Record: | CRYST1 |
| Contains: | unit cell parameters, space group, and Z value |
| Notes: |
If the structure was not determined by crystallographic means,
simply defines a unit cube
(a = b =c = 1.0, alpha = beta = gamma = 90
degrees, space group = P 1, and Z = 1)
The Hermann-Mauguin space group symbol is given without parenthesis,
e.g., P
21 21 2 and using the full symbol, e.g., C 1 2 1 instead of C 2.
The screw axis is described as a two digit number.
For a rhombohedral space group in the hexagonal setting, the lattice type symbol used is H.
The Z value is the number of polymeric chains in a unit cell. In the case of
heteropolymers,
Z is the number of occurrences of the most populous chain.
In the case of a polycrystalline fiber diffraction study,
CRYST1 and SCALE contain the normal unit cell data.
The unit cell parameters are used to calculate SCALE.
|
COLUMNS DATA TYPE CONTENTS
--------------------------------------------------------------------------------
1 - 6 Record name "CRYST1"
7 - 15 Real(9.3) a (Angstroms)
16 - 24 Real(9.3) b (Angstroms)
25 - 33 Real(9.3) c (Angstroms)
34 - 40 Real(7.2) alpha (degrees)
41 - 47 Real(7.2) beta (degrees)
48 - 54 Real(7.2) gamma (degrees)
56 - 66 LString Space group
67 - 70 Integer Z value
Example:
1 2 3 4 5 6 7
1234567890123456789012345678901234567890123456789012345678901234567890
CRYST1 117.000 15.000 39.000 90.00 90.00 90.00 P 21 21 21 8
|
Record: | ORIGXn |
| Contains: | the transformation from the orthogonal coordinates contained
in the database entry to the submitted coordinates |
| Notes: |
If the original submitted coordinates are Xsub, Ysub, Zsub and the orthogonal Angstroms coordinates
contained in the data entry are X, Y, Z, then:
Xsub = O11X + O12Y + O13Z + T1
Ysub = O21X + O22Y + O23Z + T2
Zsub = O31X + O32Y + O33Z + T3
|
COLUMNS DATA TYPE CONTENTS
--------------------------------------------------------------------------------
1 - 6 Record name "ORIGXn" (n=1, 2, or 3)
11 - 20 Real(10.6) o[n][1]
21 - 30 Real(10.6) o[n][2]
31 - 40 Real(10.6) o[n][3]
46 - 55 Real(10.5) t[n]
Example:
1 2 3 4 5 6 7
1234567890123456789012345678901234567890123456789012345678901234567890
ORIGX1 0.963457 0.136613 0.230424 16.61000
ORIGX2 -0.158977 0.983924 0.081383 13.72000
ORIGX3 -0.215598 -0.115048 0.969683 37.65000
|
Record: | SCALEn |
| Contains: |
the transformation from the orthogonal coordinates contained in the entry to fractional
crystallographic
coordinates |
| Notes: |
If the orthogonal Angstroms coordinates are X, Y, Z, and the fractional
cell coordinates are xfrac, yfrac, zfrac, then:
xfrac = S11X + S12Y + S13Z + U1
yfrac = S21X + S22Y + S23Z + U2
zfrac = S31X + S32Y + S33Z + U3
For NMR and fiber diffraction submissions, SCALE is given as an identity
matrix with no translation.
|
COLUMNS DATA TYPE CONTENTS
--------------------------------------------------------------------------------
1 - 6 Record name "SCALEn" (n=1, 2, or 3)
11 - 20 Real(10.6) s[n][1]
21 - 30 Real(10.6) s[n][2]
31 - 40 Real(10.6) s[n][3]
46 - 55 Real(10.5) u[n]
Example:
1 2 3 4 5 6 7
1234567890123456789012345678901234567890123456789012345678901234567890
SCALE1 0.019231 0.000000 0.000000 0.00000
SCALE2 0.000000 0.017065 0.000000 0.00000
SCALE3 0.000000 0.000000 0.016155 0.00000
|
Record: | MTRIXn |
| Contains: | the transformations expressing non-crystallographic symmetry |
| Notes: |
The MTRIX transformations operate on the coordinates in the entry to yield
equivalent representations of the molecule in the same coordinate frame. One
trio of MTRIX records with a constant serial number is given for each
non-crystallographic symmetry operation defined.
|
COLUMNS DATA TYPE CONTENTS
--------------------------------------------------------------------------------
1 - 6 Record name "MTRIXn" (n=1, 2, or 3)
8 - 10 Integer Serial number
11 - 20 Real(10.6) m[n][1]
21 - 30 Real(10.6) m[n][2]
31 - 40 Real(10.6) m[n][3]
46 - 55 Real(10.5) v[n]
60 Integer 1 if coordinates for the related molecule are present;
otherwise, blank.
Example:
1 2 3 4 5 6 7
1234567890123456789012345678901234567890123456789012345678901234567890
MTRIX1 1 -1.000000 0.000000 -0.000000 0.00001 1
MTRIX2 1 -0.000000 1.000000 0.000000 0.00002 1
MTRIX3 1 0.000000 -0.000000 -1.000000 0.00002 1
|
Record: | TVECT |
| Contains: | the translation vector which have infinite covalent connections |
| Notes: |
For structures not comprised of discrete molecules (e.g., infinite
polysaccharide chains), the entry contains a fragment which can be built into
the full structure by the simple translation vectors of TVECT records.
|
COLUMNS DATA TYPE CONTENTS
--------------------------------------------------------------------------------
1 - 6 Record name "TVECT "
8 - 10 Integer Serial number
11 - 20 Real(10.5) t[1]
21 - 30 Real(10.5) t[2]
31 - 40 Real(10.5) t[3]
41 - 70 String Text comment
Example:
1 2 3 4 5 6 7
1234567890123456789012345678901234567890123456789012345678901234567890
TVECT 1 0.00000 0.00000 28.30000
|
Record: | MODEL |
| Contains: | the model serial number when a single coordinate entry contains
multiple structures |
| Notes: |
Models are numbered sequentially beginning with 1.
If an entry contains more than 99,999 total atoms,
then it must be divided among multiple models.
Each MODEL must have a corresponding ENDMDL record.
In the case of an NMR entry the EXPDTA record states the number of model structures
that are present in the individual entry.
|
COLUMNS DATA TYPE CONTENTS
----------------------------------------------------------------------
1 - 6 Record name "MODEL "
11 - 14 Integer Model serial number
Example:
1 2 3 4 5 6 7 8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
MODEL 1
ATOM 1 N ALA 1 11.104 6.134 -6.504 1.00 0.00 N
ATOM 2 CA ALA 1 11.639 6.071 -5.147 1.00 0.00 C
...
...
ATOM 293 1HG GLU 18 -14.861 -4.847 0.361 1.00 0.00 H
ATOM 294 2HG GLU 18 -13.518 -3.769 0.084 1.00 0.00 H
TER 295 GLU 18
ENDMDL
MODEL 2
ATOM 1 N ALA 1 11.304 6.234 -6.104 1.00 0.00 N
ATOM 2 CA ALA 1 11.239 6.371 -5.247 1.00 0.00 C
...
...
ATOM 293 1HG GLU 18 -14.752 -4.948 0.461 1.00 0.00 H
ATOM 294 2HG GLU 18 -13.630 -3.769 0.160 1.00 0.00 H
TER 295 GLU 18
ENDMDL
|
Record: | ATOM |
| Contains: | the atomic coordinates for standard residues and the occupancy and temperature factor for each atom |
| Notes: |
ATOM records for proteins are listed from amino to carboxyl terminus.
Nucleic acid residues are listed from the 5' to the 3' terminus.
No ordering is specified for polysaccharides.
The list of ATOM records in a chain is terminated by a TER record.
If an atom is provided in more than one position, then a non-blank alternate
location indicator must be used. Within a residue, all atoms of a given
conformation are assigned the same alternate position indicator.
Additional atoms (modifying group) to side chains of standard residues are represented as a HET group
which is assigned its own residue name. The chainID, sequence
number, and insertion code assigned to the HET group is that of the
standard residue to which it is attached.
In some entries, the occupancy and temperature factor fields may be used for other quantities.
The segment identifier is a string of up to four (4) alphanumeric characters, left-justified, and may
include a space, e.g., CH86, A 1, NASE.
|
COLUMNS DATA TYPE CONTENTS
--------------------------------------------------------------------------------
1 - 6 Record name "ATOM "
7 - 11 Integer Atom serial number.
13 - 16 Atom Atom name.
17 Character Alternate location indicator.
18 - 20 Residue name Residue name.
22 Character Chain identifier.
23 - 26 Integer Residue sequence number.
27 AChar Code for insertion of residues.
31 - 38 Real(8.3) Orthogonal coordinates for X in Angstroms.
39 - 46 Real(8.3) Orthogonal coordinates for Y in Angstroms.
47 - 54 Real(8.3) Orthogonal coordinates for Z in Angstroms.
55 - 60 Real(6.2) Occupancy.
61 - 66 Real(6.2) Temperature factor (Default = 0.0).
73 - 76 LString(4) Segment identifier, left-justified.
77 - 78 LString(2) Element symbol, right-justified.
79 - 80 LString(2) Charge on the atom.
Example:
1 2 3 4 5 6 7 8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
ATOM 145 N VAL A 25 32.433 16.336 57.540 1.00 11.92 A1 N
ATOM 146 CA VAL A 25 31.132 16.439 58.160 1.00 11.85 A1 C
ATOM 147 C VAL A 25 30.447 15.105 58.363 1.00 12.34 A1 C
ATOM 148 O VAL A 25 29.520 15.059 59.174 1.00 15.65 A1 O
ATOM 149 CB AVAL A 25 30.385 17.437 57.230 0.28 13.88 A1 C
ATOM 150 CB BVAL A 25 30.166 17.399 57.373 0.72 15.41 A1 C
ATOM 151 CG1AVAL A 25 28.870 17.401 57.336 0.28 12.64 A1 C
ATOM 152 CG1BVAL A 25 30.805 18.788 57.449 0.72 15.11 A1 C
ATOM 153 CG2AVAL A 25 30.835 18.826 57.661 0.28 13.58 A1 C
ATOM 154 CG2BVAL A 25 29.909 16.996 55.922 0.72 13.25 A1 C
|
Record: | ANISOU |
| Contains: | the anisotropic temperature factors |
| Notes: |
Columns 7 - 27 and 73 - 80 are identical to the corresponding ATOM/HETATM record.
The anisotropic temperature factors (columns 29 - 70) are scaled by a factor of 10**4
(Angstroms**2) and are presented as integers.
The anisotropic temperature factors are stored in the same coordinate frame as the
atomic coordinate records.
ANISOU values are listed only if they have been provided by the depositor.
|
COLUMNS DATA TYPE CONTENTS
----------------------------------------------------------------------
1 - 6 Record name "ANISOU"
7 - 11 Integer Atom serial number
13 - 16 Atom Atom name
17 Character Alternate location indicator
18 - 20 Residue name Residue name
22 Character Chain identifier
23 - 26 Integer Residue sequence number
27 AChar Insertion code
29 - 35 Integer u[1][1]
36 - 42 Integer u[2][2]
43 - 49 Integer u[3][3]
50 - 56 Integer u[1][2]
57 - 63 Integer u[1][3]
64 - 70 Integer u[2][3]
73 - 76 LString(4) Segment identifier, left-justified
77 - 78 LString(2) Element symbol, right-justified
79 - 80 LString(2) Charge on the atom
Example:
1 2 3 4 5 6 7 8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
ATOM 107 N GLY 13 12.681 37.302 -25.211 1.000 15.56 N
ANISOU 107 N GLY 13 2406 1892 1614 198 519 -328 N
ATOM 108 CA GLY 13 11.982 37.996 -26.241 1.000 16.92 C
ANISOU 108 CA GLY 13 2748 2004 1679 -21 155 -419 C
ATOM 109 C GLY 13 11.678 39.447 -26.008 1.000 15.73 C
ANISOU 109 C GLY 13 2555 1955 1468 87 357 -109 C
ATOM 110 O GLY 13 11.444 40.201 -26.971 1.000 20.93 O
ANISOU 110 O GLY 13 3837 2505 1611 164 -121 189 O
ATOM 111 N ASN 14 11.608 39.863 -24.755 1.000 13.68 N
ANISOU 111 N ASN 14 2059 1674 1462 27 244 -96 N
|
Record: | TER |
| Contains: | indicates the end of a list of ATOM/HETATM records for a chain |
| Notes: |
The TER records occur in the coordinate section of the entry, and indicate
the last residue presented for each polypeptide and/or nucleic acid chain for
which there are coordinates. For proteins, the residue defined on the TER
record is the carboxy-terminal residue; for nucleic acids it is the
3'-terminal residue.
For a cyclic molecule, the choice of termini is arbitrary.
Terminal oxygen atoms are presented as OXT for proteins, and as O5T or O3T for nucleic acids.
The TER record has the same residue name, chain identifier, sequence number
and insertion code as the terminal residue. The serial number of the TER
record is one number greater than the serial number of the ATOM/HETATM
preceding the TER.
For chains with gaps due to disorder, it is recommended that the C-terminus
atoms be labeled O and OXT.
The residue name appearing on the TER record must be the same as the residue name
of the immediately preceding ATOM or non-water HETATM record.
|
COLUMNS DATA TYPE CONTENTS
--------------------------------------------------------------------------------
1 - 6 Record name "TER "
7 - 11 Integer Serial number
18 - 20 Residue name Residue name
22 Character Chain identifier
23 - 26 Integer Residue sequence number
27 AChar Insertion code
Example:
1 2 3 4 5 6 7 8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
ATOM 4150 H ALA A 431 8.674 16.036 12.858 1.00 0.00 H
TER 4151 ALA A 431
ATOM 1403 O PRO P 22 12.701 33.564 15.827 1.09 18.03 O
ATOM 1404 CB PRO P 22 13.512 32.617 18.642 1.09 9.32 C
ATOM 1405 CG PRO P 22 12.828 33.382 19.740 1.09 12.23 C
ATOM 1406 CD PRO P 22 12.324 34.603 18.985 1.09 11.47 C
HETATM 1407 CA BLE P 1 14.625 32.240 14.151 1.09 16.76 C
HETATM 1408 CB BLE P 1 15.610 33.091 13.297 1.09 16.56 C
HETATM 1409 CG BLE P 1 15.558 34.629 13.373 1.09 14.27 C
HETATM 1410 CD1 BLE P 1 16.601 35.208 12.440 1.09 14.75 C
HETATM 1411 CD2 BLE P 1 14.209 35.160 12.930 1.09 15.60 C
HETATM 1412 N BLE P 1 14.777 32.703 15.531 1.09 14.79 N
HETATM 1413 B BLE P 1 14.921 30.655 14.194 1.09 15.56 B
HETATM 1414 O1 BLE P 1 14.852 30.178 12.832 1.09 16.10 O
HETATM 1415 O2 BLE P 1 13.775 30.147 14.862 1.09 20.95 O
TER 1416 BLE P 1
|
Record: | HETATM |
| Contains: | the atomic coordinate records for atoms within "non-standard"
groups. These records are used for water molecules and atoms presented in HET
groups. |
| Notes: |
Insertion codes, segment id, and element naming are fully described in the
ATOM section of this document.
Disordered solvents may be represented by the residue name DIS.
No ordering is specified for polysaccharides.
HETATM records must have corresponding HET, HETNAM, FORMUL
and CONECT records, except for waters.
|
COLUMNS DATA TYPE CONTENTS
--------------------------------------------------------------------------------
1 - 6 Record name "HETATM"
7 - 11 Integer Atom serial number.
13 - 16 Atom Atom name
17 Character Alternate location indicator
18 - 20 Residue name Residue name
22 Character Chain identifier
23 - 26 Integer Residue sequence number
27 AChar Code for insertion of residues
31 - 38 Real(8.3) Orthogonal coordinates for X
39 - 46 Real(8.3) Orthogonal coordinates for Y
47 - 54 Real(8.3) Orthogonal coordinates for Z
55 - 60 Real(6.2) Occupancy
61 - 66 Real(6.2) Temperature factor
73 - 76 LString(4) Segment identifier, left-justified
77 - 78 LString(2) Element symbol, right-justified
79 - 80 LString(2) Charge on the atom
Example:
1 2 3 4 5 6 7 8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
HETATM 1357 MG MG 168 4.669 34.118 19.123 1.00 3.16 MG2+
HETATM 3835 FE HEM 1 17.140 3.115 15.066 1.00 14.14 FE3+
|
Record: | ENDMDL |
| Contains: | these records are paired with MODEL records to group individual structures found in a coordinate entry |
| Notes: |
MODEL/ENDMDL records are used only when more than one structure
is presented in the entry, or if there are more than 99,999 atoms.
Every MODEL record has an associated ENDMDL record.
|
COLUMNS DATA TYPE CONTENTS
------------------------------------------------------------------
1 - 6 Record name "ENDMDL"
Example:
1 2 3 4 5 6 7 8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
...
...
ATOM 14550 1HG GLU 122 -14.364 14.787 -14.258 1.00 0.00 H
ATOM 14551 2HG GLU 122 -13.794 13.738 -12.961 1.00 0.00 H
TER 14552 GLU 122
ENDMDL
MODEL 9
ATOM 14553 N SER 1 -28.280 1.567 12.004 1.00 0.00 N
ATOM 14554 CA SER 1 -27.749 0.392 11.256 1.00 0.00 C
...
...
ATOM 16369 1HG GLU 122 -3.757 18.546 -8.439 1.00 0.00 H
ATOM 16370 2HG GLU 122 -3.066 17.166 -7.584 1.00 0.00 H
TER 16371 GLU 122
ENDMDL
MODEL 10
ATOM 16372 N SER 1 -22.285 7.041 10.003 1.00 0.00 N
ATOM 16373 CA SER 1 -23.026 6.872 8.720 1.00 0.00 C
...
...
ATOM 18188 1HG GLU 122 -1.467 18.282 -17.144 1.00 0.00 H
ATOM 18189 2HG GLU 122 -2.711 18.067 -15.913 1.00 0.00 H
TER 18190 GLU 122
ENDMDL
|