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PDBsum entry 3k0o

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Isomerase PDB id
3k0o
Jmol
Contents
Protein chain
164 a.a.
Waters ×119
HEADER    ISOMERASE                               24-SEP-09   3K0O
TITLE     ROOM TEMPERATURE STRUCTURE OF CYPA MUTANT SER99THR
COMPND    MOL_ID: 1;
COMPND   2 MOLECULE: CYCLOPHILIN A;
COMPND   3 CHAIN: A;
COMPND   4 SYNONYM: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE A, PPIASE A, ROTAMASE A,
COMPND   5 CYCLOSPORIN A-BINDING PROTEIN;
COMPND   6 EC: 5.2.1.8;
COMPND   7 ENGINEERED: YES;
COMPND   8 MUTATION: YES
SOURCE    MOL_ID: 1;
SOURCE   2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE   3 ORGANISM_COMMON: HUMAN;
SOURCE   4 ORGANISM_TAXID: 9606;
SOURCE   5 GENE: PPIA, CYPA;
SOURCE   6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE   7 EXPRESSION_SYSTEM_TAXID: 562
KEYWDS    PROLINE ISOMERASE, CYCLOSPORIN, HOST-VIRUS INTERACTION, ISOMERASE,
KEYWDS   2 ISOPEPTIDE BOND, PHOSPHOPROTEIN, ROTAMASE
EXPDTA    X-RAY DIFFRACTION
AUTHOR    J.S.FRASER,T.ALBER
REVDAT   2   19-JUN-13 3K0O    1       JRNL   VERSN
REVDAT   1   08-DEC-09 3K0O    0
JRNL        AUTH   J.S.FRASER,M.W.CLARKSON,S.C.DEGNAN,R.ERION,D.KERN,T.ALBER
JRNL        TITL   HIDDEN ALTERNATIVE STRUCTURES OF PROLINE ISOMERASE ESSENTIAL
JRNL        TITL 2 FOR CATALYSIS.
JRNL        REF    NATURE                        V. 462   669 2009
JRNL        REFN                   ISSN 0028-0836
JRNL        PMID   19956261
JRNL        DOI    10.1038/NATURE08615
REMARK   2
REMARK   2 RESOLUTION.    1.55 ANGSTROMS.
REMARK   3
REMARK   3 REFINEMENT.
REMARK   3   PROGRAM     : PHENIX (PHENIX.REFINE: 1.4_162)
REMARK   3   AUTHORS     : PAUL ADAMS,PAVEL AFONINE,VICENT CHEN,IAN
REMARK   3               : DAVIS,KRESHNA GOPAL,RALF GROSSE-
REMARK   3               : KUNSTLEVE,LI-WEI HUNG,ROBERT IMMORMINO,
REMARK   3               : TOM IOERGER,AIRLIE MCCOY,ERIK MCKEE,NIGEL
REMARK   3               : MORIARTY,REETAL PAI,RANDY READ,JANE
REMARK   3               : RICHARDSON,DAVID RICHARDSON,TOD ROMO,JIM
REMARK   3               : SACCHETTINI,NICHOLAS SAUTER,JACOB SMITH,
REMARK   3               : LAURENT STORONI,TOM TERWILLIGER,PETER
REMARK   3               : ZWART
REMARK   3
REMARK   3    REFINEMENT TARGET : ML
REMARK   3
REMARK   3  DATA USED IN REFINEMENT.
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 1.55
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 35.27
REMARK   3   MIN(FOBS/SIGMA_FOBS)              : 0.140
REMARK   3   COMPLETENESS FOR RANGE        (%) : 87.6
REMARK   3   NUMBER OF REFLECTIONS             : 26234
REMARK   3
REMARK   3  FIT TO DATA USED IN REFINEMENT.
REMARK   3   R VALUE     (WORKING + TEST SET) : 0.110
REMARK   3   R VALUE            (WORKING SET) : 0.107
REMARK   3   FREE R VALUE                     : 0.148
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 7.340
REMARK   3   FREE R VALUE TEST SET COUNT      : 1926
REMARK   3
REMARK   3  FIT TO DATA USED IN REFINEMENT (IN BINS).
REMARK   3   BIN  RESOLUTION RANGE  COMPL.    NWORK NFREE   RWORK  RFREE
REMARK   3     1 35.2774 -  3.7336    0.99     2115   158  0.1074 0.1170
REMARK   3     2  3.7336 -  2.9639    0.99     2009   160  0.1153 0.1542
REMARK   3     3  2.9639 -  2.5894    0.98     1959   155  0.1235 0.1562
REMARK   3     4  2.5894 -  2.3527    0.97     1930   161  0.1080 0.1532
REMARK   3     5  2.3527 -  2.1841    0.96     1901   148  0.0893 0.1189
REMARK   3     6  2.1841 -  2.0554    0.96     1899   145  0.0861 0.1364
REMARK   3     7  2.0554 -  1.9524    0.95     1861   149  0.0848 0.1354
REMARK   3     8  1.9524 -  1.8674    0.94     1858   148  0.0834 0.1317
REMARK   3     9  1.8674 -  1.7956    0.92     1806   146  0.0840 0.1395
REMARK   3    10  1.7956 -  1.7336    0.91     1772   137  0.0892 0.1587
REMARK   3    11  1.7336 -  1.6794    0.89     1725   141  0.0986 0.1945
REMARK   3    12  1.6794 -  1.6314    0.72     1414   108  0.1030 0.2010
REMARK   3    13  1.6314 -  1.5884    0.58     1116    96  0.1003 0.1902
REMARK   3    14  1.5884 -  1.5497    0.48      943    74  0.1004 0.1952
REMARK   3
REMARK   3  BULK SOLVENT MODELLING.
REMARK   3   METHOD USED        : FLAT BULK SOLVENT MODEL
REMARK   3   SOLVENT RADIUS     : 1.11
REMARK   3   SHRINKAGE RADIUS   : 0.90
REMARK   3   K_SOL              : 0.39
REMARK   3   B_SOL              : 34.56
REMARK   3
REMARK   3  ERROR ESTIMATES.
REMARK   3   COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED)     : 0.130
REMARK   3   PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 12.910
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) : 1.05760
REMARK   3    B22 (A**2) : 1.05760
REMARK   3    B33 (A**2) : -2.11510
REMARK   3    B12 (A**2) : 0.00000
REMARK   3    B13 (A**2) : -0.00000
REMARK   3    B23 (A**2) : -0.00000
REMARK   3
REMARK   3  TWINNING INFORMATION.
REMARK   3   FRACTION: NULL
REMARK   3   OPERATOR: NULL
REMARK   3
REMARK   3  DEVIATIONS FROM IDEAL VALUES.
REMARK   3                 RMSD          COUNT
REMARK   3   BOND      :  0.011           1287
REMARK   3   ANGLE     :  1.310           1727
REMARK   3   CHIRALITY :  0.078            179
REMARK   3   PLANARITY :  0.006            229
REMARK   3   DIHEDRAL  : 16.840            467
REMARK   3
REMARK   3  TLS DETAILS
REMARK   3   NUMBER OF TLS GROUPS  : NULL
REMARK   3
REMARK   3  NCS DETAILS
REMARK   3   NUMBER OF NCS GROUPS : NULL
REMARK   3
REMARK   3  OTHER REFINEMENT REMARKS: NULL
REMARK   4
REMARK   4 3K0O COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-SEP-09.
REMARK 100 THE RCSB ID CODE IS RCSB055397.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION
REMARK 200  DATE OF DATA COLLECTION        : 01-MAY-08
REMARK 200  TEMPERATURE           (KELVIN) : 288
REMARK 200  PH                             : 7
REMARK 200  NUMBER OF CRYSTALS USED        : 1
REMARK 200
REMARK 200  SYNCHROTRON              (Y/N) : Y
REMARK 200  RADIATION SOURCE               : ALS
REMARK 200  BEAMLINE                       : 12.3.1
REMARK 200  X-RAY GENERATOR MODEL          : NULL
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M
REMARK 200  WAVELENGTH OR RANGE        (A) : 1.1158
REMARK 200  MONOCHROMATOR                  : KOHZU DUAL DOUBLE CRYSTAL
REMARK 200                                   MONOCHROMATOR (DDCM)
REMARK 200  OPTICS                         : NULL
REMARK 200
REMARK 200  DETECTOR TYPE                  : CCD
REMARK 200  DETECTOR MANUFACTURER          : ADSC QUANTUM 315R
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200  DATA SCALING SOFTWARE          : HKL-2000
REMARK 200
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 27237
REMARK 200  RESOLUTION RANGE HIGH      (A) : 1.550
REMARK 200  RESOLUTION RANGE LOW       (A) : 50.000
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : 0.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200  COMPLETENESS FOR RANGE     (%) : 90.8
REMARK 200  DATA REDUNDANCY                : 13.300
REMARK 200  R MERGE                    (I) : NULL
REMARK 200  R SYM                      (I) : 0.12000
REMARK 200   FOR THE DATA SET  : 21.0000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.55
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 1.61
REMARK 200  COMPLETENESS FOR SHELL     (%) : 55.0
REMARK 200  DATA REDUNDANCY IN SHELL       : 5.60
REMARK 200  R MERGE FOR SHELL          (I) : NULL
REMARK 200  R SYM FOR SHELL            (I) : 0.43600
REMARK 200   FOR SHELL         : 3.000
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: PHASER
REMARK 200 STARTING MODEL: PDB ENTRY 2CPL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS   (%): 55.89
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.79
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 1.8 M DL-MALIC ACID, PH 7, VAPOR
REMARK 280  DIFFUSION, HANGING DROP, TEMPERATURE 291K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1
REMARK 290
REMARK 290      SYMOP   SYMMETRY
REMARK 290     NNNMMM   OPERATOR
REMARK 290       1555   X,Y,Z
REMARK 290       2555   -Y,X-Y,Z+2/3
REMARK 290       3555   -X+Y,-X,Z+1/3
REMARK 290       4555   Y,X,-Z
REMARK 290       5555   X-Y,-Y,-Z+1/3
REMARK 290       6555   -X,-X+Y,-Z+2/3
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 -0.500000 -0.866025  0.000000        0.00000
REMARK 290   SMTRY2   2  0.866025 -0.500000  0.000000        0.00000
REMARK 290   SMTRY3   2  0.000000  0.000000  1.000000       63.64133
REMARK 290   SMTRY1   3 -0.500000  0.866025  0.000000        0.00000
REMARK 290   SMTRY2   3 -0.866025 -0.500000  0.000000        0.00000
REMARK 290   SMTRY3   3  0.000000  0.000000  1.000000       31.82067
REMARK 290   SMTRY1   4 -0.500000  0.866025  0.000000        0.00000
REMARK 290   SMTRY2   4  0.866025  0.500000  0.000000        0.00000
REMARK 290   SMTRY3   4  0.000000  0.000000 -1.000000        0.00000
REMARK 290   SMTRY1   5  1.000000  0.000000  0.000000        0.00000
REMARK 290   SMTRY2   5  0.000000 -1.000000  0.000000        0.00000
REMARK 290   SMTRY3   5  0.000000  0.000000 -1.000000       31.82067
REMARK 290   SMTRY1   6 -0.500000 -0.866025  0.000000        0.00000
REMARK 290   SMTRY2   6 -0.866025  0.500000  0.000000        0.00000
REMARK 290   SMTRY3   6  0.000000  0.000000 -1.000000       63.64133
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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PISA
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 375
REMARK 375 SPECIAL POSITION
REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS
REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL
REMARK 375 POSITIONS.
REMARK 375
REMARK 375 ATOM RES CSSEQI
REMARK 375      HOH A 211  LIES ON A SPECIAL POSITION.
REMARK 375      HOH A 269  LIES ON A SPECIAL POSITION.
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: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT
REMARK 500
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.
REMARK 500
REMARK 500  ATM1  RES C  SSEQI   ATM2  RES C  SSEQI           DISTANCE
REMARK 500   N    VAL A     2     O    HOH A   265              2.17
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS
REMARK 500
REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC
REMARK 500 SYMMETRY ARE IN CLOSE CONTACT.  AN ATOM LOCATED WITHIN 0.15
REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A
REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375
REMARK 500 INSTEAD OF REMARK 500.  ATOMS WITH NON-BLANK ALTERNATE
REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS.
REMARK 500
REMARK 500 DISTANCE CUTOFF:
REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS
REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS
REMARK 500
REMARK 500  ATM1  RES C  SSEQI   ATM2  RES C  SSEQI  SSYMOP   DISTANCE
REMARK 500   OE2  GLU A   165     O    HOH A   184     6454     1.91
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      -74.99   -138.20
REMARK 500    THR A 119       66.65   -110.64
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 3K0M   RELATED DB: PDB
REMARK 900 RELATED ID: 3K0N   RELATED DB: PDB
REMARK 900 RELATED ID: 3K0P   RELATED DB: PDB
REMARK 900 RELATED ID: 3K0Q   RELATED DB: PDB
REMARK 900 RELATED ID: 3K0R   RELATED DB: PDB
DBREF  3K0O A    1   165  UNP    P62937   PPIA_HUMAN       1    165
SEQADV 3K0O THR A   99  UNP  P62937    SER    99 ENGINEERED
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 THR 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   1 VAL A   29  GLY A   42  1                                  14
HELIX    2   2 THR A  119  ASP A  123  5                                   5
HELIX    3   3 GLY A  135  ARG A  144  1                                  10
HELIX    4   4 PHE A  145  GLY A  146  5                                   2
HELIX    5   5 SER A  147  LYS A  151  5                                   5
SHEET    1   A 8 PHE A  53  ILE A  57  0
SHEET    2   A 8 MET A  61  GLY A  64 -1  O  GLN A  63   N  ARG A  55
SHEET    3   A 8 PHE A 112  CYS A 115 -1  O  ILE A 114   N  CYS A  62
SHEET    4   A 8 ILE A  97  MET A 100 -1  N  THR A  99   O  PHE A 113
SHEET    5   A 8 VAL A 128  GLU A 134 -1  O  GLY A 130   N  LEU A  98
SHEET    6   A 8 GLU A  15  LEU A  24 -1  N  SER A  21   O  LYS A 133
SHEET    7   A 8 THR A   5  VAL A  12 -1  N  ILE A  10   O  LEU A  17
SHEET    8   A 8 ILE A 156  GLN A 163 -1  O  ASP A 160   N  ASP A   9
CRYST1   60.438   60.438   95.462  90.00  90.00 120.00 P 32 2 1      6
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      0.016546  0.009553  0.000000        0.00000
SCALE2      0.000000  0.019106  0.000000        0.00000
SCALE3      0.000000  0.000000  0.010475        0.00000
      
PROCHECK
Go to PROCHECK summary
 References