CRYST1 |
ORIGXn |
SCALEn |
MTRIXn |
TVECT |
MODEL
ATOM |
ANISOU |
TER |
HETATM |
ENDMDL
Record: | CRYST1 |
Contains: | unit cell parameters, space group, and Z value |
Notes: |
(a = b =c = 1.0, alpha = beta = gamma = 90 degrees, space group = P 1, and Z = 1) e.g., P 21 21 2 and using the full symbol, e.g., C 1 2 1 instead of C 2. Z is the number of occurrences of the most populous chain. CRYST1 and SCALE contain the normal unit cell data. |
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: |
cell coordinates are xfrac, yfrac, zfrac, then: xfrac = S11X + S12Y + S13Z + U1 yfrac = S21X + S22Y + S23Z + U2 zfrac = S31X + S32Y + S33Z + U3 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: |
then it must be divided among multiple models. 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 296 N ALA 1 10.883 6.779 -6.464 1.00 0.00 N ATOM 297 CA ALA 1 11.451 6.531 -5.142 1.00 0.00 C ... ... ATOM 588 1HG GLU 18 -13.363 -4.163 -2.372 1.00 0.00 H ATOM 589 2HG GLU 18 -12.634 -3.023 -3.475 1.00 0.00 H TER 590 GLU 18 ENDMDL |
|
Record: | ATOM |
Contains: | the atomic coordinates for standard residues and the occupancy and temperature factor for each atom |
Notes: |
location indicator must be used. Within a residue, all atoms of a given conformation are assigned the same alternate position indicator. 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. 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: |
(Angstroms**2) and are presented as integers. atomic coordinate records. |
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 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. 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. atoms be labeled O and OXT. 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: |
ATOM section of this document. 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: |
is presented in the entry, or if there are more than 99,999 atoms. |
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 |