HEADER ELECTRON TRANSPORT 20-AUG-98 1BQX TITLE ARTIFICIAL FE8S8 FERREDOXIN: THE D13C VARIANT OF BACILLUS SCHLEGELII TITLE 2 FE7S8 FERREDOXIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (FERREDOXIN); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SCHLEGELII; SOURCE 3 ORGANISM_TAXID: 1484; SOURCE 4 ATCC: ATCC 43741; SOURCE 5 COLLECTION: ATCC 43741; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: JM 109; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PKKFD D13C KEYWDS IRON-SULFUR PROTEIN, ELECTRON TRANSPORT EXPDTA SOLUTION NMR AUTHOR S.AONO,D.BENTROP,I.BERTINI,G.COSENZA,C.LUCHINAT REVDAT 5 03-NOV-21 1BQX 1 REMARK SEQADV LINK REVDAT 4 06-FEB-19 1BQX 1 REMARK ATOM REVDAT 3 24-FEB-09 1BQX 1 VERSN REVDAT 2 29-DEC-99 1BQX 4 HEADER COMPND REMARK JRNL REVDAT 2 2 4 ATOM SOURCE SEQRES REVDAT 1 26-AUG-98 1BQX 0 JRNL AUTH S.AONO,D.BENTROP,I.BERTINI,G.COSENZA,C.LUCHINAT JRNL TITL SOLUTION STRUCTURE OF AN ARTIFICIAL FE8S8 FERREDOXIN: THE JRNL TITL 2 D13C VARIANT OF BACILLUS SCHLEGELII FE7S8 FERREDOXIN. JRNL REF EUR.J.BIOCHEM. V. 258 502 1998 JRNL REFN ISSN 0014-2956 JRNL PMID 9874217 JRNL DOI 10.1046/J.1432-1327.1998.2580502.X REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.AONO,D.BENTROP,I.BERTINI,C.LUCHINAT,R.MACINAI REMARK 1 TITL THE D13C VARIANT OF BACILLUS SCHLEGELII 7FE FERREDOXIN IS AN REMARK 1 TITL 2 8FE FERREDOXIN AS REVEALED BY 1H-NMR SPECTROSCOPY REMARK 1 REF FEBS LETT. V. 412 501 1997 REMARK 1 REFN ISSN 0014-5793 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 4.1 REMARK 3 AUTHORS : PEARLMAN,CASE,CALDWELL,ROSS,CHEATHAM, REMARK 3 FERGUSON,SEIBEL,SINGH,WEINER,KOLLMAN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 THE STRUCTURE CALCULATIONS WERE CARRIED OUT WITH THE TORSION ANGLE REMARK 3 DYNAMICS REMARK 3 PROGRAM DYANA (BY GUENTERT,MUMENTHALER,WUETHRICH). THE 20 REMARK 3 STRUCTURES OF THE REMARK 3 DYANA FAMILY WITH THE LOWEST TARGET FUNCTION VALUES WERE REFINED REMARK 3 BY RESTRAINED REMARK 3 ENERGY MINIMIZATION(REM) AND RESTRAINED MOLECULAR DYNAMICS (RMD) REMARK 3 IN VACUO. THE REMARK 3 STRUCTURE IN THIS ENTRY REPRESENTS THE MINIMIZED AVERAGE STRUCTURE REMARK 3 OF THE RMD REMARK 3 FAMILY. REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE. REMARK 4 REMARK 4 1BQX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB. REMARK 100 THE DEPOSITION ID IS D_1000008319. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 300 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 20 MM REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY; COSY; TOCSY; 1D-NOE REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE500; AVANCE600; AVANCE800 REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : DYANA, AMBER REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS, REMARK 210 RESTRAINED ENERGY MINIMIZATION, REMARK 210 RESTRAINED MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 500 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : LEAST RESTRAINT VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: REMARK 210 MINIMIZED AVERAGE STRUCTURE. THE STRUCTURE WAS DETERMINED USING 1H REMARK 210 NMR REMARK 210 SPECTROSCOPY. EXPERIMENTAL DETAILS CAN BE FOUND IN THE JRNL REMARK 210 CITATION ABOVE. REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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: 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 THR A 5 -97.71 -143.92 REMARK 500 GLU A 6 -52.54 -127.18 REMARK 500 PRO A 7 31.35 -70.37 REMARK 500 THR A 11 84.85 15.48 REMARK 500 LYS A 12 58.38 75.99 REMARK 500 SER A 15 -57.44 -155.84 REMARK 500 VAL A 17 -92.22 -126.74 REMARK 500 GLU A 18 32.18 -75.69 REMARK 500 ASP A 23 61.96 36.71 REMARK 500 GLU A 29 -61.84 65.24 REMARK 500 ILE A 40 38.60 -90.99 REMARK 500 PRO A 50 26.02 -75.15 REMARK 500 SER A 52 98.48 63.12 REMARK 500 ALA A 53 -21.37 -154.43 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 TYR A 33 0.10 SIDE CHAIN REMARK 500 TYR A 55 0.21 SIDE CHAIN REMARK 500 ARG A 72 0.15 SIDE CHAIN 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 SF4 A 78 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 8 SG REMARK 620 2 SF4 A 78 S2 110.8 REMARK 620 3 SF4 A 78 S3 120.0 106.0 REMARK 620 4 SF4 A 78 S4 114.5 103.2 100.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 78 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 13 SG REMARK 620 2 SF4 A 78 S1 105.6 REMARK 620 3 SF4 A 78 S3 114.8 103.0 REMARK 620 4 SF4 A 78 S4 111.3 113.1 108.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 78 FE3 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 16 SG REMARK 620 2 SF4 A 78 S1 108.8 REMARK 620 3 SF4 A 78 S2 121.8 102.6 REMARK 620 4 SF4 A 78 S4 105.8 107.0 110.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 79 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 20 SG REMARK 620 2 SF4 A 79 S2 116.4 REMARK 620 3 SF4 A 79 S3 117.0 103.4 REMARK 620 4 SF4 A 79 S4 112.9 102.6 102.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 79 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 39 SG REMARK 620 2 SF4 A 79 S1 105.5 REMARK 620 3 SF4 A 79 S3 114.2 103.7 REMARK 620 4 SF4 A 79 S4 111.7 110.9 110.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 79 FE3 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 42 SG REMARK 620 2 SF4 A 79 S1 108.1 REMARK 620 3 SF4 A 79 S2 112.9 103.8 REMARK 620 4 SF4 A 79 S4 114.5 105.4 111.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 79 FE4 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 45 SG REMARK 620 2 SF4 A 79 S1 99.2 REMARK 620 3 SF4 A 79 S2 110.2 106.6 REMARK 620 4 SF4 A 79 S3 125.5 106.4 107.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 78 FE4 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 49 SG REMARK 620 2 SF4 A 78 S1 107.6 REMARK 620 3 SF4 A 78 S2 110.2 105.7 REMARK 620 4 SF4 A 78 S3 117.4 105.2 109.9 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 SF4 A 78 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SF4 A 79 DBREF 1BQX A 1 77 UNP Q45560 FER_BACSC 1 77 SEQADV 1BQX CYS A 13 UNP Q45560 ASP 13 ENGINEERED MUTATION SEQRES 1 A 77 ALA TYR VAL ILE THR GLU PRO CYS ILE GLY THR LYS CYS SEQRES 2 A 77 ALA SER CYS VAL GLU VAL CYS PRO VAL ASP CYS ILE HIS SEQRES 3 A 77 GLU GLY GLU ASP GLN TYR TYR ILE ASP PRO ASP VAL CYS SEQRES 4 A 77 ILE ASP CYS GLY ALA CYS GLU ALA VAL CYS PRO VAL SER SEQRES 5 A 77 ALA ILE TYR HIS GLU ASP PHE VAL PRO GLU GLU TRP LYS SEQRES 6 A 77 SER TYR ILE GLN LYS ASN ARG ASP PHE PHE LYS LYS HET SF4 A 78 8 HET SF4 A 79 8 HETNAM SF4 IRON/SULFUR CLUSTER FORMUL 2 SF4 2(FE4 S4) HELIX 1 1 ALA A 44 VAL A 48 1 5 HELIX 2 2 GLU A 62 PHE A 75 1 14 SHEET 1 A 2 ILE A 25 GLU A 27 0 SHEET 2 A 2 TYR A 32 ILE A 34 -1 N TYR A 33 O HIS A 26 LINK SG CYS A 8 FE1 SF4 A 78 1555 1555 2.03 LINK SG CYS A 13 FE2 SF4 A 78 1555 1555 2.05 LINK SG CYS A 16 FE3 SF4 A 78 1555 1555 2.10 LINK SG CYS A 20 FE1 SF4 A 79 1555 1555 2.07 LINK SG CYS A 39 FE2 SF4 A 79 1555 1555 2.05 LINK SG CYS A 42 FE3 SF4 A 79 1555 1555 2.10 LINK SG CYS A 45 FE4 SF4 A 79 1555 1555 2.04 LINK SG CYS A 49 FE4 SF4 A 78 1555 1555 2.03 SITE 1 AC1 7 CYS A 8 CYS A 13 SER A 15 CYS A 16 SITE 2 AC1 7 TYR A 32 CYS A 49 ILE A 54 SITE 1 AC2 7 CYS A 20 CYS A 24 ILE A 34 CYS A 39 SITE 2 AC2 7 ILE A 40 CYS A 42 CYS A 45 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000