PDB Short entry for 2PPN
HEADER    ISOMERASE                               30-APR-07   2PPN              
TITLE     CRYSTAL STRUCTURE OF FKBP12                                           
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: FK506-BINDING PROTEIN 1A;                                  
COMPND   3 CHAIN: A;                                                            
COMPND   4 FRAGMENT: FKBP12;                                                    
COMPND   5 SYNONYM: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE, PPIASE, ROTAMASE, 12   
COMPND   6 KDA FKBP, FKBP-12, IMMUNOPHILIN FKBP12;                              
COMPND   7 EC: 5.2.1.8;                                                         
COMPND   8 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: FKBP1A, FKBP1, FKBP12;                                         
SOURCE   6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;                                 
SOURCE   7 EXPRESSION_SYSTEM_TAXID: 562                                         
KEYWDS    HIGH RESOLUTION PROTEIN STRUCTURE, ISOMERASE                          
EXPDTA    X-RAY DIFFRACTION                                                     
AUTHOR    S.SZEP,S.PARK,G.D.VANDUYNE,J.G.SAVEN                                  
REVDAT   4   21-FEB-24 2PPN    1       REMARK                                   
REVDAT   3   31-MAR-10 2PPN    1       JRNL                                     
REVDAT   2   24-FEB-09 2PPN    1       VERSN                                    
REVDAT   1   27-MAY-08 2PPN    0                                                
JRNL        AUTH   S.SZEP,S.PARK,E.T.BODER,G.D.VAN DUYNE,J.G.SAVEN              
JRNL        TITL   STRUCTURAL COUPLING BETWEEN FKBP12 AND BURIED WATER.         
JRNL        REF    PROTEINS                      V.  74   603 2009              
JRNL        REFN                   ISSN 0887-3585                               
JRNL        PMID   18704951                                                     
JRNL        DOI    10.1002/PROT.22176                                           
REMARK   2                                                                      
REMARK   2 RESOLUTION.    0.92 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) : 0.92                           
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 50.00                          
REMARK   3   DATA CUTOFF            (SIGMA(F)) : NULL                           
REMARK   3   COMPLETENESS FOR RANGE        (%) : 98.6                           
REMARK   3   CROSS-VALIDATION METHOD           : THROUGHOUT                     
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) : 0.213                  
REMARK   3   R VALUE          (WORKING SET, NO CUTOFF) : 0.209                  
REMARK   3   FREE R VALUE                  (NO CUTOFF) : 0.199                  
REMARK   3   FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL                   
REMARK   3   FREE R VALUE TEST SET COUNT   (NO CUTOFF) : 3561                   
REMARK   3   TOTAL NUMBER OF REFLECTIONS   (NO CUTOFF) : 61906                  
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)) : NULL                   
REMARK   3   FREE R VALUE                  (F>4SIG(F)) : NULL                   
REMARK   3   FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL                   
REMARK   3   FREE R VALUE TEST SET COUNT   (F>4SIG(F)) : NULL                   
REMARK   3   TOTAL NUMBER OF REFLECTIONS   (F>4SIG(F)) : NULL                   
REMARK   3                                                                      
REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.                    
REMARK   3   PROTEIN ATOMS      : 832                                           
REMARK   3   NUCLEIC ACID ATOMS : 0                                             
REMARK   3   HETEROGEN ATOMS    : 0                                             
REMARK   3   SOLVENT ATOMS      : 118                                           
REMARK   3                                                                      
REMARK   3  MODEL REFINEMENT.                                                   
REMARK   3   OCCUPANCY SUM OF NON-HYDROGEN ATOMS      : NULL                    
REMARK   3   OCCUPANCY SUM OF HYDROGEN ATOMS          : NULL                    
REMARK   3   NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL                    
REMARK   3   NUMBER OF LEAST-SQUARES PARAMETERS       : NULL                    
REMARK   3   NUMBER OF RESTRAINTS                     : NULL                    
REMARK   3                                                                      
REMARK   3  RMS DEVIATIONS FROM RESTRAINT TARGET VALUES.                        
REMARK   3   BOND LENGTHS                         (A) : 0.006                   
REMARK   3   ANGLE DISTANCES                      (A) : 1.152                   
REMARK   3   SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL                    
REMARK   3   DISTANCES FROM RESTRAINT PLANES      (A) : NULL                    
REMARK   3   ZERO CHIRAL VOLUMES               (A**3) : NULL                    
REMARK   3   NON-ZERO CHIRAL VOLUMES           (A**3) : NULL                    
REMARK   3   ANTI-BUMPING DISTANCE RESTRAINTS     (A) : NULL                    
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: NULL                                                  
REMARK   3                                                                      
REMARK   3  STEREOCHEMISTRY TARGET VALUES : ENGH & HUBER                        
REMARK   3   SPECIAL CASE: NULL                                                 
REMARK   3                                                                      
REMARK   3  OTHER REFINEMENT REMARKS: USED ANISOTROPIC B FACTOR                 
REMARK   3  REFINEMENT IN SHELX                                                 
REMARK   4                                                                      
REMARK   4 2PPN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-MAY-07.                  
REMARK 100 THE DEPOSITION ID IS D_1000042645.                                   
REMARK 200                                                                      
REMARK 200 EXPERIMENTAL DETAILS                                                 
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION                  
REMARK 200  DATE OF DATA COLLECTION        : 23-NOV-05                          
REMARK 200  TEMPERATURE           (KELVIN) : 200                                
REMARK 200  PH                             : 7.0                                
REMARK 200  NUMBER OF CRYSTALS USED        : 1                                  
REMARK 200                                                                      
REMARK 200  SYNCHROTRON              (Y/N) : Y                                  
REMARK 200  RADIATION SOURCE               : ALS                                
REMARK 200  BEAMLINE                       : 8.2.2                              
REMARK 200  X-RAY GENERATOR MODEL          : NULL                               
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M                                  
REMARK 200  WAVELENGTH OR RANGE        (A) : 0.98                               
REMARK 200  MONOCHROMATOR                  : SI 111 CHANNEL                     
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   : 61906                              
REMARK 200  RESOLUTION RANGE HIGH      (A) : 0.920                              
REMARK 200  RESOLUTION RANGE LOW       (A) : 50.000                             
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : 8.900                              
REMARK 200                                                                      
REMARK 200 OVERALL.                                                             
REMARK 200  COMPLETENESS FOR RANGE     (%) : 96.4                               
REMARK 200  DATA REDUNDANCY                : 3.300                              
REMARK 200  R MERGE                    (I) : 0.07900                            
REMARK 200  R SYM                      (I) : 0.07900                            
REMARK 200  <I/SIGMA(I)> FOR THE DATA SET  : 8.9000                             
REMARK 200                                                                      
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.                                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.92                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 0.97                     
REMARK 200  COMPLETENESS FOR SHELL     (%) : 96.4                               
REMARK 200  DATA REDUNDANCY IN SHELL       : 2.40                               
REMARK 200  R MERGE FOR SHELL          (I) : 0.18000                            
REMARK 200  R SYM FOR SHELL            (I) : 0.18000                            
REMARK 200  <I/SIGMA(I)> FOR SHELL         : 5.500                              
REMARK 200                                                                      
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH                              
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT        
REMARK 200 SOFTWARE USED: MOLREP CCP4                                           
REMARK 200 STARTING MODEL: DMSO BOUND WILD TYPE FKBP12 STRUCTURE FROM PDB       
REMARK 200                                                                      
REMARK 200 REMARK: NULL                                                         
REMARK 280                                                                      
REMARK 280 CRYSTAL                                                              
REMARK 280 SOLVENT CONTENT, VS   (%): 45.36                                     
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.25                     
REMARK 280                                                                      
REMARK 280 CRYSTALLIZATION CONDITIONS: 1.9-2.1 M SODIUM MALEONATE 50 MM DMSO    
REMARK 280  SLOW BUFFER EXCHANGE INTO 2.5 M SODIUM MALEONEATE NO DMSO, IN 10    
REMARK 280  MINUTE STEPS FOR FREEZING, PH 7.0, VAPOR DIFFUSION, HANGING DROP,   
REMARK 280  TEMPERATURE 298K                                                    
REMARK 290                                                                      
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY                                            
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1                         
REMARK 290                                                                      
REMARK 290      SYMOP   SYMMETRY                                                
REMARK 290     NNNMMM   OPERATOR                                                
REMARK 290       1555   X,Y,Z                                                   
REMARK 290       2555   -X,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        0.00000            
REMARK 290   SMTRY2   2  0.000000  1.000000  0.000000       31.35000            
REMARK 290   SMTRY3   2  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 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    ARG A  40   CZ    ARG A  40   NH2     0.111                       
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  13   NE  -  CZ  -  NH2 ANGL. DEV. =  -3.9 DEGREES          
REMARK 500    ARG A  18   NH1 -  CZ  -  NH2 ANGL. DEV. =   8.4 DEGREES          
REMARK 500    ARG A  18   NE  -  CZ  -  NH2 ANGL. DEV. =  -6.6 DEGREES          
REMARK 500    GLU A  31   OE1 -  CD  -  OE2 ANGL. DEV. =   8.5 DEGREES          
REMARK 500    ARG A  40   NE  -  CZ  -  NH1 ANGL. DEV. =  -8.8 DEGREES          
REMARK 500    ARG A  40   NE  -  CZ  -  NH2 ANGL. DEV. =  11.5 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    ARG A  13      -32.94   -136.33                                   
REMARK 500    ALA A  81     -111.46   -132.83                                   
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
REMARK 900                                                                      
REMARK 900 RELATED ENTRIES                                                      
REMARK 900 RELATED ID: 2PPO   RELATED DB: PDB                                   
REMARK 900 CRYSTAL STRUCTURE OF E60A MUTANT OF FKBP12                           
REMARK 900 RELATED ID: 2PPP   RELATED DB: PDB                                   
REMARK 900 CRYSTAL STRUCTURE OF E60Q MUTANT OF FKBP12                           
DBREF  2PPN A    1   107  UNP    P62942   FKB1A_HUMAN      2    108             
SEQRES   1 A  107  GLY VAL GLN VAL GLU THR ILE SER PRO GLY ASP GLY ARG          
SEQRES   2 A  107  THR PHE PRO LYS ARG GLY GLN THR CYS VAL VAL HIS TYR          
SEQRES   3 A  107  THR GLY MET LEU GLU ASP GLY LYS LYS PHE ASP SER SER          
SEQRES   4 A  107  ARG ASP ARG ASN LYS PRO PHE LYS PHE MET LEU GLY LYS          
SEQRES   5 A  107  GLN GLU VAL ILE ARG GLY TRP GLU GLU GLY VAL ALA GLN          
SEQRES   6 A  107  MET SER VAL GLY GLN ARG ALA LYS LEU THR ILE SER PRO          
SEQRES   7 A  107  ASP TYR ALA TYR GLY ALA THR GLY HIS PRO GLY ILE ILE          
SEQRES   8 A  107  PRO PRO HIS ALA THR LEU VAL PHE ASP VAL GLU LEU LEU          
SEQRES   9 A  107  LYS LEU GLU                                                  
FORMUL   2  HOH   *118(H2 O)                                                    
HELIX    1   1 SER A   39  ASN A   43  1                                   5    
HELIX    2   2 ILE A   56  ALA A   64  1                                   9    
HELIX    3   3 PRO A   78  ALA A   81  5                                   4    
SHEET    1   A 5 VAL A   2  SER A   8  0                                        
SHEET    2   A 5 ARG A  71  ILE A  76 -1  O  LYS A  73   N  GLU A   5           
SHEET    3   A 5 LEU A  97  GLU A 107 -1  O  LEU A  97   N  ILE A  76           
SHEET    4   A 5 THR A  21  LEU A  30 -1  N  HIS A  25   O  GLU A 102           
SHEET    5   A 5 LYS A  35  SER A  38 -1  O  ASP A  37   N  GLY A  28           
SHEET    1   B 5 VAL A   2  SER A   8  0                                        
SHEET    2   B 5 ARG A  71  ILE A  76 -1  O  LYS A  73   N  GLU A   5           
SHEET    3   B 5 LEU A  97  GLU A 107 -1  O  LEU A  97   N  ILE A  76           
SHEET    4   B 5 THR A  21  LEU A  30 -1  N  HIS A  25   O  GLU A 102           
SHEET    5   B 5 PHE A  46  MET A  49 -1  O  PHE A  48   N  CYS A  22           
CRYST1   28.767   62.700   32.277  90.00 113.66  90.00 P 1 21 1      2          
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      0.034762  0.000000  0.015231        0.00000                         
SCALE2      0.000000  0.015949  0.000000        0.00000                         
SCALE3      0.000000  0.000000  0.033825        0.00000