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
(ATOM LINES ARE NOT SHOWN.)
END