HEADER ELECTRON TRANSPORT 28-AUG-96 1XER TITLE STRUCTURE OF FERREDOXIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: FERREDOXIN; COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SULFOLOBUS TOKODAII STR. 7; SOURCE 3 ORGANISM_TAXID: 273063; SOURCE 4 STRAIN: STRAIN 7 KEYWDS ELECTRON TRANSPORT, IRON-SULFUR, DUPLICATION EXPDTA X-RAY DIFFRACTION AUTHOR T.FUJII,Y.HATA,H.MORIYAMA,T.WAKAGI,N.TANAKA,T.OSHIMA REVDAT 2 24-FEB-09 1XER 1 VERSN REVDAT 1 04-SEP-97 1XER 0 JRNL AUTH T.FUJII,Y.HATA,T.WAKAGI,N.TANAKA,T.OSHIMA JRNL TITL NOVEL ZINC-BINDING CENTRE IN THERMOACIDOPHILIC JRNL TITL 2 ARCHAEAL FERREDOXINS. JRNL REF NAT.STRUCT.BIOL. V. 3 834 1996 JRNL REFN ISSN 1072-8368 JRNL PMID 8836097 JRNL DOI 10.1038/NSB1096-834 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH T.FUJII,H.MORIYAMA,A.TAKENAKA,N.TANAKA,T.WAKAGI, REMARK 1 AUTH 2 T.OSHIMA REMARK 1 TITL CRYSTALLIZATION AND PRELIMINARY X-RAY STUDIES ON REMARK 1 TITL 2 SULFOLOBUS ACIDOCALDARIUS FERREDOXIN REMARK 1 REF J.BIOCHEM.(TOKYO) V. 110 472 1991 REMARK 1 REFN ISSN 0021-924X REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 3.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 89.9 REMARK 3 NUMBER OF REFLECTIONS : 5008 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.173 REMARK 3 FREE R VALUE : 0.244 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.09 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 73.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 555 REMARK 3 BIN R VALUE (WORKING SET) : 0.2200 REMARK 3 BIN FREE R VALUE : 0.2290 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 71 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 772 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 15 REMARK 3 SOLVENT ATOMS : 31 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.25 REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.011 REMARK 3 BOND ANGLES (DEGREES) : 1.74 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 26.89 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.41 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1XER 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 : 24-OCT-92 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RUH2R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NI FILTER REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU REMARK 200 INTENSITY-INTEGRATION SOFTWARE : R-AXIS IIC REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8689 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.710 REMARK 200 RESOLUTION RANGE LOW (A) : 35.590 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 86.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.07100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIRAS REMARK 200 SOFTWARE USED: PHASES REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 33.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.88 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 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+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 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 34.76000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 25.06000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 25.06000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 52.14000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 25.06000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 25.06000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 17.38000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 25.06000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 25.06000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 52.14000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 25.06000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 25.06000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 17.38000 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 34.76000 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: DIMERIC 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 350 BIOMT1 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 69.52000 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS(M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 MLZ A 29 CM 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 ZN A 106 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 16 ND1 REMARK 620 2 HIS A 19 NE2 110.7 REMARK 620 3 HIS A 34 ND1 105.1 109.1 REMARK 620 4 ASP A 76 OD1 112.0 114.1 105.3 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 ZN A 106 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE F3S A 104 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE F3S A 105 REMARK 999 REMARK 999 SEQUENCE REMARK 999 REMARK 999 BECAUSE OF THE ELECTRON DENSITY OF THE SIDE CHAIN OF LYS REMARK 999 29 IS NOT CLEAR, THE EXACT POSITION OF THE SIDE CHAIN OF REMARK 999 LYS 29 IS UNDEFINED. ALTHOUGH IT IS KNOWN FROM CHEMICAL REMARK 999 ANALYSIS THAT THE N-ZETA ATOM OF LYS 29 IS MONOMETHYLATED, REMARK 999 THE COORDINATES CONTAIN ONLY NORMAL SIDE CHAIN REMARK 999 COORDINATES FOR LYS 29. DBREF 1XER A 1 103 UNP P55907 FER1_SULTO 2 104 SEQADV 1XER MLZ A 29 UNP P55907 LYS 30 MODIFIED RESIDUE SEQRES 1 A 103 GLY ILE ASP PRO ASN TYR ARG THR ASN ARG GLN VAL VAL SEQRES 2 A 103 GLY GLU HIS SER GLY HIS LYS VAL TYR GLY PRO VAL GLU SEQRES 3 A 103 PRO PRO MLZ VAL LEU GLY ILE HIS GLY THR ILE VAL GLY SEQRES 4 A 103 VAL ASP PHE ASP LEU CYS ILE ALA ASP GLY SER CYS ILE SEQRES 5 A 103 ASN ALA CYS PRO VAL ASN VAL PHE GLN TRP TYR ASP THR SEQRES 6 A 103 PRO GLY HIS PRO ALA SER GLU LYS LYS ALA ASP PRO VAL SEQRES 7 A 103 ASN GLU GLN ALA CYS ILE PHE CYS MET ALA CYS VAL ASN SEQRES 8 A 103 VAL CYS PRO VAL ALA ALA ILE ASP VAL LYS PRO PRO MODRES 1XER MLZ A 29 LYS N-METHYL-LYSINE HET MLZ A 29 9 HET ZN A 106 1 HET F3S A 104 7 HET F3S A 105 7 HETNAM MLZ N-METHYL-LYSINE HETNAM ZN ZINC ION HETNAM F3S FE3-S4 CLUSTER FORMUL 1 MLZ C7 H16 N2 O2 FORMUL 2 ZN ZN 2+ FORMUL 3 F3S 2(FE3 S4) FORMUL 5 HOH *31(H2 O) HELIX 1 1 TYR A 6 ASN A 9 1 4 HELIX 2 2 SER A 50 ALA A 54 1 5 HELIX 3 3 GLU A 80 ALA A 82 5 3 HELIX 4 4 ALA A 88 VAL A 92 1 5 SHEET 1 A 2 VAL A 38 VAL A 40 0 SHEET 2 A 2 ILE A 98 VAL A 100 -1 N ASP A 99 O GLY A 39 SHEET 1 B 2 GLN A 61 ASP A 64 0 SHEET 2 B 2 LYS A 73 ASP A 76 -1 N ASP A 76 O GLN A 61 SHEET 1 C 2 VAL A 12 HIS A 16 0 SHEET 2 C 2 HIS A 19 TYR A 22 -1 N VAL A 21 O VAL A 13 LINK N MLZ A 29 C PRO A 28 1555 1555 1.32 LINK C MLZ A 29 N VAL A 30 1555 1555 1.33 LINK FE1 F3S A 104 SG CYS A 45 1555 1555 2.28 LINK FE3 F3S A 104 SG CYS A 93 1555 1555 2.30 LINK FE1 F3S A 105 SG CYS A 83 1555 1555 2.31 LINK FE3 F3S A 105 SG CYS A 55 1555 1555 2.31 LINK ZN ZN A 106 ND1 HIS A 16 1555 1555 2.07 LINK ZN ZN A 106 NE2 HIS A 19 1555 1555 1.95 LINK ZN ZN A 106 ND1 HIS A 34 1555 1555 1.96 LINK ZN ZN A 106 OD1 ASP A 76 1555 1555 1.85 LINK SG CYS A 51 FE4 F3S A 104 1555 1555 2.30 LINK SG CYS A 89 FE4 F3S A 105 1555 1555 2.31 CISPEP 1 GLY A 23 PRO A 24 0 0.05 CISPEP 2 PRO A 27 PRO A 28 0 0.23 SITE 1 AC1 4 HIS A 16 HIS A 19 HIS A 34 ASP A 76 SITE 1 AC2 10 CYS A 45 ILE A 46 ALA A 47 ASP A 48 SITE 2 AC2 10 GLY A 49 SER A 50 CYS A 51 TRP A 62 SITE 3 AC2 10 CYS A 93 ILE A 98 SITE 1 AC3 9 CYS A 55 VAL A 57 VAL A 59 PHE A 60 SITE 2 AC3 9 CYS A 83 ILE A 84 CYS A 86 MET A 87 SITE 3 AC3 9 CYS A 89 CRYST1 50.120 50.120 69.520 90.00 90.00 90.00 P 43 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 0.019952 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019952 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014384 0.00000