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PDBsum entry 2dsx

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Electron transport PDB id
2dsx
Jmol
Contents
Protein chain
52 a.a.
Metals
_FE
Waters ×101
HEADER    ELECTRON TRANSPORT                      07-JUL-06   2DSX
TITLE     CRYSTAL STRUCTURE OF RUBREDOXIN FROM DESULFOVIBRIO GIGAS TO
TITLE    2 ULTRA-HIGH 0.68 A RESOLUTION
COMPND    MOL_ID: 1;
COMPND   2 MOLECULE: RUBREDOXIN;
COMPND   3 CHAIN: A;
COMPND   4 SYNONYM: RD
SOURCE    MOL_ID: 1;
SOURCE   2 ORGANISM_SCIENTIFIC: DESULFOVIBRIO GIGAS;
SOURCE   3 ORGANISM_TAXID: 879
KEYWDS    RUBREDOXIN, DESULFOVIBRIO GIGAS, REDOX, ELECTRON TRANSPORT
EXPDTA    X-RAY DIFFRACTION
AUTHOR    C.-J.CHEN,Y.-H.LIN,Y.-C.HUANG,M.-Y.LIU
REVDAT   3   24-FEB-09 2DSX    1       VERSN
REVDAT   2   19-DEC-06 2DSX    1       REMARK
REVDAT   1   10-OCT-06 2DSX    0
JRNL        AUTH   C.J.CHEN,Y.H.LIN,Y.C.HUANG,M.Y.LIU
JRNL        TITL   CRYSTAL STRUCTURE OF RUBREDOXIN FROM DESULFOVIBRIO
JRNL        TITL 2 GIGAS TO ULTRA-HIGH 0.68A RESOLUTION
JRNL        REF    BIOCHEM.BIOPHYS.RES.COMMUN.   V. 349    79 2006
JRNL        REFN                   ISSN 0006-291X
JRNL        PMID   16930541
JRNL        DOI    10.1016/J.BBRC.2006.07.205
REMARK   1
REMARK   2
REMARK   2 RESOLUTION.    0.68 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) : 0.68
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 10.00
REMARK   3   DATA CUTOFF            (SIGMA(F)) : 4.000
REMARK   3   COMPLETENESS FOR RANGE        (%) : 96.0
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) : 0.103
REMARK   3   R VALUE          (WORKING SET, NO CUTOFF) : 0.099
REMARK   3   FREE R VALUE                  (NO CUTOFF) : 0.111
REMARK   3   FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL
REMARK   3   FREE R VALUE TEST SET COUNT   (NO CUTOFF) : 5239
REMARK   3   TOTAL NUMBER OF REFLECTIONS   (NO CUTOFF) : 47119
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      : 399
REMARK   3   NUCLEIC ACID ATOMS : 0
REMARK   3   HETEROGEN ATOMS    : 1
REMARK   3   SOLVENT ATOMS      : 101
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) : NULL
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: NULL
REMARK   4
REMARK   4 2DSX COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-JUL-06.
REMARK 100 THE RCSB ID CODE IS RCSB025806.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION
REMARK 200  DATE OF DATA COLLECTION        : 20-MAY-03
REMARK 200  TEMPERATURE           (KELVIN) : 110
REMARK 200  PH                             : 4.6
REMARK 200  NUMBER OF CRYSTALS USED        : 1
REMARK 200
REMARK 200  SYNCHROTRON              (Y/N) : Y
REMARK 200  RADIATION SOURCE               : SPRING-8
REMARK 200  BEAMLINE                       : BL12B2
REMARK 200  X-RAY GENERATOR MODEL          : NULL
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M
REMARK 200  WAVELENGTH OR RANGE        (A) : 0.689
REMARK 200  MONOCHROMATOR                  : SI 111 CHANNEL
REMARK 200  OPTICS                         : NULL
REMARK 200
REMARK 200  DETECTOR TYPE                  : CCD
REMARK 200  DETECTOR MANUFACTURER          : ADSC QUANTUM 4
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200  DATA SCALING SOFTWARE          : HKL-2000
REMARK 200
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 52365
REMARK 200  RESOLUTION RANGE HIGH      (A) : 0.680
REMARK 200  RESOLUTION RANGE LOW       (A) : 10.000
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : 0.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200  COMPLETENESS FOR RANGE     (%) : 92.6
REMARK 200  DATA REDUNDANCY                : 16.600
REMARK 200  R MERGE                    (I) : 0.07300
REMARK 200  R SYM                      (I) : NULL
REMARK 200   FOR THE DATA SET  : 24.2000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.68
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 0.75
REMARK 200  COMPLETENESS FOR SHELL     (%) : 57.1
REMARK 200  DATA REDUNDANCY IN SHELL       : 7.30
REMARK 200  R MERGE FOR SHELL          (I) : 0.26100
REMARK 200  R SYM FOR SHELL            (I) : NULL
REMARK 200   FOR SHELL         : 3.600
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD
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   (%): 24.15
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.62
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 4.2M AMMONIUM SULFATE, 0.1M
REMARK 280  CITRITE, PH 4.6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE
REMARK 280  296K
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       20.66200
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 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    LYS A  51   CD  -  CE  -  NZ  ANGL. DEV. =  21.3 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    ASP A  19       77.76   -157.22
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                              FE A 501  FE
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS A   6   SG
REMARK 620 2 CYS A   9   SG  114.7
REMARK 620 3 CYS A  39   SG  113.7 102.8
REMARK 620 4 CYS A  42   SG  105.8 109.6 110.3
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 FE A 501
DBREF  2DSX A    1    52  UNP    P00270   RUBR_DESGI       1     52
SEQRES   1 A   52  MET ASP ILE TYR VAL CYS THR VAL CYS GLY TYR GLU TYR
SEQRES   2 A   52  ASP PRO ALA LYS GLY ASP PRO ASP SER GLY ILE LYS PRO
SEQRES   3 A   52  GLY THR LYS PHE GLU ASP LEU PRO ASP ASP TRP ALA CYS
SEQRES   4 A   52  PRO VAL CYS GLY ALA SER LYS ASP ALA PHE GLU LYS GLN
HET     FE  A 501       1
HETNAM      FE FE (III) ION
FORMUL   2   FE    FE 3+
FORMUL   3  HOH   *101(H2 O)
HELIX    1   1 ASP A   19  GLY A   23  5                                   5
HELIX    2   2 LYS A   29  LEU A   33  5                                   5
HELIX    3   3 SER A   45  ASP A   47  5                                   3
SHEET    1   A 3 GLU A  12  TYR A  13  0
SHEET    2   A 3 TYR A   4  CYS A   6 -1  N  TYR A   4   O  TYR A  13
SHEET    3   A 3 PHE A  49  LYS A  51 -1  O  GLU A  50   N  VAL A   5
LINK        FE    FE A 501                 SG  CYS A   6     1555   1555  2.34
LINK        FE    FE A 501                 SG  CYS A   9     1555   1555  2.31
LINK        FE    FE A 501                 SG  CYS A  39     1555   1555  2.33
LINK        FE    FE A 501                 SG  CYS A  42     1555   1555  2.31
SITE     1 AC1  4 CYS A   6  CYS A   9  CYS A  39  CYS A  42
CRYST1   19.474   41.324   24.129  90.00 108.20  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      0.051351  0.000000  0.016883        0.00000
SCALE2      0.000000  0.024199  0.000000        0.00000
SCALE3      0.000000  0.000000  0.043626        0.00000
      
PROCHECK
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