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 v5.368:
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
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.
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
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.
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.
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.
<PD