HEADER ELECTRON TRANSPORT 05-FEB-04 1UWM
TITLE REDUCED FERREDOXIN 6 FROM RHODOBACTER CAPSULATUS
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: FERREDOXIN VI;
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: FDVI;
COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: RHODOBACTER CAPSULATUS;
SOURCE 3 ORGANISM_TAXID: 1061;
SOURCE 4 STRAIN: B10;
SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008;
SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3);
SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PAJ66
KEYWDS FERREDOXIN, ELECTRON TRANSPORT, METAL-BINDING, IRON-SULFUR, IRON,
KEYWDS 2 2FE-2S
EXPDTA X-RAY DIFFRACTION
AUTHOR G.SAINZ,J.JAKONCIC,L.C.SIEKER,V.STOJANOFF,N.SANISHVILI,M.ASSO,
AUTHOR 2 P.BERTRAND,J.ARMENGAUD,Y.JOUANNEAU
REVDAT 5 13-DEC-23 1UWM 1 LINK
REVDAT 4 15-MAY-19 1UWM 1 REMARK
REVDAT 3 24-FEB-09 1UWM 1 VERSN
REVDAT 2 05-OCT-06 1UWM 1 JRNL
REVDAT 1 18-JAN-06 1UWM 0
JRNL AUTH G.SAINZ,J.JAKONCIC,L.C.SIEKER,V.STOJANOFF,N.SANISHVILI,
JRNL AUTH 2 M.ASSO,P.BERTRAND,J.ARMENGAUD,Y.JOUANNEAU
JRNL TITL STRUCTURE OF A [2FE-2S] FERREDOXIN FROM RHODOBACTER
JRNL TITL 2 CAPSULATUS LIKELY INVOLVED IN FE-S CLUSTER BIOGENESIS AND
JRNL TITL 3 CONFORMATIONAL CHANGES OBSERVED UPON REDUCTION.
JRNL REF J.BIOL.INORG.CHEM. V. 11 235 2006
JRNL REFN ISSN 0949-8257
JRNL PMID 16402206
JRNL DOI 10.1007/S00775-005-0069-2
REMARK 2
REMARK 2 RESOLUTION. 2.00 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : CNS 1.1
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) : 2.00
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.83
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 465410.330
REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000
REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 96.2
REMARK 3 NUMBER OF REFLECTIONS : 8680
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) : 0.230
REMARK 3 FREE R VALUE : 0.257
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.500
REMARK 3 FREE R VALUE TEST SET COUNT : 912
REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.009
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : 10
REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.00
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.07
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.20
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 708
REMARK 3 BIN R VALUE (WORKING SET) : 0.3090
REMARK 3 BIN FREE R VALUE : 0.3440
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 11.80
REMARK 3 BIN FREE R VALUE TEST SET COUNT : 95
REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.035
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 : 142
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 4.50
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.00
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -4.18000
REMARK 3 B22 (A**2) : -6.29000
REMARK 3 B33 (A**2) : 10.47000
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) : 0.26
REMARK 3 ESD FROM SIGMAA (A) : 0.24
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) : 0.31
REMARK 3 ESD FROM C-V SIGMAA (A) : 0.27
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 BOND LENGTHS (A) : 0.014
REMARK 3 BOND ANGLES (DEGREES) : 1.700
REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.30
REMARK 3 IMPROPER ANGLES (DEGREES) : 1.190
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) : 2.100 ; 1.500
REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.670 ; 2.000
REMARK 3 SIDE-CHAIN BOND (A**2) : 2.980 ; 2.000
REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.790 ; 2.500
REMARK 3
REMARK 3 BULK SOLVENT MODELING.
REMARK 3 METHOD USED : FLAT MODEL
REMARK 3 KSOL : 0.42
REMARK 3 BSOL : 70.01
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.PARAM
REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM
REMARK 3 PARAMETER FILE 4 : NULL
REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP
REMARK 3 TOPOLOGY FILE 2 : CLUSTER150.TOP
REMARK 3 TOPOLOGY FILE 3 : WATER.TOP
REMARK 3 TOPOLOGY FILE 4 : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 1UWM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 05-FEB-04.
REMARK 100 THE DEPOSITION ID IS D_1290014483.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 15-JUN-01
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 : ESRF
REMARK 200 BEAMLINE : ID14-4
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.9393
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : ADSC CCD
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO
REMARK 200 DATA SCALING SOFTWARE : SCALEPACK
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9100
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000
REMARK 200 RESOLUTION RANGE LOW (A) : 30.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 98.6
REMARK 200 DATA REDUNDANCY : 11.00
REMARK 200 R MERGE (I) : 0.08200
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.2900
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.03
REMARK 200 COMPLETENESS FOR SHELL (%) : 96.6
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : 0.27300
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 5.620
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: AMORE
REMARK 200 STARTING MODEL: PDB ENTRY 1E9M
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 54.00
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.80
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 7.2 M SODIUM FORMATE, IMIDAZOLE PH
REMARK 280 7.6, 15 DEG, REDUCTION WITH SODIUM DITHIONITE UNDER 2PPM O2, PH
REMARK 280 7.60, VAPOR 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 22.77100
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 27.67450
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.16750
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 27.67450
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.77100
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 25.16750
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 400
REMARK 400 COMPOUND
REMARK 400 FERREDOXIN ARE IRON-SULFUR PROTEINS THAT TRANSFER
REMARK 400 ELECTRONS IN METABOLIC REACTIONS.
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 -34.80 -131.65
REMARK 500 ALA A 44 -92.28 -78.41
REMARK 500 CYS A 45 -29.73 -36.11
REMARK 500
REMARK 500 REMARK: NULL
REMARK 525
REMARK 525 SOLVENT
REMARK 525
REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT
REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST
REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT
REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE
REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER;
REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE
REMARK 525 NUMBER; I=INSERTION CODE):
REMARK 525
REMARK 525 M RES CSSEQI
REMARK 525 HOH A2010 DISTANCE = 6.47 ANGSTROMS
REMARK 525 HOH A2020 DISTANCE = 5.87 ANGSTROMS
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 A1107 FE1
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS A 39 SG
REMARK 620 2 FES A1107 S1 110.6
REMARK 620 3 FES A1107 S2 120.8 101.9
REMARK 620 4 CYS A 45 SG 110.3 105.5 106.5
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 FES A1107 FE2
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS A 48 SG
REMARK 620 2 FES A1107 S1 115.0
REMARK 620 3 FES A1107 S2 101.0 105.9
REMARK 620 4 CYS A 86 SG 100.3 112.1 122.2
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 A1107
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1E9M RELATED DB: PDB
REMARK 900 FERREDOXIN VI FROM RHODOBACTER CAPSULATUS
DBREF 1UWM 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 A1107 4
HETNAM FES FE2/S2 (INORGANIC) CLUSTER
FORMUL 2 FES FE2 S2
FORMUL 3 HOH *142(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 AA 5 ARG A 12 GLU A 16 0
SHEET 2 AA 5 LYS A 2 ILE A 6 -1 O ILE A 3 N VAL A 15
SHEET 3 AA 5 LEU A 97 HIS A 100 1 O LEU A 97 N ILE A 4
SHEET 4 AA 5 HIS A 49 VAL A 52 -1 O TYR A 51 N HIS A 100
SHEET 5 AA 5 SER A 82 LEU A 84 -1 O ARG A 83 N ALA A 50
LINK SG CYS A 39 FE1 FES A1107 1555 1555 2.21
LINK SG CYS A 45 FE1 FES A1107 1555 1555 2.26
LINK SG CYS A 48 FE2 FES A1107 1555 1555 2.34
LINK SG CYS A 86 FE2 FES A1107 1555 1555 2.25
SITE 1 AC1 10 MET A 24 ALA A 37 CYS A 39 GLY A 41
SITE 2 AC1 10 CYS A 43 ALA A 44 CYS A 45 SER A 46
SITE 3 AC1 10 CYS A 48 CYS A 86
CRYST1 45.542 50.335 55.349 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 0.021958 0.000000 0.000000 0.00000
SCALE2 0.000000 0.019867 0.000000 0.00000
SCALE3 0.000000 0.000000 0.018067 0.00000
(ATOM LINES ARE NOT SHOWN.)
END