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Database: PDB
Entry: 6FD1
LinkDB: 6FD1
Original site: 6FD1 
HEADER    ELECTRON TRANSPORT                      17-SEP-97   6FD1              
TITLE     7-FE FERREDOXIN FROM AZOTOBACTER VINELANDII LOW TEMPERATURE,          
TITLE    2 1.35 A                                                               
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: 7-FE FERREDOXIN I (FD1);                                   
COMPND   3 CHAIN: A;                                                            
COMPND   4 SYNONYM: FD1                                                         
SOURCE    MOL_ID: 1;                                                            
SOURCE   2 ORGANISM_SCIENTIFIC: AZOTOBACTER VINELANDII;                         
SOURCE   3 ORGANISM_TAXID: 354                                                  
KEYWDS    ELECTRON TRANSPORT, IRON-SULFUR                                       
EXPDTA    X-RAY DIFFRACTION                                                     
AUTHOR    C.D.STOUT,E.A.STURA,D.E.MCREE                                         
REVDAT   3   24-MAR-09 6FD1    1       ATOM   CONECT                            
REVDAT   2   24-FEB-09 6FD1    1       VERSN                                    
REVDAT   1   12-NOV-97 6FD1    0                                                
JRNL        AUTH   C.D.STOUT,E.A.STURA,D.E.MCREE                                
JRNL        TITL   STRUCTURE OF AZOTOBACTER VINELANDII 7FE FERREDOXIN           
JRNL        TITL 2 AT 1.35 A RESOLUTION AND DETERMINATION OF THE                
JRNL        TITL 3 [FE-S] BONDS WITH 0.01 A ACCURACY.                           
JRNL        REF    J.MOL.BIOL.                   V. 278   629 1998              
JRNL        REFN                   ISSN 0022-2836                               
JRNL        PMID   9600844                                                      
JRNL        DOI    10.1006/JMBI.1998.1732                                       
REMARK   1                                                                      
REMARK   2                                                                      
REMARK   2 RESOLUTION.    1.35 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) : 1.35                           
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 100.00                         
REMARK   3   DATA CUTOFF            (SIGMA(F)) : 0.000                          
REMARK   3   COMPLETENESS FOR RANGE        (%) : 96.5                           
REMARK   3   CROSS-VALIDATION METHOD           : R-FREE                         
REMARK   3   FREE R VALUE TEST SET SELECTION   : EVERY 20TH REFLECTION          
REMARK   3                                                                      
REMARK   3  FIT TO DATA USED IN REFINEMENT (NO CUTOFF).                         
REMARK   3   R VALUE   (WORKING + TEST SET, NO CUTOFF) : 0.150                  
REMARK   3   R VALUE          (WORKING SET, NO CUTOFF) : 0.153                  
REMARK   3   FREE R VALUE                  (NO CUTOFF) : 0.213                  
REMARK   3   FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.000                  
REMARK   3   FREE R VALUE TEST SET COUNT   (NO CUTOFF) : 1544                   
REMARK   3   TOTAL NUMBER OF REFLECTIONS   (NO CUTOFF) : 30880                  
REMARK   3                                                                      
REMARK   3  FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F).                     
REMARK   3   R VALUE   (WORKING + TEST SET, F>4SIG(F)) : 0.138                  
REMARK   3   R VALUE          (WORKING SET, F>4SIG(F)) : 0.139                  
REMARK   3   FREE R VALUE                  (F>4SIG(F)) : 0.201                  
REMARK   3   FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.000                  
REMARK   3   FREE R VALUE TEST SET COUNT   (F>4SIG(F)) : 1218                   
REMARK   3   TOTAL NUMBER OF REFLECTIONS   (F>4SIG(F)) : 24118                  
REMARK   3                                                                      
REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.                    
REMARK   3   PROTEIN ATOMS      : 846                                           
REMARK   3   NUCLEIC ACID ATOMS : 0                                             
REMARK   3   HETEROGEN ATOMS    : 15                                            
REMARK   3   SOLVENT ATOMS      : 162                                           
REMARK   3                                                                      
REMARK   3  MODEL REFINEMENT.                                                   
REMARK   3   OCCUPANCY SUM OF NON-HYDROGEN ATOMS      : 1011.50                 
REMARK   3   OCCUPANCY SUM OF HYDROGEN ATOMS          : 776.00                  
REMARK   3   NUMBER OF DISCRETELY DISORDERED RESIDUES : 1                       
REMARK   3   NUMBER OF LEAST-SQUARES PARAMETERS       : 9211                    
REMARK   3   NUMBER OF RESTRAINTS                     : 10844                   
REMARK   3                                                                      
REMARK   3  RMS DEVIATIONS FROM RESTRAINT TARGET VALUES.                        
REMARK   3   BOND LENGTHS                         (A) : 0.020                   
REMARK   3   ANGLE DISTANCES                      (A) : 0.040                   
REMARK   3   SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.020                   
REMARK   3   DISTANCES FROM RESTRAINT PLANES      (A) : 0.200                   
REMARK   3   ZERO CHIRAL VOLUMES               (A**3) : 0.200                   
REMARK   3   NON-ZERO CHIRAL VOLUMES           (A**3) : 0.200                   
REMARK   3   ANTI-BUMPING DISTANCE RESTRAINTS     (A) : 0.020                   
REMARK   3   RIGID-BOND ADP COMPONENTS         (A**2) : 0.020                   
REMARK   3   SIMILAR ADP COMPONENTS            (A**2) : 0.300                   
REMARK   3   APPROXIMATELY ISOTROPIC ADPS      (A**2) : 0.200                   
REMARK   3                                                                      
REMARK   3  BULK SOLVENT MODELING.                                              
REMARK   3   METHOD USED: MOEWS & KRETSINGER                                    
REMARK   3                                                                      
REMARK   3  STEREOCHEMISTRY TARGET VALUES : ENGH & HUBER                        
REMARK   3   SPECIAL CASE: FE CLUSTERS NOT RESTRAINED                           
REMARK   3                                                                      
REMARK   3  OTHER REFINEMENT REMARKS: FREE R USED UNTIL LAST CYCLE WHEN         
REMARK   3  ALL DATA WAS INCLUDED.                                              
REMARK   4                                                                      
REMARK   4 6FD1 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        : APR-97                             
REMARK 200  TEMPERATURE           (KELVIN) : 100                                
REMARK 200  PH                             : 7.8                                
REMARK 200  NUMBER OF CRYSTALS USED        : 1                                  
REMARK 200                                                                      
REMARK 200  SYNCHROTRON              (Y/N) : Y                                  
REMARK 200  RADIATION SOURCE               : SSRL                               
REMARK 200  BEAMLINE                       : BL7-1                              
REMARK 200  X-RAY GENERATOR MODEL          : NULL                               
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M                                  
REMARK 200  WAVELENGTH OR RANGE        (A) : 1.08                               
REMARK 200  MONOCHROMATOR                  : NULL                               
REMARK 200  OPTICS                         : NULL                               
REMARK 200                                                                      
REMARK 200  DETECTOR TYPE                  : IMAGE PLATE                        
REMARK 200  DETECTOR MANUFACTURER          : MARRESEARCH                        
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : DENZO                              
REMARK 200  DATA SCALING SOFTWARE          : SCALEPACK                          
REMARK 200                                                                      
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 57315                              
REMARK 200  RESOLUTION RANGE HIGH      (A) : 1.350                              
REMARK 200  RESOLUTION RANGE LOW       (A) : 100.000                            
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : NULL                               
REMARK 200                                                                      
REMARK 200 OVERALL.                                                             
REMARK 200  COMPLETENESS FOR RANGE     (%) : 96.5                               
REMARK 200  DATA REDUNDANCY                : 3.300                              
REMARK 200  R MERGE                    (I) : NULL                               
REMARK 200  R SYM                      (I) : 0.05700                            
REMARK 200  <I/SIGMA(I)> FOR THE DATA SET  : 21.3000                            
REMARK 200                                                                      
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.                                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.35                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 1.38                     
REMARK 200  COMPLETENESS FOR SHELL     (%) : 72.0                               
REMARK 200  DATA REDUNDANCY IN SHELL       : 2.40                               
REMARK 200  R MERGE FOR SHELL          (I) : NULL                               
REMARK 200  R SYM FOR SHELL            (I) : 0.74700                            
REMARK 200  <I/SIGMA(I)> FOR SHELL         : 1.700                              
REMARK 200                                                                      
REMARK 200 DIFFRACTION PROTOCOL: NULL                                           
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT        
REMARK 200 SOFTWARE USED: TRIVIAL CASE                                          
REMARK 200 STARTING MODEL: PDB ENTRY 5FD1                                       
REMARK 200                                                                      
REMARK 200 REMARK: ALL DATA INCLUDING NEGATIVE I'S WERE USED WERE               
REMARK 200  PROCESSED IN POINT GROUP 422 - PRESERVE BIJVOET PAIRS               
REMARK 280                                                                      
REMARK 280 CRYSTAL                                                              
REMARK 280 SOLVENT CONTENT, VS   (%): 57.38                                     
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.89                     
REMARK 280                                                                      
REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN CRYSTALLIZED FROM 4.8M           
REMARK 280  AMMONIUM SULFATE, 0.45M TRIS-HCL, PH 7.8                            
REMARK 290                                                                      
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY                                            
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2                        
REMARK 290                                                                      
REMARK 290      SYMOP   SYMMETRY                                                
REMARK 290     NNNMMM   OPERATOR                                                
REMARK 290       1555   X,Y,Z                                                   
REMARK 290       2555   -X,-Y,Z+1/2                                             
REMARK 290       3555   -Y+1/2,X+1/2,Z+1/4                                      
REMARK 290       4555   Y+1/2,-X+1/2,Z+3/4                                      
REMARK 290       5555   -X+1/2,Y+1/2,-Z+1/4                                     
REMARK 290       6555   X+1/2,-Y+1/2,-Z+3/4                                     
REMARK 290       7555   Y,X,-Z                                                  
REMARK 290       8555   -Y,-X,-Z+1/2                                            
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        0.00000            
REMARK 290   SMTRY3   2  0.000000  0.000000  1.000000       46.32000            
REMARK 290   SMTRY1   3  0.000000 -1.000000  0.000000       27.42000            
REMARK 290   SMTRY2   3  1.000000  0.000000  0.000000       27.42000            
REMARK 290   SMTRY3   3  0.000000  0.000000  1.000000       23.16000            
REMARK 290   SMTRY1   4  0.000000  1.000000  0.000000       27.42000            
REMARK 290   SMTRY2   4 -1.000000  0.000000  0.000000       27.42000            
REMARK 290   SMTRY3   4  0.000000  0.000000  1.000000       69.48000            
REMARK 290   SMTRY1   5 -1.000000  0.000000  0.000000       27.42000            
REMARK 290   SMTRY2   5  0.000000  1.000000  0.000000       27.42000            
REMARK 290   SMTRY3   5  0.000000  0.000000 -1.000000       23.16000            
REMARK 290   SMTRY1   6  1.000000  0.000000  0.000000       27.42000            
REMARK 290   SMTRY2   6  0.000000 -1.000000  0.000000       27.42000            
REMARK 290   SMTRY3   6  0.000000  0.000000 -1.000000       69.48000            
REMARK 290   SMTRY1   7  0.000000  1.000000  0.000000        0.00000            
REMARK 290   SMTRY2   7  1.000000  0.000000  0.000000        0.00000            
REMARK 290   SMTRY3   7  0.000000  0.000000 -1.000000        0.00000            
REMARK 290   SMTRY1   8  0.000000 -1.000000  0.000000        0.00000            
REMARK 290   SMTRY2   8 -1.000000  0.000000  0.000000        0.00000            
REMARK 290   SMTRY3   8  0.000000  0.000000 -1.000000       46.32000            
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 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    ASP A  15   CB  -  CG  -  OD1 ANGL. DEV. =   5.8 DEGREES          
REMARK 500    HIS A  35   CB  -  CG  -  CD2 ANGL. DEV. =   7.2 DEGREES          
REMARK 500    ASP A  90   C   -  N   -  CA  ANGL. DEV. = -15.1 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    THR A   5     -169.17   -117.40                                   
REMARK 500    ASP A  90       41.20    -99.57                                   
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
REMARK 800                                                                      
REMARK 800 SITE                                                                 
REMARK 800 SITE_IDENTIFIER: AC1                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SF4 A 107                 
REMARK 800 SITE_IDENTIFIER: AC2                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE F3S A 108                 
DBREF  6FD1 A    1   106  UNP    P00214   FER1_AZOVI       1    106             
SEQRES   1 A  106  ALA PHE VAL VAL THR ASP ASN CYS ILE LYS CYS LYS TYR          
SEQRES   2 A  106  THR ASP CYS VAL GLU VAL CYS PRO VAL ASP CYS PHE TYR          
SEQRES   3 A  106  GLU GLY PRO ASN PHE LEU VAL ILE HIS PRO ASP GLU CYS          
SEQRES   4 A  106  ILE ASP CYS ALA LEU CYS GLU PRO GLU CYS PRO ALA GLN          
SEQRES   5 A  106  ALA ILE PHE SER GLU ASP GLU VAL PRO GLU ASP MET GLN          
SEQRES   6 A  106  GLU PHE ILE GLN LEU ASN ALA GLU LEU ALA GLU VAL TRP          
SEQRES   7 A  106  PRO ASN ILE THR GLU LYS LYS ASP PRO LEU PRO ASP ALA          
SEQRES   8 A  106  GLU ASP TRP ASP GLY VAL LYS GLY LYS LEU GLN HIS LEU          
SEQRES   9 A  106  GLU ARG                                                      
HET    SF4  A 107       8                                                       
HET    F3S  A 108       7                                                       
HETNAM     SF4 IRON/SULFUR CLUSTER                                              
HETNAM     F3S FE3-S4 CLUSTER                                                   
FORMUL   2  SF4    FE4 S4                                                       
FORMUL   3  F3S    FE3 S4                                                       
FORMUL   4  HOH   *162(H2 O)                                                    
HELIX    1   1 ASP A    6  CYS A    8  5                                   3    
HELIX    2   2 ASP A   15  VAL A   19  5                                   5    
HELIX    3   3 GLU A   46  GLU A   48  5                                   3    
HELIX    4   4 GLU A   57  GLU A   59  5                                   3    
HELIX    5   5 GLU A   62  GLU A   76  5                                  15    
HELIX    6   6 ALA A   91  TRP A   94  1                                   4    
HELIX    7   7 LYS A  100  HIS A  103  5                                   4    
SHEET    1   A 2 PHE A   2  VAL A   4  0                                        
SHEET    2   A 2 ILE A  54  SER A  56 -1  N  PHE A  55   O  VAL A   3           
SHEET    1   B 2 PHE A  25  GLU A  27  0                                        
SHEET    2   B 2 LEU A  32  ILE A  34 -1  N  VAL A  33   O  TYR A  26           
LINK        FE1  SF4 A 107                 SG  CYS A  39     1555   1555  2.30  
LINK        FE2  SF4 A 107                 SG  CYS A  42     1555   1555  2.27  
LINK        FE3  SF4 A 107                 SG  CYS A  45     1555   1555  2.26  
LINK        FE4  SF4 A 107                 SG  CYS A  20     1555   1555  2.29  
LINK        FE1  F3S A 108                 SG  CYS A  16     1555   1555  2.31  
LINK        FE3  F3S A 108                 SG  CYS A   8     1555   1555  2.29  
LINK         SG  CYS A  49                FE4  F3S A 108     1555   1555  2.32  
SITE     1 AC1 10 PHE A   2  CYS A  20  VAL A  22  CYS A  24                    
SITE     2 AC1 10 PHE A  25  CYS A  39  ILE A  40  CYS A  42                    
SITE     3 AC1 10 ALA A  43  CYS A  45                                          
SITE     1 AC2  7 CYS A   8  LYS A  12  TYR A  13  THR A  14                    
SITE     2 AC2  7 ASP A  15  CYS A  16  CYS A  49                               
CRYST1   54.840   54.840   92.640  90.00  90.00  90.00 P 41 21 2     8          
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      0.018235  0.000000  0.000000        0.00000                         
SCALE2      0.000000  0.018235  0.000000        0.00000                         
SCALE3      0.000000  0.000000  0.010794        0.00000                         
(ATOM LINES ARE NOT SHOWN.)
END                                                                             
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