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PDBsum entry 2cpl

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Isomerase(peptidyl-prolyl cis-trans) PDB id
2cpl
Jmol
Contents
Protein chain
164 a.a.
Waters ×119
HEADER    ISOMERASE(PEPTIDYL-PROLYL CIS-TRANS)    30-JUN-92   2CPL
TITLE     SIMILARITIES AND DIFFERENCES BETWEEN HUMAN CYCLOPHILIN A
TITLE    2 AND OTHER BETA-BARREL STRUCTURES. STRUCTURAL REFINEMENT AT
TITLE    3 1.63 ANGSTROMS RESOLUTION
COMPND    MOL_ID: 1;
COMPND   2 MOLECULE: CYCLOPHILIN A;
COMPND   3 CHAIN: A;
COMPND   4 ENGINEERED: YES
SOURCE    MOL_ID: 1;
SOURCE   2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE   3 ORGANISM_COMMON: HUMAN;
SOURCE   4 ORGANISM_TAXID: 9606;
SOURCE   5 GENE: CYCLOPHILIN;
SOURCE   6 EXPRESSION_SYSTEM_GENE: CYCLOPHILIN
KEYWDS    ISOMERASE(PEPTIDYL-PROLYL CIS-TRANS)
EXPDTA    X-RAY DIFFRACTION
AUTHOR    H.KE
REVDAT   3   24-FEB-09 2CPL    1       VERSN
REVDAT   2   01-APR-03 2CPL    1       JRNL
REVDAT   1   31-OCT-93 2CPL    0
JRNL        AUTH   H.KE
JRNL        TITL   SIMILARITIES AND DIFFERENCES BETWEEN HUMAN
JRNL        TITL 2 CYCLOPHILIN A AND OTHER BETA-BARREL STRUCTURES.
JRNL        TITL 3 STRUCTURAL REFINEMENT AT 1.63 A RESOLUTION.
JRNL        REF    J.MOL.BIOL.                   V. 228   539 1992
JRNL        REFN                   ISSN 0022-2836
JRNL        PMID   1453463
JRNL        DOI    10.1016/0022-2836(92)90841-7
REMARK   1
REMARK   1 REFERENCE 1
REMARK   1  AUTH   H.KE,L.D.ZYDOWSKY,J.LIU,C.T.WALSH
REMARK   1  TITL   CRYSTAL STRUCTURE OF RECOMBINANT HUMAN T CELL
REMARK   1  TITL 2 CYCLOPHILIN A AT 2.5 ANGSTROMS RESOLUTION
REMARK   1  REF    PROC.NATL.ACAD.SCI.USA        V.  88  9483 1991
REMARK   1  REFN                   ISSN 0027-8424
REMARK   2
REMARK   2 RESOLUTION.    1.63 ANGSTROMS.
REMARK   3
REMARK   3 REFINEMENT.
REMARK   3   PROGRAM     : X-PLOR
REMARK   3   AUTHORS     : BRUNGER
REMARK   3
REMARK   3  DATA USED IN REFINEMENT.
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 1.63
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : NULL
REMARK   3   DATA CUTOFF            (SIGMA(F)) : NULL
REMARK   3   DATA CUTOFF HIGH         (ABS(F)) : NULL
REMARK   3   DATA CUTOFF LOW          (ABS(F)) : NULL
REMARK   3   COMPLETENESS (WORKING+TEST)   (%) : NULL
REMARK   3   NUMBER OF REFLECTIONS             : NULL
REMARK   3
REMARK   3  FIT TO DATA USED IN REFINEMENT.
REMARK   3   CROSS-VALIDATION METHOD          : NULL
REMARK   3   FREE R VALUE TEST SET SELECTION  : NULL
REMARK   3   R VALUE            (WORKING SET) : 0.180
REMARK   3   FREE R VALUE                     : NULL
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : NULL
REMARK   3   FREE R VALUE TEST SET COUNT      : NULL
REMARK   3   ESTIMATED ERROR OF FREE R VALUE  : NULL
REMARK   3
REMARK   3  FIT IN THE HIGHEST RESOLUTION BIN.
REMARK   3   TOTAL NUMBER OF BINS USED           : NULL
REMARK   3   BIN RESOLUTION RANGE HIGH       (A) : NULL
REMARK   3   BIN RESOLUTION RANGE LOW        (A) : NULL
REMARK   3   BIN COMPLETENESS (WORKING+TEST) (%) : NULL
REMARK   3   REFLECTIONS IN BIN    (WORKING SET) : NULL
REMARK   3   BIN R VALUE           (WORKING SET) : NULL
REMARK   3   BIN FREE R VALUE                    : NULL
REMARK   3   BIN FREE R VALUE TEST SET SIZE  (%) : NULL
REMARK   3   BIN FREE R VALUE TEST SET COUNT     : NULL
REMARK   3   ESTIMATED ERROR OF BIN FREE R VALUE : NULL
REMARK   3
REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK   3   PROTEIN ATOMS            : 1258
REMARK   3   NUCLEIC ACID ATOMS       : 0
REMARK   3   HETEROGEN ATOMS          : 0
REMARK   3   SOLVENT ATOMS            : 119
REMARK   3
REMARK   3  B VALUES.
REMARK   3   FROM WILSON PLOT           (A**2) : NULL
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : NULL
REMARK   3   OVERALL ANISOTROPIC B VALUE.
REMARK   3    B11 (A**2) : NULL
REMARK   3    B22 (A**2) : NULL
REMARK   3    B33 (A**2) : NULL
REMARK   3    B12 (A**2) : NULL
REMARK   3    B13 (A**2) : NULL
REMARK   3    B23 (A**2) : NULL
REMARK   3
REMARK   3  ESTIMATED COORDINATE ERROR.
REMARK   3   ESD FROM LUZZATI PLOT        (A) : NULL
REMARK   3   ESD FROM SIGMAA              (A) : NULL
REMARK   3   LOW RESOLUTION CUTOFF        (A) : NULL
REMARK   3
REMARK   3  CROSS-VALIDATED ESTIMATED COORDINATE ERROR.
REMARK   3   ESD FROM C-V LUZZATI PLOT    (A) : NULL
REMARK   3   ESD FROM C-V SIGMAA          (A) : NULL
REMARK   3
REMARK   3  RMS DEVIATIONS FROM IDEAL VALUES.
REMARK   3   BOND LENGTHS                 (A) : 0.013
REMARK   3   BOND ANGLES            (DEGREES) : 2.50
REMARK   3   DIHEDRAL ANGLES        (DEGREES) : NULL
REMARK   3   IMPROPER ANGLES        (DEGREES) : NULL
REMARK   3
REMARK   3  ISOTROPIC THERMAL MODEL : NULL
REMARK   3
REMARK   3  ISOTROPIC THERMAL FACTOR RESTRAINTS.    RMS    SIGMA
REMARK   3   MAIN-CHAIN BOND              (A**2) : NULL  ; NULL
REMARK   3   MAIN-CHAIN ANGLE             (A**2) : NULL  ; NULL
REMARK   3   SIDE-CHAIN BOND              (A**2) : NULL  ; NULL
REMARK   3   SIDE-CHAIN ANGLE             (A**2) : NULL  ; NULL
REMARK   3
REMARK   3  NCS MODEL : NULL
REMARK   3
REMARK   3  NCS RESTRAINTS.                         RMS   SIGMA/WEIGHT
REMARK   3   GROUP  1  POSITIONAL            (A) : NULL  ; NULL
REMARK   3   GROUP  1  B-FACTOR           (A**2) : NULL  ; NULL
REMARK   3
REMARK   3  PARAMETER FILE  1  : NULL
REMARK   3  TOPOLOGY FILE  1   : NULL
REMARK   3
REMARK   3  OTHER REFINEMENT REMARKS: NULL
REMARK   4
REMARK   4 2CPL COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION
REMARK 200  DATE OF DATA COLLECTION        : NULL
REMARK 200  TEMPERATURE           (KELVIN) : NULL
REMARK 200  PH                             : NULL
REMARK 200  NUMBER OF CRYSTALS USED        : NULL
REMARK 200
REMARK 200  SYNCHROTRON              (Y/N) : NULL
REMARK 200  RADIATION SOURCE               : NULL
REMARK 200  BEAMLINE                       : NULL
REMARK 200  X-RAY GENERATOR MODEL          : NULL
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : NULL
REMARK 200  WAVELENGTH OR RANGE        (A) : NULL
REMARK 200  MONOCHROMATOR                  : NULL
REMARK 200  OPTICS                         : NULL
REMARK 200
REMARK 200  DETECTOR TYPE                  : NULL
REMARK 200  DETECTOR MANUFACTURER          : NULL
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : NULL
REMARK 200  DATA SCALING SOFTWARE          : NULL
REMARK 200
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : NULL
REMARK 200  RESOLUTION RANGE HIGH      (A) : NULL
REMARK 200  RESOLUTION RANGE LOW       (A) : NULL
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200  COMPLETENESS FOR RANGE     (%) : NULL
REMARK 200  DATA REDUNDANCY                : NULL
REMARK 200  R MERGE                    (I) : NULL
REMARK 200  R SYM                      (I) : NULL
REMARK 200   FOR THE DATA SET  : NULL
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : NULL
REMARK 200  COMPLETENESS FOR SHELL     (%) : NULL
REMARK 200  DATA REDUNDANCY IN SHELL       : NULL
REMARK 200  R MERGE FOR SHELL          (I) : NULL
REMARK 200  R SYM FOR SHELL            (I) : NULL
REMARK 200   FOR SHELL         : NULL
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: NULL
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL
REMARK 200 SOFTWARE USED: X-PLOR
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS   (%): 56.00
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.80
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: NULL
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21
REMARK 290
REMARK 290      SYMOP   SYMMETRY
REMARK 290     NNNMMM   OPERATOR
REMARK 290       1555   X,Y,Z
REMARK 290       2555   -X+1/2,-Y,Z+1/2
REMARK 290       3555   -X,Y+1/2,-Z+1/2
REMARK 290       4555   X+1/2,-Y+1/2,-Z
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       21.50000
REMARK 290   SMTRY2   2  0.000000 -1.000000  0.000000        0.00000
REMARK 290   SMTRY3   2  0.000000  0.000000  1.000000       44.60000
REMARK 290   SMTRY1   3 -1.000000  0.000000  0.000000        0.00000
REMARK 290   SMTRY2   3  0.000000  1.000000  0.000000       26.30000
REMARK 290   SMTRY3   3  0.000000  0.000000 -1.000000       44.60000
REMARK 290   SMTRY1   4  1.000000  0.000000  0.000000       21.50000
REMARK 290   SMTRY2   4  0.000000 -1.000000  0.000000       26.30000
REMARK 290   SMTRY3   4  0.000000  0.000000 -1.000000        0.00000
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 350
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 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC
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     MET A     1
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS
REMARK 500
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3)
REMARK 500
REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999
REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996
REMARK 500
REMARK 500  M RES CSSEQI ATM1   RES CSSEQI ATM2   DEVIATION
REMARK 500    HIS A 126   NE2   HIS A 126   CD2    -0.072
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND ANGLES
REMARK 500
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1)
REMARK 500
REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999
REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996
REMARK 500
REMARK 500  M RES CSSEQI ATM1   ATM2   ATM3
REMARK 500    ARG A  69   NE  -  CZ  -  NH1 ANGL. DEV. =   5.0 DEGREES
REMARK 500    ARG A  69   NE  -  CZ  -  NH2 ANGL. DEV. =  -4.4 DEGREES
REMARK 500    TRP A 121   CD1 -  CG  -  CD2 ANGL. DEV. =   7.3 DEGREES
REMARK 500    TRP A 121   CG  -  CD1 -  NE1 ANGL. DEV. =  -6.3 DEGREES
REMARK 500    TRP A 121   CE2 -  CD2 -  CG  ANGL. DEV. =  -5.5 DEGREES
REMARK 500    LYS A 125   CA  -  CB  -  CG  ANGL. DEV. =  15.7 DEGREES
REMARK 500
REMARK 500 REMARK: NULL
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
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  60      -71.22   -135.48
REMARK 500
REMARK 500 REMARK: NULL
DBREF  2CPL A    2   165  UNP    P62937   PPIA_HUMAN       1    164
SEQRES   1 A  165  MET VAL ASN PRO THR VAL PHE PHE ASP ILE ALA VAL ASP
SEQRES   2 A  165  GLY GLU PRO LEU GLY ARG VAL SER PHE GLU LEU PHE ALA
SEQRES   3 A  165  ASP LYS VAL PRO LYS THR ALA GLU ASN PHE ARG ALA LEU
SEQRES   4 A  165  SER THR GLY GLU LYS GLY PHE GLY TYR LYS GLY SER CYS
SEQRES   5 A  165  PHE HIS ARG ILE ILE PRO GLY PHE MET CYS GLN GLY GLY
SEQRES   6 A  165  ASP PHE THR ARG HIS ASN GLY THR GLY GLY LYS SER ILE
SEQRES   7 A  165  TYR GLY GLU LYS PHE GLU ASP GLU ASN PHE ILE LEU LYS
SEQRES   8 A  165  HIS THR GLY PRO GLY ILE LEU SER MET ALA ASN ALA GLY
SEQRES   9 A  165  PRO ASN THR ASN GLY SER GLN PHE PHE ILE CYS THR ALA
SEQRES  10 A  165  LYS THR GLU TRP LEU ASP GLY LYS HIS VAL VAL PHE GLY
SEQRES  11 A  165  LYS VAL LYS GLU GLY MET ASN ILE VAL GLU ALA MET GLU
SEQRES  12 A  165  ARG PHE GLY SER ARG ASN GLY LYS THR SER LYS LYS ILE
SEQRES  13 A  165  THR ILE ALA ASP CYS GLY GLN LEU GLU
FORMUL   2  HOH   *119(H2 O)
HELIX    1  H1 PHE A   25  VAL A   29  5                                   5
HELIX    2  H2 PRO A   30  THR A   41  1                                  12
HELIX    3  H3 THR A  119  ASP A  123  5                                   5
HELIX    4  H4 GLY A  135  MET A  142  1                                   8
HELIX    5  H5 GLU A  143  GLY A  146  5                                   4
SHEET    1   A 9 PRO A   4  ALA A  11  0
SHEET    2   A 9 PRO A  16  LEU A  24 -1
SHEET    3   A 9 VAL A 127  GLU A 134 -1
SHEET    4   A 9 GLY A  96  ALA A 101 -1
SHEET    5   A 9 GLN A 111  THR A 116 -1
SHEET    6   A 9 MET A  61  GLY A  64 -1
SHEET    7   A 9 GLY A  50  ILE A  56 -1
SHEET    8   A 9 LYS A 155  LEU A 164 -1
SHEET    9   A 9 PRO A   4  ALA A  11 -1
CRYST1   43.000   52.600   89.200  90.00  90.00  90.00 P 21 21 21    4
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      0.023256  0.000000  0.000000        0.00000
SCALE2      0.000000  0.019011  0.000000        0.00000
SCALE3      0.000000  0.000000  0.011211        0.00000
      
PROCHECK
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