PDB Short entry for 3K0N
HEADER    ISOMERASE                               24-SEP-09   3K0N              
TITLE     ROOM TEMPERATURE STRUCTURE OF CYPA                                    
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                                                      
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 3K0N    1       JRNL   VERSN                             
REVDAT   1   08-DEC-09 3K0N    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.    1.39 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) : 1.39                           
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 33.33                          
REMARK   3   MIN(FOBS/SIGMA_FOBS)              : 0.000                          
REMARK   3   COMPLETENESS FOR RANGE        (%) : 94.5                           
REMARK   3   NUMBER OF REFLECTIONS             : 39216                          
REMARK   3                                                                      
REMARK   3  FIT TO DATA USED IN REFINEMENT.                                     
REMARK   3   R VALUE     (WORKING + TEST SET) : 0.124                           
REMARK   3   R VALUE            (WORKING SET) : 0.122                           
REMARK   3   FREE R VALUE                     : 0.160                           
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 4.840                           
REMARK   3   FREE R VALUE TEST SET COUNT      : 1900                            
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 33.3435 -  3.3512    0.99     2990   153  0.1196 0.1347        
REMARK   3     2  3.3512 -  2.6603    0.99     2866   145  0.1338 0.1563        
REMARK   3     3  2.6603 -  2.3241    0.99     2828   144  0.1253 0.1717        
REMARK   3     4  2.3241 -  2.1117    0.99     2810   141  0.1090 0.1478        
REMARK   3     5  2.1117 -  1.9603    0.99     2784   142  0.1034 0.1335        
REMARK   3     6  1.9603 -  1.8448    0.99     2772   143  0.1008 0.1510        
REMARK   3     7  1.8448 -  1.7524    0.98     2734   137  0.1018 0.1561        
REMARK   3     8  1.7524 -  1.6761    0.97     2714   138  0.1051 0.1492        
REMARK   3     9  1.6761 -  1.6116    0.95     2682   132  0.0991 0.1791        
REMARK   3    10  1.6116 -  1.5560    0.95     2607   133  0.1063 0.1540        
REMARK   3    11  1.5560 -  1.5073    0.92     2586   126  0.1100 0.1945        
REMARK   3    12  1.5073 -  1.4642    0.89     2476   130  0.1262 0.1931        
REMARK   3    13  1.4642 -  1.4257    0.86     2394   125  0.1478 0.2256        
REMARK   3    14  1.4257 -  1.3909    0.76     2073   111  0.1783 0.2775        
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              : 0.36                                          
REMARK   3   B_SOL              : 34.95                                         
REMARK   3                                                                      
REMARK   3  ERROR ESTIMATES.                                                    
REMARK   3   COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED)     : 0.140            
REMARK   3   PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 14.710           
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) : -0.78400                                             
REMARK   3    B22 (A**2) : 1.72500                                              
REMARK   3    B33 (A**2) : -0.94090                                             
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           1564                                  
REMARK   3   ANGLE     :  1.264           2118                                  
REMARK   3   CHIRALITY :  0.076            223                                  
REMARK   3   PLANARITY :  0.008            281                                  
REMARK   3   DIHEDRAL  : 15.948            576                                  
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 3K0N COMPLIES WITH FORMAT V. 3.30, 13-JUL-11                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-DEC-09.                  
REMARK 100 THE RCSB ID CODE IS RCSB055396.                                      
REMARK 200                                                                      
REMARK 200 EXPERIMENTAL DETAILS                                                 
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION                  
REMARK 200  DATE OF DATA COLLECTION        : 31-MAR-08                          
REMARK 200  TEMPERATURE           (KELVIN) : 288                                
REMARK 200  PH                             : 7.5                                
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) : 1.115831                           
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 315                   
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : HKL-2000                           
REMARK 200  DATA SCALING SOFTWARE          : HKL-2000                           
REMARK 200                                                                      
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 39216                              
REMARK 200  RESOLUTION RANGE HIGH      (A) : 1.390                              
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     (%) : 94.5                               
REMARK 200  DATA REDUNDANCY                : 7.400                              
REMARK 200  R MERGE                    (I) : NULL                               
REMARK 200  R SYM                      (I) : 0.10100                            
REMARK 200  <I/SIGMA(I)> FOR THE DATA SET  : 21.0000                            
REMARK 200                                                                      
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.                                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.39                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 1.44                     
REMARK 200  COMPLETENESS FOR SHELL     (%) : 87.0                               
REMARK 200  DATA REDUNDANCY IN SHELL       : 2.80                               
REMARK 200  R MERGE FOR SHELL          (I) : NULL                               
REMARK 200  R SYM FOR SHELL            (I) : 0.50700                            
REMARK 200  <I/SIGMA(I)> FOR SHELL         : 1.900                              
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   (%): 56.13                                     
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.80                     
REMARK 280                                                                      
REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM HEPES PH 7.5, 22% PEG 3350, 5     
REMARK 280  MM TCEP, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K            
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       21.54800            
REMARK 290   SMTRY2   2  0.000000 -1.000000  0.000000        0.00000            
REMARK 290   SMTRY3   2  0.000000  0.000000  1.000000       44.62450            
REMARK 290   SMTRY1   3 -1.000000  0.000000  0.000000        0.00000            
REMARK 290   SMTRY2   3  0.000000  1.000000  0.000000       26.29600            
REMARK 290   SMTRY3   3  0.000000  0.000000 -1.000000       44.62450            
REMARK 290   SMTRY1   4  1.000000  0.000000  0.000000       21.54800            
REMARK 290   SMTRY2   4  0.000000 -1.000000  0.000000       26.29600            
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 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 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 465     GLU A   165                                                      
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      -80.40   -136.20                                   
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
REMARK 900                                                                      
REMARK 900 RELATED ENTRIES                                                      
REMARK 900 RELATED ID: 3K0M   RELATED DB: PDB                                   
REMARK 900 RELATED ID: 3K0O   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  3K0N A    1   165  UNP    P62937   PPIA_HUMAN       1    165             
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   *132(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    
SHEET    1   A 8 PHE A  53  ILE A  57  0                                        
SHEET    2   A 8 MET A  61  GLY A  64 -1  O  MET A  61   N  ILE A  57           
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  SER A  99   O  PHE A 113           
SHEET    5   A 8 VAL A 128  GLU A 134 -1  O  PHE A 129   N  LEU A  98           
SHEET    6   A 8 GLU A  15  LEU A  24 -1  N  SER A  21   O  GLU A 134           
SHEET    7   A 8 THR A   5  VAL A  12 -1  N  ILE A  10   O  GLY A  18           
SHEET    8   A 8 ILE A 156  GLN A 163 -1  O  ASP A 160   N  ASP A   9           
CRYST1   43.096   52.592   89.249  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      0.023204  0.000000  0.000000        0.00000                         
SCALE2      0.000000  0.019014  0.000000        0.00000                         
SCALE3      0.000000  0.000000  0.011205        0.00000