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PDBsum entry 1dyw

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Isomerase(peptidyl-prolyl cis-trans) PDB id
1dyw
Jmol
Contents
Protein chain
172 a.a. *
Waters ×252
* Residue conservation analysis
HEADER    ISOMERASE(PEPTIDYL-PROLYL CIS-TRANS)    10-FEB-00   1DYW
TITLE     BIOCHEMICAL AND STRUCTURAL CHARACTERIZATION OF A DIVERGENT
TITLE    2 LOOP CYCLOPHILIN FROM CAENORHABDITIS ELEGANS
COMPND    MOL_ID: 1;
COMPND   2 MOLECULE: CYCLOPHILIN 3;
COMPND   3 CHAIN: A;
COMPND   4 SYNONYM: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE 3, PPIASE,
COMPND   5  ROTAMASE;
COMPND   6 EC: 5.2.1.8;
COMPND   7 ENGINEERED: YES
SOURCE    MOL_ID: 1;
SOURCE   2 ORGANISM_SCIENTIFIC: CAENORHABDITIS ELEGANS;
SOURCE   3 ORGANISM_TAXID: 6239;
SOURCE   4 PLASMID: PET-5A;
SOURCE   5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE   6 EXPRESSION_SYSTEM_TAXID: 562
KEYWDS    ISOMERASE(PEPTIDYL-PROLYL CIS-TRANS), ISOMERASE, ROTAMASE
EXPDTA    X-RAY DIFFRACTION
AUTHOR    J.DORNAN,A.P.PAGE,P.TAYLOR,S.Y.WU,A.D.WINTER,H.HUSI,
AUTHOR   2 M.D.WALKINSHAW
REVDAT   2   24-FEB-09 1DYW    1       VERSN
REVDAT   1   22-JUN-00 1DYW    0
JRNL        AUTH   J.DORNAN,A.P.PAGE,P.TAYLOR,S.Y.WU,A.D.WINTER,
JRNL        AUTH 2 H.HUSI,M.D.WALKINSHAW
JRNL        TITL   BIOCHEMICAL AND STRUCTURAL CHARACTERIZATION OF A
JRNL        TITL 2 DIVERGENT LOOP CYCLOPHILIN FROM CAENORHABDITIS
JRNL        TITL 3 ELEGANS
JRNL        REF    J.BIOL.CHEM.                  V. 274 34877 1999
JRNL        REFN                   ISSN 0021-9258
JRNL        PMID   10574961
JRNL        DOI    10.1074/JBC.274.49.34877
REMARK   1
REMARK   1 REFERENCE 1
REMARK   1  AUTH   V.MIKOL,J.KALLEN,G.PFLUEGL,M.D.WALKINSHAW
REMARK   1  TITL   X-RAY STRUCTURE OF A MONOMERIC CYCLOPHILIN
REMARK   1  REF    J.MOL.BIOL.                   V. 234  1119 1993
REMARK   1  REFN                   ISSN 0022-2836
REMARK   1  PMID   8263916
REMARK   1  DOI    10.1006/JMBI.1993.1664
REMARK   2
REMARK   2 RESOLUTION.    1.8  ANGSTROMS.
REMARK   3
REMARK   3 REFINEMENT.
REMARK   3   PROGRAM     : SHELXL-97
REMARK   3   AUTHORS     : G.M.SHELDRICK
REMARK   3
REMARK   3  DATA USED IN REFINEMENT.
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 15.00
REMARK   3   DATA CUTOFF            (SIGMA(F)) : 0.0
REMARK   3   COMPLETENESS FOR RANGE        (%) : 97.0
REMARK   3   CROSS-VALIDATION METHOD           : FREE R
REMARK   3   FREE R VALUE TEST SET SELECTION   : RANDOM
REMARK   3
REMARK   3  FIT TO DATA USED IN REFINEMENT (NO CUTOFF).
REMARK   3   R VALUE   (WORKING + TEST SET, NO CUTOFF) : NULL
REMARK   3   R VALUE          (WORKING SET, NO CUTOFF) : 0.2152
REMARK   3   FREE R VALUE                  (NO CUTOFF) : 0.2861
REMARK   3   FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5
REMARK   3   FREE R VALUE TEST SET COUNT   (NO CUTOFF) : 1064
REMARK   3   TOTAL NUMBER OF REFLECTIONS   (NO CUTOFF) : 20135
REMARK   3
REMARK   3  FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F).
REMARK   3   R VALUE   (WORKING + TEST SET, F>4SIG(F)) : NULL
REMARK   3   R VALUE          (WORKING SET, F>4SIG(F)) : 0.2035
REMARK   3   FREE R VALUE                  (F>4SIG(F)) : 0.2678
REMARK   3   FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5
REMARK   3   FREE R VALUE TEST SET COUNT   (F>4SIG(F)) : 934
REMARK   3   TOTAL NUMBER OF REFLECTIONS   (F>4SIG(F)) : 17786
REMARK   3
REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK   3   PROTEIN ATOMS      : 1297
REMARK   3   NUCLEIC ACID ATOMS : 0
REMARK   3   HETEROGEN ATOMS    : 0
REMARK   3   SOLVENT ATOMS      : 252
REMARK   3
REMARK   3  MODEL REFINEMENT.
REMARK   3   OCCUPANCY SUM OF NON-HYDROGEN ATOMS      : 1561.00
REMARK   3   OCCUPANCY SUM OF HYDROGEN ATOMS          : 0.00
REMARK   3   NUMBER OF DISCRETELY DISORDERED RESIDUES : 0
REMARK   3   NUMBER OF LEAST-SQUARES PARAMETERS       : 6247
REMARK   3   NUMBER OF RESTRAINTS                     : 5295
REMARK   3
REMARK   3  RMS DEVIATIONS FROM RESTRAINT TARGET VALUES.
REMARK   3   BOND LENGTHS                         (A) : 0.007
REMARK   3   ANGLE DISTANCES                      (A) : 0.024
REMARK   3   SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000
REMARK   3   DISTANCES FROM RESTRAINT PLANES      (A) : NULL
REMARK   3   ZERO CHIRAL VOLUMES               (A**3) : 0.039
REMARK   3   NON-ZERO CHIRAL VOLUMES           (A**3) : 0.040
REMARK   3   ANTI-BUMPING DISTANCE RESTRAINTS     (A) : 0.019
REMARK   3   RIGID-BOND ADP COMPONENTS         (A**2) : NULL
REMARK   3   SIMILAR ADP COMPONENTS            (A**2) : NULL
REMARK   3   APPROXIMATELY ISOTROPIC ADPS      (A**2) : NULL
REMARK   3
REMARK   3  BULK SOLVENT MODELING.
REMARK   3   METHOD USED: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-2
REMARK   3
REMARK   3  STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER
REMARK   3   SPECIAL CASE: NULL
REMARK   3
REMARK   3  OTHER REFINEMENT REMARKS: THE C-TERMINAL RESIDUE WAS NOT SEEN
REMARK   3  IN THE DENSITY MAPS
REMARK   4
REMARK   4 1DYW COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 10-FEB-00.
REMARK 100 THE PDBE ID CODE IS EBI-4343.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION
REMARK 200  DATE OF DATA COLLECTION        : NULL
REMARK 200  TEMPERATURE           (KELVIN) : 100.0
REMARK 200  PH                             : 5.60
REMARK 200  NUMBER OF CRYSTALS USED        : 1
REMARK 200
REMARK 200  SYNCHROTRON              (Y/N) : N
REMARK 200  RADIATION SOURCE               : ROTATING ANODE
REMARK 200  BEAMLINE                       : NULL
REMARK 200  X-RAY GENERATOR MODEL          : BRUKER NONIUS FR571
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M
REMARK 200  WAVELENGTH OR RANGE        (A) : 1.5418
REMARK 200  MONOCHROMATOR                  : GRAPHITE(002)
REMARK 200  OPTICS                         : COLLIMATOR
REMARK 200
REMARK 200  DETECTOR TYPE                  : IMAGE PLATE
REMARK 200  DETECTOR MANUFACTURER          : MARRESEARCH
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : DENZO
REMARK 200  DATA SCALING SOFTWARE          : SCALEPACK
REMARK 200
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 21337
REMARK 200  RESOLUTION RANGE HIGH      (A) : 1.800
REMARK 200  RESOLUTION RANGE LOW       (A) : 15.000
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200  COMPLETENESS FOR RANGE     (%) : 97.0
REMARK 200  DATA REDUNDANCY                : 6.590
REMARK 200  R MERGE                    (I) : NULL
REMARK 200  R SYM                      (I) : 0.08300
REMARK 200   FOR THE DATA SET  : 11.7500
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 1.83
REMARK 200  COMPLETENESS FOR SHELL     (%) : 96.2
REMARK 200  DATA REDUNDANCY IN SHELL       : NULL
REMARK 200  R MERGE FOR SHELL          (I) : NULL
REMARK 200  R SYM FOR SHELL            (I) : 0.27800
REMARK 200   FOR SHELL         : 2.587
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: AMORE
REMARK 200 STARTING MODEL: 1CWA
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS  (%): 59.32
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.05
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS:
REMARK 280 MPEG5000, SODIUM CITRATE, PH 5.6
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2
REMARK 290
REMARK 290      SYMOP   SYMMETRY
REMARK 290     NNNMMM   OPERATOR
REMARK 290       1555   X,Y,Z
REMARK 290       2555   -X,-Y,Z+1/2
REMARK 290       3555   -Y+1/2,X+1/2,Z+1/4
REMARK 290       4555   Y+1/2,-X+1/2,Z+3/4
REMARK 290       5555   -X+1/2,Y+1/2,-Z+1/4
REMARK 290       6555   X+1/2,-Y+1/2,-Z+3/4
REMARK 290       7555   Y,X,-Z
REMARK 290       8555   -Y,-X,-Z+1/2
REMARK 290
REMARK 290     WHERE NNN -> OPERATOR NUMBER
REMARK 290           MMM -> TRANSLATION VECTOR
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY
REMARK 290 RELATED MOLECULES.
REMARK 290   SMTRY1   1  1.000000  0.000000  0.000000        0.00000
REMARK 290   SMTRY2   1  0.000000  1.000000  0.000000        0.00000
REMARK 290   SMTRY3   1  0.000000  0.000000  1.000000        0.00000
REMARK 290   SMTRY1   2 -1.000000  0.000000  0.000000        0.00000
REMARK 290   SMTRY2   2  0.000000 -1.000000  0.000000        0.00000
REMARK 290   SMTRY3   2  0.000000  0.000000  1.000000       61.56200
REMARK 290   SMTRY1   3  0.000000 -1.000000  0.000000       30.30400
REMARK 290   SMTRY2   3  1.000000  0.000000  0.000000       30.30400
REMARK 290   SMTRY3   3  0.000000  0.000000  1.000000       30.78100
REMARK 290   SMTRY1   4  0.000000  1.000000  0.000000       30.30400
REMARK 290   SMTRY2   4 -1.000000  0.000000  0.000000       30.30400
REMARK 290   SMTRY3   4  0.000000  0.000000  1.000000       92.34300
REMARK 290   SMTRY1   5 -1.000000  0.000000  0.000000       30.30400
REMARK 290   SMTRY2   5  0.000000  1.000000  0.000000       30.30400
REMARK 290   SMTRY3   5  0.000000  0.000000 -1.000000       30.78100
REMARK 290   SMTRY1   6  1.000000  0.000000  0.000000       30.30400
REMARK 290   SMTRY2   6  0.000000 -1.000000  0.000000       30.30400
REMARK 290   SMTRY3   6  0.000000  0.000000 -1.000000       92.34300
REMARK 290   SMTRY1   7  0.000000  1.000000  0.000000        0.00000
REMARK 290   SMTRY2   7  1.000000  0.000000  0.000000        0.00000
REMARK 290   SMTRY3   7  0.000000  0.000000 -1.000000        0.00000
REMARK 290   SMTRY1   8  0.000000 -1.000000  0.000000        0.00000
REMARK 290   SMTRY2   8 -1.000000  0.000000  0.000000        0.00000
REMARK 290   SMTRY3   8  0.000000  0.000000 -1.000000       61.56200
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN
REMARK 300 THIS ENTRY.  THE REMARK MAY ALSO PROVIDE INFORMATION ON
REMARK 300 BURIED SURFACE AREA.
REMARK 300
REMARK 300 DETAILS:BIOLOGICAL_UNIT: MONOMER
REMARK 350
REMARK 350 GENERATING THE BIOMOLECULE
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW.  BOTH NON-CRYSTALLOGRAPHIC AND
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
REMARK 350
REMARK 350 BIOMOLECULE:  1
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PQS
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
REMARK 350   BIOMT1   1  1.000000  0.000000  0.000000        0.00000
REMARK 350   BIOMT2   1  0.000000  1.000000  0.000000        0.00000
REMARK 350   BIOMT3   1  0.000000  0.000000  1.000000        0.00000
REMARK 465
REMARK 465 MISSING RESIDUES
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE
REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
REMARK 465
REMARK 465   M RES C SSSEQI
REMARK 465     ALA A   173
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: TORSION ANGLES
REMARK 500
REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS:
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2)
REMARK 500
REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI-
REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400
REMARK 500
REMARK 500  M RES CSSEQI        PSI       PHI
REMARK 500    PHE A  67      -81.28   -142.02
REMARK 500    GLU A  88      -60.06    165.36
REMARK 500    THR A 126       54.03   -115.65
REMARK 500    LEU A 171      -62.10   -106.32
REMARK 500
REMARK 500 REMARK: NULL
REMARK 525
REMARK 525 SOLVENT
REMARK 525
REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT
REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST
REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT
REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE
REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER;
REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE
REMARK 525 NUMBER; I=INSERTION CODE):
DBREF  1DYW A    1   173  UNP    P52011   CYP3_CAEEL       1    173
SEQRES   1 A  173  MET SER ARG SER LYS VAL PHE PHE ASP ILE THR ILE GLY
SEQRES   2 A  173  GLY LYS ALA SER GLY ARG ILE VAL MET GLU LEU TYR ASP
SEQRES   3 A  173  ASP VAL VAL PRO LYS THR ALA GLY ASN PHE ARG ALA LEU
SEQRES   4 A  173  CYS THR GLY GLU ASN GLY ILE GLY LYS SER GLY LYS PRO
SEQRES   5 A  173  LEU HIS PHE LYS GLY SER LYS PHE HIS ARG ILE ILE PRO
SEQRES   6 A  173  ASN PHE MET ILE GLN GLY GLY ASP PHE THR ARG GLY ASN
SEQRES   7 A  173  GLY THR GLY GLY GLU SER ILE TYR GLY GLU LYS PHE PRO
SEQRES   8 A  173  ASP GLU ASN PHE LYS GLU LYS HIS THR GLY PRO GLY VAL
SEQRES   9 A  173  LEU SER MET ALA ASN ALA GLY PRO ASN THR ASN GLY SER
SEQRES  10 A  173  GLN PHE PHE LEU CYS THR VAL LYS THR GLU TRP LEU ASP
SEQRES  11 A  173  GLY LYS HIS VAL VAL PHE GLY ARG VAL VAL GLU GLY LEU
SEQRES  12 A  173  ASP VAL VAL LYS ALA VAL GLU SER ASN GLY SER GLN SER
SEQRES  13 A  173  GLY LYS PRO VAL LYS ASP CYS MET ILE ALA ASP CYS GLY
SEQRES  14 A  173  GLN LEU LYS ALA
FORMUL   2  HOH   *252(H2 O1)
HELIX    1   1 VAL A   29  GLY A   42  1                                  14
HELIX    2   2 THR A  126  ASP A  130  5                                   5
HELIX    3   3 GLY A  142  SER A  151  1                                  10
SHEET    1   A 8 ARG A  62  ILE A  64  0
SHEET    2   A 8 MET A  68  GLY A  71 -1  O  MET A  68   N  ILE A  64
SHEET    3   A 8 PHE A 119  CYS A 122 -1  O  PHE A 119   N  GLY A  71
SHEET    4   A 8 VAL A 104  MET A 107 -1  O  VAL A 104   N  CYS A 122
SHEET    5   A 8 VAL A 135  GLU A 141 -1  N  PHE A 136   O  LEU A 105
SHEET    6   A 8 LYS A  15  LEU A  24 -1  O  VAL A  21   N  VAL A 140
SHEET    7   A 8 LYS A   5  ILE A  12 -1  O  VAL A   6   N  MET A  22
SHEET    8   A 8 CYS A 163  LYS A 172
CRYST1   60.608   60.608  123.124  90.00  90.00  90.00 P 41 21 2     8
ORIGX1      1.000000  0.000000  0.000000        0.00000
ORIGX2      0.000000  1.000000  0.000000        0.00000
ORIGX3      0.000000  0.000000  1.000000        0.00000
SCALE1      0.016499  0.000000  0.000000        0.00000
SCALE2      0.000000  0.016499  0.000000        0.00000
SCALE3      0.000000  0.000000  0.008122        0.00000
      
PROCHECK
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 References