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 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 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