HEADER ELECTRON TRANSPORT 11-OCT-99 1QN1 TITLE SOLUTION STRUCTURE OF DESULFOVIBRIO GIGAS FERRICYTOCHROME C3, NMR, 15 TITLE 2 STRUCTURES COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOCHROME C3; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: TETRAHEME CYTOCHROME; COMPND 5 OTHER_DETAILS: CLASS III OF C-TYPE CYTOCHROMES, FULLY OXIDISED FORM SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DESULFOVIBRIO GIGAS; SOURCE 3 ORGANISM_TAXID: 879; SOURCE 4 CELLULAR_LOCATION: PERIPLASM KEYWDS ELECTRON TRANSPORT, HEMEPROTEIN, CYTOCHROME C3, REDOX COOPERATIVITY, KEYWDS 2 REDOX-BOHR COOPERATIVITY, ENERGY TRANSDUCTION, PARAMAGNETIC EXPDTA SOLUTION NMR NUMMDL 15 AUTHOR L.BRENNAN,A.C.MESSIAS,J.LEGALL,D.L.TURNER,A.V.XAVIER REVDAT 3 06-NOV-19 1QN1 1 SEQADV LINK REVDAT 2 24-FEB-09 1QN1 1 VERSN REVDAT 1 12-OCT-00 1QN1 0 JRNL AUTH L.BRENNAN,D.L.TURNER,A.C.MESSIAS,M.L.TEODORO,J.LEGALL, JRNL AUTH 2 H.SANTOS,A.V.XAVIER JRNL TITL STRUCTURAL BASIS FOR THE NETWORK OF FUNCTIONAL JRNL TITL 2 COOPERATIVITIES IN CYTOCHROMES C3 FROM DESULFOVIBRIO GIGAS: JRNL TITL 3 SOLUTION STRUCTURES OF THE OXIDISED AND REDUCED STATES JRNL REF J.MOL.BIOL. V. 298 61 2000 JRNL REFN ISSN 0022-2836 JRNL PMID 10756105 JRNL DOI 10.1006/JMBI.2000.3652 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH R.O.LOURO,T.CATARINO,D.L.TURNER,M.A.PICARRA-PEREIRA, REMARK 1 AUTH 2 I.PACHECO,J.LEGALL,A.V.XAVIER REMARK 1 TITL FUNCTIONAL AND MECHANISTIC STUDIES OF CYTOCHROME C3 FROM REMARK 1 TITL 2 DESULFOVIBRIO GIGAS: THERMODYNAMICS OF A 'PROTON THRUSTER' REMARK 1 REF BIOCHEMISTRY V. 37 15808 1998 REMARK 1 REFN ISSN 0006-2960 REMARK 1 PMID 9843386 REMARK 1 DOI 10.1021/BI981505T REMARK 1 REFERENCE 2 REMARK 1 AUTH P.M.MATIAS,J.MORAIS,M.A.CARRONDO,K.WILSON,Z.DAUTER,L.SIEKER REMARK 1 TITL CYTOCHROMES C3 FROM DESULFOVIBRIO GIGAS: CRYSTAL STRUCTURE REMARK 1 TITL 2 AT 1.8 A RESOLUTION AND EVIDENCE FOR A SPECIFIC REMARK 1 TITL 3 CALCIUM-BINDING SITE REMARK 1 REF PROTEIN SCI. V. 5 1342 1996 REMARK 1 REFN ISSN 0961-8368 REMARK 1 PMID 8819167 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PARADYANA REMARK 3 AUTHORS : D.L.TURNER,L.BRENNAN,S.G.CHAMBERLIN, R.O.LOURO, REMARK 3 A.V.XAVIER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: DIPOLAR SHIFTS WERE USED AS RESTRAINTS REMARK 3 IN AN EXTENDED VERSION OF DYANA CALLED PARADYANA. D.L.TURNER,L, REMARK 3 BRENNAN,S.G.CHAMBERLIN, R.O.LOURO,A.V.XAVIER (1998)DETERMINATION REMARK 3 OF SOLUTION STRUCTURES OF PARAMAGNETIC PROTEINS BY REMARK 3 NMR.EUR.BIOPHYS.J.27,367-375. REMARK 4 REMARK 4 1QN1 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 11-OCT-99. REMARK 100 THE DEPOSITION ID IS D_1290004221. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 306.4 REMARK 210 PH : 5.1 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D-1H-NOESY; 2D-1H-TOCSY; 2D-1H REMARK 210 -COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : PARADYANA REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS WITH REMARK 210 SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 600 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 15 REMARK 210 CONFORMERS, SELECTION CRITERIA : LEAST RESTRAINT VIOLATION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL 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: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O ILE A 84 H LYS A 88 1.52 REMARK 500 O LYS A 44 H ALA A 47 1.52 REMARK 500 O HIS A 87 H LYS A 90 1.57 REMARK 500 O LYS A 95 H LYS A 99 1.60 REMARK 500 REMARK 500 REMARK: NULL 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 1 ASP A 2 164.37 -44.47 REMARK 500 1 PRO A 4 109.70 -55.46 REMARK 500 1 ALA A 5 -84.46 -42.44 REMARK 500 1 ASP A 11 69.29 -150.91 REMARK 500 1 GLU A 17 -96.87 38.77 REMARK 500 1 ASN A 19 158.33 -40.46 REMARK 500 1 THR A 28 25.98 -147.26 REMARK 500 1 HIS A 29 32.03 -163.75 REMARK 500 1 HIS A 39 33.97 -89.30 REMARK 500 1 THR A 51 -141.76 34.77 REMARK 500 1 CYS A 54 -124.64 -144.29 REMARK 500 1 HIS A 55 59.00 -104.16 REMARK 500 1 ILE A 57 114.77 -39.60 REMARK 500 1 LEU A 58 42.03 -104.98 REMARK 500 1 LYS A 63 -155.88 -88.23 REMARK 500 1 SER A 64 157.44 81.75 REMARK 500 1 VAL A 65 35.80 -91.69 REMARK 500 1 TYR A 69 53.40 -92.20 REMARK 500 1 LYS A 70 -58.65 -144.49 REMARK 500 1 THR A 82 -107.52 -108.01 REMARK 500 1 CYS A 83 -48.32 -135.99 REMARK 500 1 SER A 85 -81.37 -55.87 REMARK 500 1 ALA A 91 -65.37 179.67 REMARK 500 1 LYS A 95 -30.50 -39.16 REMARK 500 1 LEU A 101 -25.59 156.15 REMARK 500 1 THR A 102 -45.17 -140.41 REMARK 500 1 CYS A 104 -73.75 -95.57 REMARK 500 1 ALA A 108 49.65 -83.04 REMARK 500 1 CYS A 109 -49.87 -153.02 REMARK 500 2 ASP A 2 -160.25 38.40 REMARK 500 2 ALA A 5 -160.49 -64.45 REMARK 500 2 ASP A 11 89.09 -154.61 REMARK 500 2 ALA A 14 162.88 -42.26 REMARK 500 2 GLU A 17 49.83 -177.79 REMARK 500 2 LYS A 18 61.65 64.83 REMARK 500 2 ASN A 19 -155.70 -86.00 REMARK 500 2 HIS A 29 35.06 -162.32 REMARK 500 2 LYS A 33 132.76 -39.87 REMARK 500 2 THR A 50 43.21 -84.58 REMARK 500 2 ASP A 52 131.30 -38.60 REMARK 500 2 CYS A 54 -133.81 -149.75 REMARK 500 2 HIS A 55 63.05 -100.77 REMARK 500 2 LEU A 58 42.64 -106.01 REMARK 500 2 LYS A 63 -138.45 -64.59 REMARK 500 2 SER A 64 163.86 68.05 REMARK 500 2 VAL A 65 35.00 -92.06 REMARK 500 2 TYR A 69 55.42 -90.68 REMARK 500 2 LYS A 70 -58.06 -143.68 REMARK 500 2 THR A 82 -104.24 -108.74 REMARK 500 2 CYS A 83 -46.55 -142.40 REMARK 500 REMARK 500 THIS ENTRY HAS 402 RAMACHANDRAN OUTLIERS. 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 HEC A 113 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 26 NE2 REMARK 620 2 HEC A 113 NA 92.5 REMARK 620 3 HEC A 113 NB 91.8 91.1 REMARK 620 4 HEC A 113 NC 90.3 176.9 90.2 REMARK 620 5 HEC A 113 ND 90.7 90.4 176.9 88.1 REMARK 620 6 HIS A 38 NE2 177.8 89.6 88.9 87.6 88.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEC A 115 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 29 NE2 REMARK 620 2 HEC A 115 NA 90.8 REMARK 620 3 HEC A 115 NB 92.6 89.6 REMARK 620 4 HEC A 115 NC 91.8 177.2 91.3 REMARK 620 5 HEC A 115 ND 91.2 89.1 176.0 89.9 REMARK 620 6 HIS A 87 NE2 177.6 88.0 89.6 89.3 86.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEC A 114 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 39 NE2 REMARK 620 2 HEC A 114 NA 90.4 REMARK 620 3 HEC A 114 NB 92.4 89.6 REMARK 620 4 HEC A 114 NC 92.1 177.0 91.8 REMARK 620 5 HEC A 114 ND 92.3 88.8 175.0 89.5 REMARK 620 6 HIS A 55 NE2 177.7 88.7 89.6 88.7 85.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEC A 116 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 73 NE2 REMARK 620 2 HEC A 116 NA 90.8 REMARK 620 3 HEC A 116 NB 92.5 89.4 REMARK 620 4 HEC A 116 NC 91.7 176.9 92.3 REMARK 620 5 HEC A 116 ND 91.3 87.8 175.3 90.3 REMARK 620 6 HIS A 110 NE2 178.4 88.2 88.6 89.3 87.4 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEC A 113 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEC A 114 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEC A 115 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEC A 116 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1WAD RELATED DB: PDB REMARK 900 CYTOCHROME C3 WITH 4 HEME GROUPS AND ONE CALCIUM ION REMARK 900 RELATED ID: 1A2I RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF DESULFOVIBRIO VULGARIS (HILDENBOROUGH) REMARK 900 FERROCYTOCHROME C3, NMR, 20 STRUCTURES REMARK 900 RELATED ID: 1QN0 RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF DESULFOVIBRIO GIGAS FERROCYTOCHROME C3, NMR, REMARK 900 20 STRUCTURES REMARK 999 REMARK 999 SEQUENCE REMARK 999 RESIDUE 40 WAS FOUND TO BE GLN DBREF 1QN1 A 1 112 UNP P00133 CYC3_DESGI 1 112 SEQADV 1QN1 GLN A 40 UNP P00133 ASP 40 CONFLICT SEQRES 1 A 112 VAL ASP VAL PRO ALA ASP GLY ALA LYS ILE ASP PHE ILE SEQRES 2 A 112 ALA GLY GLY GLU LYS ASN LEU THR VAL VAL PHE ASN HIS SEQRES 3 A 112 SER THR HIS LYS ASP VAL LYS CYS ASP ASP CYS HIS HIS SEQRES 4 A 112 GLN PRO GLY ASP LYS GLN TYR ALA GLY CYS THR THR ASP SEQRES 5 A 112 GLY CYS HIS ASN ILE LEU ASP LYS ALA ASP LYS SER VAL SEQRES 6 A 112 ASN SER TRP TYR LYS VAL VAL HIS ASP ALA LYS GLY GLY SEQRES 7 A 112 ALA LYS PRO THR CYS ILE SER CYS HIS LYS ASP LYS ALA SEQRES 8 A 112 GLY ASP ASP LYS GLU LEU LYS LYS LYS LEU THR GLY CYS SEQRES 9 A 112 LYS GLY SER ALA CYS HIS PRO SER HET HEC A 113 75 HET HEC A 114 75 HET HEC A 115 75 HET HEC A 116 75 HETNAM HEC HEME C FORMUL 2 HEC 4(C34 H34 FE N4 O4) HELIX 1 1 SER A 27 HIS A 29 5 3 HELIX 2 2 LYS A 33 HIS A 38 1 6 HELIX 3 3 CYS A 83 ASP A 89 1 7 HELIX 4 4 ASP A 94 LYS A 100 1 7 SHEET 1 A 2 ASP A 6 ILE A 10 0 SHEET 2 A 2 VAL A 22 ASN A 25 -1 N PHE A 24 O GLY A 7 LINK NE2 HIS A 26 FE HEC A 113 1555 1555 1.91 LINK NE2 HIS A 29 FE HEC A 115 1555 1555 1.89 LINK SG CYS A 34 CAB HEC A 113 1555 1555 1.87 LINK SG CYS A 37 CAC HEC A 113 1555 1555 1.81 LINK NE2 HIS A 38 FE HEC A 113 1555 1555 2.00 LINK NE2 HIS A 39 FE HEC A 114 1555 1555 1.90 LINK SG CYS A 49 CAB HEC A 114 1555 1555 1.87 LINK SG CYS A 54 CAC HEC A 114 1555 1555 1.81 LINK NE2 HIS A 55 FE HEC A 114 1555 1555 2.00 LINK NE2 HIS A 73 FE HEC A 116 1555 1555 1.88 LINK SG CYS A 83 CAB HEC A 115 1555 1555 1.86 LINK SG CYS A 86 CAC HEC A 115 1555 1555 1.81 LINK NE2 HIS A 87 FE HEC A 115 1555 1555 2.00 LINK SG CYS A 104 CAB HEC A 116 1555 1555 1.91 LINK SG CYS A 109 CAC HEC A 116 1555 1555 1.81 LINK NE2 HIS A 110 FE HEC A 116 1555 1555 2.00 SITE 1 AC1 9 VAL A 3 PHE A 12 PHE A 24 HIS A 26 SITE 2 AC1 9 HIS A 29 CYS A 34 CYS A 37 HIS A 38 SITE 3 AC1 9 CYS A 49 SITE 1 AC2 14 CYS A 37 HIS A 39 GLN A 40 LYS A 44 SITE 2 AC2 14 GLY A 48 CYS A 49 GLY A 53 CYS A 54 SITE 3 AC2 14 HIS A 55 VAL A 65 VAL A 71 ALA A 79 SITE 4 AC2 14 LYS A 80 PRO A 81 SITE 1 AC3 8 THR A 28 HIS A 29 ASP A 36 THR A 82 SITE 2 AC3 8 CYS A 83 CYS A 86 HIS A 87 ALA A 108 SITE 1 AC4 11 ILE A 13 LEU A 20 VAL A 22 TYR A 69 SITE 2 AC4 11 VAL A 72 HIS A 73 LEU A 101 THR A 102 SITE 3 AC4 11 CYS A 104 CYS A 109 HIS A 110 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 MODEL 1