pdbx_chem_comp_nonstandard
cross-reference from pdbx_chem_comp_nonstandard.
pdbx_chem_comp_nonstandard.comp_id
This data item is a pointer to attribute id in category chem_comp in the
CHEM_COMP category.
base modification
sugar modification
phosphate modification
This data item describes modification type.
0
pdbx_chem_comp_pcm
Data items in the PDBX_CHEM_COMP_PCM category provide
information about the protein modifications that are described
by the chemical component.
An example of the category for the phosphoserine (SEP) chemical component.
<PDBx:pdbx_chem_comp_pcmCategory>
<PDBx:pdbx_chem_comp_pcm pcm_id="1">
<PDBx:category>Named protein modification</PDBx:category>
<PDBx:comp_id>SEP</PDBx:comp_id>
<PDBx:comp_id_linking_atom xsi:nil="true" />
<PDBx:modified_residue_id>SER</PDBx:modified_residue_id>
<PDBx:modified_residue_id_linking_atom xsi:nil="true" />
<PDBx:polypeptide_position>Any position</PDBx:polypeptide_position>
<PDBx:position>Amino-acid side chain</PDBx:position>
<PDBx:type>Phosphorylation</PDBx:type>
<PDBx:uniprot_specific_ptm_accession>PTM-0253</PDBx:uniprot_specific_ptm_accession>
</PDBx:pdbx_chem_comp_pcm>
</PDBx:pdbx_chem_comp_pcmCategory>
An example of the category for the Alpha-L-fucopyranose (FUC) chemical component.
<PDBx:pdbx_chem_comp_pcmCategory>
<PDBx:pdbx_chem_comp_pcm pcm_id="1">
<PDBx:category>Carbohydrate</PDBx:category>
<PDBx:comp_id>FUC</PDBx:comp_id>
<PDBx:comp_id_linking_atom>C1</PDBx:comp_id_linking_atom>
<PDBx:modified_residue_id>SER</PDBx:modified_residue_id>
<PDBx:modified_residue_id_linking_atom>OG</PDBx:modified_residue_id_linking_atom>
<PDBx:polypeptide_position>Any position</PDBx:polypeptide_position>
<PDBx:position>Amino-acid side chain</PDBx:position>
<PDBx:type xsi:nil="true" />
</PDBx:pdbx_chem_comp_pcm>
<PDBx:pdbx_chem_comp_pcm pcm_id="2">
<PDBx:category>Carbohydrate</PDBx:category>
<PDBx:comp_id>FUC</PDBx:comp_id>
<PDBx:comp_id_linking_atom>C1</PDBx:comp_id_linking_atom>
<PDBx:modified_residue_id>THR</PDBx:modified_residue_id>
<PDBx:modified_residue_id_linking_atom>OG1</PDBx:modified_residue_id_linking_atom>
<PDBx:polypeptide_position>Any position</PDBx:polypeptide_position>
<PDBx:position>Amino-acid side chain</PDBx:position>
<PDBx:type xsi:nil="true" />
</PDBx:pdbx_chem_comp_pcm>
</PDBx:pdbx_chem_comp_pcmCategory>
1
1
1
1
0
1
0
1
0
1
0
1
1
1
1
1
0
1
0
1
0
1
1
pdbx_chem_comp_pcmCategory
This property indicates that datablock
has a category holder pdbx_chem_comp_pcmCategory.
pdbx_chem_comp_pcmCategory
This property indicates that pdbx_chem_comp_pcmCategory.
has a category pdbx_chem_comp_pcm.
pdbx_chem_comp_pcmItem
Abstract datatype property for pdbx_chem_comp_pcm items.
reference_to_pdbx_chem_comp_pcm
cross-reference to pdbx_chem_comp_pcm.
referenced_by_pdbx_chem_comp_pcm
cross-reference from pdbx_chem_comp_pcm.
ADP-Ribose
Biotin
Carbohydrate
Chromophore/chromophore-like
Covalent chemical modification
Crosslinker
Disulfide bridge
Flavin
Heme/heme-like
Isopeptide bond
Lipid/lipid-like
Named protein modification
Non-standard linkage
Non-standard residue
Nucleotide monophosphate
Terminal acetylation
Terminal amidation
The category of protein modification.
Named protein modification
pdbx_chem_comp_pcm.comp_id
Chemical component identifier for the CCD that contains the modification group.
SEP
pdbx_chem_comp_pcm.comp_id_linking_atom
The atom on the modification group that covalently links the
modification to the residue that is being modified. This is
only added when the protein modification is linked and so the
amino acid group and the modification group are described by
separate CCDs.
C1
pdbx_chem_comp_pcm.first_instance_model_db_code
The PDB Entry ID for the first model that contains the protein modification.
4PEP
pdbx_chem_comp_pcm.modified_residue_id
Chemical component identifier for the amino acid residue that is being modified.
SER
pdbx_chem_comp_pcm.modified_residue_id_linking_atom
The atom on the polypeptide residue group that covalently links
the modification to the residue that is being modified. This is
only added when the protein modification is linked and so the
amino acid group and the modification group are described by
separate CCDs.
OG
C-terminal
N-terminal
Any position
The position of the modification on the polypeptide.
Any position
Amino-acid side chain
Amino-acid backbone
Amino-acid side chain and backbone
The position of the modification on the amino acid.
Amino acid side chain
12-Hydroxyfarnesylation
12-Oxomyristoylation
12R-Hydroxymyristoylation
14-Hydroxy-10,13-dioxo-7-heptadecenoic acid
(3-Aminopropyl)(5'-adenosyl)phosphono amidation
2-Aminoadipylation
2-Aminoethylphosphorylation
2-Cholinephosphorylation
2-Hydroxyisobutyrylation
2-Oxo-5,5-dimethylhexanoylation
2-Oxobutanoic acid
2,3-Dicarboxypropylation
3-Oxoalanine
3-Phenyllactic acid
(3R)-3-Hydroxybutyrylation
4-Phosphopantetheine
ADP-ribosylation
ADP-riboxanation
AMPylation
Acetamidation
Acetamidomethylation
Acetylation
Allysine
Amination
Arachidoylation
Archaeol
Arsenylation
Bacillithiolation
Benzoylation
Benzylation
Beta-amino acid
Beta-hydroxybutyrylation
Beta-lysylation
Beta-mercaptoethanol
Biotinylation
Bromination
Butyrylation
Carbamoylation
Carboxyethylation
Carboxylation
Carboxymethylation
cGMPylation
Chlorination
Cholesterylation
Citrullination
Crotonylation
Cyanation
D-amino acid
Deamidation
Decanoylation
Decarboxylation
Dehydroamino acid
Dehydrocoelenterazination
Dehydrogenation
Dehydroxylation
Deoxidation
Deoxyhypusine
Diacylglycerol
Dihydroxyacetonation
Diphosphorylation
Diphthamide
Dipyrromethane methylation
D-lactate
Dopaminylation
Ethylation
Ethylsulfanylation
Farnesylation
Fluorination
Formylation
GMPylation
Geranylgeranylation
Glutarylation
Glutathionylation
Glycerophosphorylation
Glycerylphosphorylethanolamination
Heptanoylation
Hexanoylation
Histaminylation
Hydrogenation
Hydroperoxylation
Hydroxyamination
Hydroxyethylation
Hydroxylation
Hydroxymethylation
Hydroxysulfanylation
Hypusine
Iodination
Lactoylation
Laurylation
Lipoylation
L-lactate
Malonylation
Methoxylation
Methylamination
Methylation
Methylsulfanylation
Methylsulfation
Myristoylation
N-pyruvic acid 2-iminylation
N-methylcarbamoylation
Nitration
Nitrosylation
Noradrenylation
Norleucine
Norvaline
Octanoylation
Oleoylation
Ornithine
Oxidation
Palmitoleoylation
Palmitoylation
Pentadecanoylation
Pentanoylation
Phosphatidylethanolamine amidation
Phosphoenolpyruvate
Phosphorylation
Propionylation
Pyridoxal phosphate
Pyrrolidone carboxylic acid
Pyruvic acid
Retinoylation
Selanylation
Selenomethionine
Serotonylation
Stearoylation