PDB Short entry for 1E9M
HEADER    IRON-SULFUR PROTEIN                     24-OCT-00   1E9M              
TITLE     FERREDOXIN VI FROM RHODOBACTER CAPSULATUS                             
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: FERREDOXIN VI;                                             
COMPND   3 CHAIN: A;                                                            
COMPND   4 ENGINEERED: YES                                                      
SOURCE    MOL_ID: 1;                                                            
SOURCE   2 ORGANISM_SCIENTIFIC: RHODOBACTER CAPSULATUS;                         
SOURCE   3 ORGANISM_TAXID: 1061;                                                
SOURCE   4 STRAIN: B10;                                                         
SOURCE   5 GENE: FDXE;                                                          
SOURCE   6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;                                 
SOURCE   7 EXPRESSION_SYSTEM_TAXID: 469008;                                     
SOURCE   8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3);                                 
SOURCE   9 EXPRESSION_SYSTEM_PLASMID: PAJ66;                                    
SOURCE  10 EXPRESSION_SYSTEM_GENE: FDXE                                         
KEYWDS    IRON-SULFUR PROTEIN, FERREDOXIN, [2FE-2S], BACTERIUM, ELECTRON        
KEYWDS   2 TRANSPORT                                                            
EXPDTA    X-RAY DIFFRACTION                                                     
AUTHOR    G.SAINZ,J.ARMENGAUD,V.STOJANOFF,N.SANISHVILI,Y.JOUANNEAU,S.LARRY      
REVDAT   4   15-MAY-19 1E9M    1       REMARK                                   
REVDAT   3   24-FEB-09 1E9M    1       VERSN                                    
REVDAT   2   16-JUL-02 1E9M    1       REMARK HETATM                            
REVDAT   1   09-APR-01 1E9M    0                                                
JRNL        AUTH   J.ARMENGAUD,G.SAINZ,Y.JOUANNEAU,L.C.SIEKER                   
JRNL        TITL   CRYSTALLIZATION AND PRELIMINARY X-RAY DIFFRACTION ANALYSIS   
JRNL        TITL 2 OF A [2FE-2S] FERREDOXIN (FDVI) FROM RHODOBACTER CAPSULATUS  
JRNL        REF    ACTA CRYSTALLOGR.,SECT.D      V.  57   301 2001              
JRNL        REFN                   ISSN 0907-4449                               
JRNL        PMID   11173487                                                     
JRNL        DOI    10.1107/S0907444900017832                                    
REMARK   2                                                                      
REMARK   2 RESOLUTION.    2.07 ANGSTROMS.                                       
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : CNS 1.0                                              
REMARK   3   AUTHORS     : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-              
REMARK   3               : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,              
REMARK   3               : READ,RICE,SIMONSON,WARREN                            
REMARK   3                                                                      
REMARK   3  REFINEMENT TARGET : NULL                                            
REMARK   3                                                                      
REMARK   3  DATA USED IN REFINEMENT.                                            
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 2.07                           
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 19.27                          
REMARK   3   DATA CUTOFF            (SIGMA(F)) : 0.000                          
REMARK   3   DATA CUTOFF HIGH         (ABS(F)) : 939932.990                     
REMARK   3   DATA CUTOFF LOW          (ABS(F)) : NULL                           
REMARK   3   COMPLETENESS (WORKING+TEST)   (%) : 97.4                           
REMARK   3   NUMBER OF REFLECTIONS             : 7653                           
REMARK   3                                                                      
REMARK   3  FIT TO DATA USED IN REFINEMENT.                                     
REMARK   3   CROSS-VALIDATION METHOD          : THROUGHOUT                      
REMARK   3   FREE R VALUE TEST SET SELECTION  : RANDOM                          
REMARK   3   R VALUE            (WORKING SET) : 0.196                           
REMARK   3   FREE R VALUE                     : 0.214                           
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 5.200                           
REMARK   3   FREE R VALUE TEST SET COUNT      : 397                             
REMARK   3   ESTIMATED ERROR OF FREE R VALUE  : 0.011                           
REMARK   3                                                                      
REMARK   3  FIT IN THE HIGHEST RESOLUTION BIN.                                  
REMARK   3   TOTAL NUMBER OF BINS USED           : 6                            
REMARK   3   BIN RESOLUTION RANGE HIGH       (A) : 2.07                         
REMARK   3   BIN RESOLUTION RANGE LOW        (A) : 2.20                         
REMARK   3   BIN COMPLETENESS (WORKING+TEST) (%) : 93.00                        
REMARK   3   REFLECTIONS IN BIN    (WORKING SET) : 1122                         
REMARK   3   BIN R VALUE           (WORKING SET) : 0.2130                       
REMARK   3   BIN FREE R VALUE                    : 0.2590                       
REMARK   3   BIN FREE R VALUE TEST SET SIZE  (%) : 5.50                         
REMARK   3   BIN FREE R VALUE TEST SET COUNT     : 65                           
REMARK   3   ESTIMATED ERROR OF BIN FREE R VALUE : 0.032                        
REMARK   3                                                                      
REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.                    
REMARK   3   PROTEIN ATOMS            : 797                                     
REMARK   3   NUCLEIC ACID ATOMS       : 0                                       
REMARK   3   HETEROGEN ATOMS          : 4                                       
REMARK   3   SOLVENT ATOMS            : 57                                      
REMARK   3                                                                      
REMARK   3  B VALUES.                                                           
REMARK   3   FROM WILSON PLOT           (A**2) : 18.60                          
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : 32.80                          
REMARK   3   OVERALL ANISOTROPIC B VALUE.                                       
REMARK   3    B11 (A**2) : -7.57000                                             
REMARK   3    B22 (A**2) : -5.39000                                             
REMARK   3    B33 (A**2) : 12.96000                                             
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  ESTIMATED COORDINATE ERROR.                                         
REMARK   3   ESD FROM LUZZATI PLOT        (A) : 0.23                            
REMARK   3   ESD FROM SIGMAA              (A) : 0.13                            
REMARK   3   LOW RESOLUTION CUTOFF        (A) : 5.00                            
REMARK   3                                                                      
REMARK   3  CROSS-VALIDATED ESTIMATED COORDINATE ERROR.                         
REMARK   3   ESD FROM C-V LUZZATI PLOT    (A) : 0.27                            
REMARK   3   ESD FROM C-V SIGMAA          (A) : 0.20                            
REMARK   3                                                                      
REMARK   3  RMS DEVIATIONS FROM IDEAL VALUES.                                   
REMARK   3   BOND LENGTHS                 (A) : 0.005                           
REMARK   3   BOND ANGLES            (DEGREES) : 1.300                           
REMARK   3   DIHEDRAL ANGLES        (DEGREES) : 25.10                           
REMARK   3   IMPROPER ANGLES        (DEGREES) : 0.730                           
REMARK   3                                                                      
REMARK   3  ISOTROPIC THERMAL MODEL : RESTRAINED                                
REMARK   3                                                                      
REMARK   3  ISOTROPIC THERMAL FACTOR RESTRAINTS.    RMS    SIGMA                
REMARK   3   MAIN-CHAIN BOND              (A**2) : 1.450 ; 1.500                
REMARK   3   MAIN-CHAIN ANGLE             (A**2) : 2.240 ; 2.000                
REMARK   3   SIDE-CHAIN BOND              (A**2) : 2.260 ; 2.000                
REMARK   3   SIDE-CHAIN ANGLE             (A**2) : 3.460 ; 2.500                
REMARK   3                                                                      
REMARK   3  BULK SOLVENT MODELING.                                              
REMARK   3   METHOD USED : FLAT MODEL                                           
REMARK   3   KSOL        : 0.40                                                 
REMARK   3   BSOL        : 60.00                                                
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  : PROTEIN_REP.PARAM                              
REMARK   3  PARAMETER FILE  2  : CLUSTER150                                     
REMARK   3  PARAMETER FILE  3  : WATER_REP.PARAM                                
REMARK   3  PARAMETER FILE  4  : NULL                                           
REMARK   3  PARAMETER FILE  5  : NULL                                           
REMARK   3  TOPOLOGY FILE  1   : PROTEIN.TOP                                    
REMARK   3  TOPOLOGY FILE  2   : CLUSTER150                                     
REMARK   3  TOPOLOGY FILE  3   : WATER.TOP                                      
REMARK   3  TOPOLOGY FILE  4   : ION.TOP                                        
REMARK   3  TOPOLOGY FILE  5   : NULL                                           
REMARK   3                                                                      
REMARK   3  OTHER REFINEMENT REMARKS: NULL                                      
REMARK   4                                                                      
REMARK   4 1E9M COMPLIES WITH FORMAT V. 3.30, 13-JUL-11                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 24-OCT-00.                  
REMARK 100 THE DEPOSITION ID IS D_1290005368.                                   
REMARK 200                                                                      
REMARK 200 EXPERIMENTAL DETAILS                                                 
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION                  
REMARK 200  DATE OF DATA COLLECTION        : 15-JUL-99                          
REMARK 200  TEMPERATURE           (KELVIN) : 100.0                              
REMARK 200  PH                             : 7.60                               
REMARK 200  NUMBER OF CRYSTALS USED        : 1                                  
REMARK 200                                                                      
REMARK 200  SYNCHROTRON              (Y/N) : Y                                  
REMARK 200  RADIATION SOURCE               : APS                                
REMARK 200  BEAMLINE                       : 19-ID                              
REMARK 200  X-RAY GENERATOR MODEL          : NULL                               
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M                                  
REMARK 200  WAVELENGTH OR RANGE        (A) : 1.741,1.9815                       
REMARK 200  MONOCHROMATOR                  : SI(111)                            
REMARK 200  OPTICS                         : MIRROR                             
REMARK 200                                                                      
REMARK 200  DETECTOR TYPE                  : CCD                                
REMARK 200  DETECTOR MANUFACTURER          : ANL-ECT                            
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : DENZO                              
REMARK 200  DATA SCALING SOFTWARE          : SCALEPACK                          
REMARK 200                                                                      
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 16751                              
REMARK 200  RESOLUTION RANGE HIGH      (A) : 1.960                              
REMARK 200  RESOLUTION RANGE LOW       (A) : 40.161                             
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : 2.000                              
REMARK 200                                                                      
REMARK 200 OVERALL.                                                             
REMARK 200  COMPLETENESS FOR RANGE     (%) : 98.8                               
REMARK 200  DATA REDUNDANCY                : 3.600                              
REMARK 200  R MERGE                    (I) : NULL                               
REMARK 200  R SYM                      (I) : 0.05300                            
REMARK 200  <I/SIGMA(I)> FOR THE DATA SET  : 24.9000                            
REMARK 200                                                                      
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.                                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.96                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 2.03                     
REMARK 200  COMPLETENESS FOR SHELL     (%) : 93.7                               
REMARK 200  DATA REDUNDANCY IN SHELL       : 3.00                               
REMARK 200  R MERGE FOR SHELL          (I) : NULL                               
REMARK 200  R SYM FOR SHELL            (I) : 0.30000                            
REMARK 200  <I/SIGMA(I)> FOR SHELL         : 3.700                              
REMARK 200                                                                      
REMARK 200 DIFFRACTION PROTOCOL: MAD                                            
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD                          
REMARK 200 SOFTWARE USED: SOLVE                                                 
REMARK 200 STARTING MODEL: NULL                                                 
REMARK 200                                                                      
REMARK 200 REMARK: NULL                                                         
REMARK 280                                                                      
REMARK 280 CRYSTAL                                                              
REMARK 280 SOLVENT CONTENT, VS   (%): 53.00                                     
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.64                     
REMARK 280                                                                      
REMARK 280 CRYSTALLIZATION CONDITIONS: 7 M SODIUM FORMATE, IMIDAZOLE PH 7.6,    
REMARK 280  15 DEG SEEDING IN 3.5-4.2 SODIUM FORMATE., PH 7.60, VAPOR           
REMARK 280  DIFFUSION, TEMPERATURE 288K                                         
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       22.67000            
REMARK 290   SMTRY2   2  0.000000 -1.000000  0.000000        0.00000            
REMARK 290   SMTRY3   2  0.000000  0.000000  1.000000       27.45500            
REMARK 290   SMTRY1   3 -1.000000  0.000000  0.000000        0.00000            
REMARK 290   SMTRY2   3  0.000000  1.000000  0.000000       24.51500            
REMARK 290   SMTRY3   3  0.000000  0.000000 -1.000000       27.45500            
REMARK 290   SMTRY1   4  1.000000  0.000000  0.000000       22.67000            
REMARK 290   SMTRY2   4  0.000000 -1.000000  0.000000       24.51500            
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: 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 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    ALA A  44       20.49   -142.58                                   
REMARK 500    CYS A  45      -22.38   -140.47                                   
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
REMARK 620                                                                      
REMARK 620 METAL COORDINATION                                                   
REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;               
REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):                             
REMARK 620                                                                      
REMARK 620 COORDINATION ANGLES FOR:  M RES CSSEQI METAL                         
REMARK 620                             FES A 500  FE1                           
REMARK 620 N RES CSSEQI ATOM                                                    
REMARK 620 1 CYS A  39   SG                                                     
REMARK 620 2 FES A 500   S1  111.5                                              
REMARK 620 3 FES A 500   S2  107.6 104.4                                        
REMARK 620 4 CYS A  45   SG  111.2 109.8 112.1                                  
REMARK 620 N                    1     2     3                                   
REMARK 620                                                                      
REMARK 620 COORDINATION ANGLES FOR:  M RES CSSEQI METAL                         
REMARK 620                             FES A 500  FE2                           
REMARK 620 N RES CSSEQI ATOM                                                    
REMARK 620 1 CYS A  48   SG                                                     
REMARK 620 2 FES A 500   S1  111.3                                              
REMARK 620 3 FES A 500   S2  115.1 105.1                                        
REMARK 620 4 CYS A  86   SG  104.2 116.7 104.6                                  
REMARK 620 N                    1     2     3                                   
REMARK 800                                                                      
REMARK 800 SITE                                                                 
REMARK 800 SITE_IDENTIFIER: AC1                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FES A 500                 
DBREF  1E9M A    1   106  UNP    P80306   FER6_RHOCA       1    106             
SEQRES   1 A  106  ALA LYS ILE ILE PHE ILE GLU HIS ASN GLY THR ARG HIS          
SEQRES   2 A  106  GLU VAL GLU ALA LYS PRO GLY LEU THR VAL MET GLU ALA          
SEQRES   3 A  106  ALA ARG ASP ASN GLY VAL PRO GLY ILE ASP ALA ASP CYS          
SEQRES   4 A  106  GLY GLY ALA CYS ALA CYS SER THR CYS HIS ALA TYR VAL          
SEQRES   5 A  106  ASP PRO ALA TRP VAL ASP LYS LEU PRO LYS ALA LEU PRO          
SEQRES   6 A  106  THR GLU THR ASP MET ILE ASP PHE ALA TYR GLU PRO ASN          
SEQRES   7 A  106  PRO ALA THR SER ARG LEU THR CYS GLN ILE LYS VAL THR          
SEQRES   8 A  106  SER LEU LEU ASP GLY LEU VAL VAL HIS LEU PRO GLU LYS          
SEQRES   9 A  106  GLN ILE                                                      
HET    FES  A 500       4                                                       
HETNAM     FES FE2/S2 (INORGANIC) CLUSTER                                       
FORMUL   2  FES    FE2 S2                                                       
FORMUL   3  HOH   *57(H2 O)                                                     
HELIX    1   1 THR A   22  ASP A   29  1                                   8    
HELIX    2   2 ASP A   53  ASP A   58  1                                   6    
HELIX    3   3 LEU A   64  ASP A   72  1                                   9    
HELIX    4   4 CYS A   86  ILE A   88  5                                   3    
HELIX    5   5 THR A   91  ASP A   95  5                                   5    
SHEET    1   A 5 ARG A  12  GLU A  16  0                                        
SHEET    2   A 5 LYS A   2  ILE A   6 -1  O  ILE A   3   N  VAL A  15           
SHEET    3   A 5 LEU A  97  HIS A 100  1  O  LEU A  97   N  ILE A   4           
SHEET    4   A 5 HIS A  49  VAL A  52 -1  O  TYR A  51   N  HIS A 100           
SHEET    5   A 5 SER A  82  LEU A  84 -1  O  ARG A  83   N  ALA A  50           
LINK        FE1  FES A 500                 SG  CYS A  39     1555   1555  2.30  
LINK        FE1  FES A 500                 SG  CYS A  45     1555   1555  2.27  
LINK        FE2  FES A 500                 SG  CYS A  48     1555   1555  2.19  
LINK        FE2  FES A 500                 SG  CYS A  86     1555   1555  2.35  
SITE     1 AC1  9 ALA A  37  CYS A  39  GLY A  41  CYS A  43                    
SITE     2 AC1  9 ALA A  44  CYS A  45  SER A  46  CYS A  48                    
SITE     3 AC1  9 CYS A  86                                                     
CRYST1   45.340   49.030   54.910  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      0.022055  0.000000  0.000000        0.00000                         
SCALE2      0.000000  0.020396  0.000000        0.00000                         
SCALE3      0.000000  0.000000  0.018212        0.00000