HEADER ELECTRON TRANSPORT 30-MAY-11 2LDO TITLE SOLUTION STRUCTURE OF TRIHEME CYTOCHROME PPCA FROM GEOBACTER TITLE 2 SULFURREDUCENS REVEALS THE STRUCTURAL ORIGIN OF THE REDOX-BOHR EFFECT COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOCHROME C3; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SEQUENCE DATABASE RESIDUES 21-91; COMPND 5 SYNONYM: PPCA; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GEOBACTER SULFURREDUCENS; SOURCE 3 ORGANISM_TAXID: 35554; SOURCE 4 GENE: GSU0612, PPCA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR: PCK32 KEYWDS ELECTRON TRANSFER, ELECTRON TRANSPORT EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR L.MORGADO,V.B.PAIXAO,M.BRUIX,C.A.SALGUEIRO REVDAT 3 03-MAR-21 2LDO 1 COMPND REMARK HET HETNAM REVDAT 3 2 1 HETSYN FORMUL LINK ATOM REVDAT 2 28-DEC-11 2LDO 1 JRNL REVDAT 1 07-SEP-11 2LDO 0 JRNL AUTH L.MORGADO,V.B.PAIXAO,M.SCHIFFER,P.R.POKKULURI,M.BRUIX, JRNL AUTH 2 C.A.SALGUEIRO JRNL TITL REVEALING THE STRUCTURAL ORIGIN OF THE REDOX-BOHR EFFECT: JRNL TITL 2 THE FIRST SOLUTION STRUCTURE OF A CYTOCHROME FROM GEOBACTER JRNL TITL 3 SULFURREDUCENS. JRNL REF BIOCHEM.J. V. 441 179 2012 JRNL REFN ISSN 0264-6021 JRNL PMID 21861844 JRNL DOI 10.1042/BJ20111103 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TOPSPIN, PARADYANA REMARK 3 AUTHORS : BRUKER BIOSPIN (TOPSPIN), REMARK 3 D.L.TURNER,L,BRENNAN,S.G.CHAMBERLIN, R.O.LOURO, REMARK 3 A.V.XAVIER (PARADYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2LDO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-JUN-11. REMARK 100 THE DEPOSITION ID IS D_1000102268. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.1 REMARK 210 IONIC STRENGTH : 100 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1 MM [U-100% 15N] CYTOCHROME C3 REMARK 210 -1, 1 MM PROTOPORPHYRIN IX REMARK 210 CONTAINING FE-2, 45 MM SODIUM REMARK 210 PHOSPHATE-3, 0.04 % SODIUM AZIDE- REMARK 210 4, 93% H2O/7% D2O; 1 MM REMARK 210 CYTOCHROME C3-5, 1 MM REMARK 210 PROTOPORPHYRIN IX CONTAINING FE- REMARK 210 6, 45 MM SODIUM PHOSPHATE-7, REMARK 210 0.04 % SODIUM AZIDE-8, 93% H2O/7% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D 1H-15N NOESY; REMARK 210 3D 1H-15N TOCSY; 2D 1H-1H TOCSY; REMARK 210 2D 1H-1H NOESY; 2D 1H-1H COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN, SPARKY, PARADYANA, REMARK 210 MOLMOL, PROCHECKNMR REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY 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 GLY A 11 HD1 HIS A 69 1.50 REMARK 500 O LYS A 18 H GLN A 21 1.55 REMARK 500 O ASP A 2 H HIS A 17 1.58 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 LYS A 18 -68.06 -140.35 REMARK 500 1 LYS A 33 31.24 -91.89 REMARK 500 1 PHE A 41 150.10 -33.61 REMARK 500 1 LYS A 43 -78.20 -57.95 REMARK 500 1 GLU A 44 -37.87 -34.93 REMARK 500 1 LYS A 49 37.03 -86.83 REMARK 500 1 CYS A 51 -86.09 -128.30 REMARK 500 1 HIS A 55 -71.18 -45.76 REMARK 500 2 ASP A 2 -39.03 -37.37 REMARK 500 2 LYS A 18 -68.04 -141.32 REMARK 500 2 LYS A 33 31.41 -91.45 REMARK 500 2 PHE A 41 159.96 -38.12 REMARK 500 2 LYS A 43 -78.69 -60.95 REMARK 500 2 GLU A 44 -36.61 -34.87 REMARK 500 2 LYS A 49 39.70 -86.28 REMARK 500 2 CYS A 51 -85.75 -123.47 REMARK 500 2 HIS A 55 -71.54 -53.49 REMARK 500 3 ASP A 2 -41.39 -169.87 REMARK 500 3 LYS A 18 -68.17 -140.51 REMARK 500 3 PHE A 41 150.44 -33.67 REMARK 500 3 LYS A 43 -77.97 -57.94 REMARK 500 3 GLU A 44 -36.68 -34.99 REMARK 500 3 LYS A 49 38.87 -87.08 REMARK 500 3 CYS A 51 -85.71 -123.57 REMARK 500 3 HIS A 55 -71.53 -53.09 REMARK 500 4 ASP A 2 -40.87 -172.63 REMARK 500 4 HIS A 17 49.63 -79.48 REMARK 500 4 LYS A 18 -68.01 -138.56 REMARK 500 4 PHE A 41 158.94 -37.68 REMARK 500 4 LYS A 43 -78.37 -60.40 REMARK 500 4 GLU A 44 -36.76 -34.70 REMARK 500 4 LYS A 49 40.48 -85.03 REMARK 500 4 CYS A 51 -86.38 -124.70 REMARK 500 4 HIS A 55 -70.63 -46.15 REMARK 500 5 ASP A 2 -37.24 -38.43 REMARK 500 5 HIS A 17 48.99 -80.58 REMARK 500 5 LYS A 18 -68.13 -139.25 REMARK 500 5 LYS A 33 30.30 -92.53 REMARK 500 5 PHE A 41 159.22 -37.85 REMARK 500 5 LYS A 43 -78.61 -59.97 REMARK 500 5 GLU A 44 -37.11 -34.82 REMARK 500 5 LYS A 49 38.86 -85.52 REMARK 500 5 CYS A 51 -86.92 -126.35 REMARK 500 5 HIS A 55 -71.21 -45.73 REMARK 500 6 HIS A 17 48.08 -80.16 REMARK 500 6 LYS A 18 -69.01 -137.47 REMARK 500 6 LYS A 33 31.21 -91.77 REMARK 500 6 PHE A 41 160.32 -38.27 REMARK 500 6 LYS A 43 -78.53 -59.30 REMARK 500 6 GLU A 44 -37.37 -35.01 REMARK 500 REMARK 500 THIS ENTRY HAS 180 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 130 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 17 NE2 REMARK 620 2 HEC A 130 NA 87.5 REMARK 620 3 HEC A 130 NB 94.5 89.4 REMARK 620 4 HEC A 130 NC 94.1 174.4 95.9 REMARK 620 5 HEC A 130 ND 89.0 85.1 173.3 89.6 REMARK 620 6 HIS A 31 NE2 171.5 86.5 91.4 91.4 84.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEC A 154 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 20 NE2 REMARK 620 2 HEC A 154 NA 88.8 REMARK 620 3 HEC A 154 NB 89.6 85.7 REMARK 620 4 HEC A 154 NC 92.1 176.1 90.6 REMARK 620 5 HEC A 154 ND 92.2 89.2 174.5 94.5 REMARK 620 6 HIS A 55 NE2 175.0 87.3 87.0 91.5 90.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEC A 168 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 47 NE2 REMARK 620 2 HEC A 168 NA 84.6 REMARK 620 3 HEC A 168 NB 93.7 88.0 REMARK 620 4 HEC A 168 NC 95.1 175.5 96.6 REMARK 620 5 HEC A 168 ND 91.6 84.8 170.6 90.7 REMARK 620 6 HIS A 69 NE2 168.2 84.6 90.6 95.3 82.7 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 130 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEC A 154 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEC A 168 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 16842 RELATED DB: BMRB DBREF 2LDO A 1 71 UNP Q8GGK7 Q8GGK7_GEOSL 21 91 SEQRES 1 A 71 ALA ASP ASP ILE VAL LEU LYS ALA LYS ASN GLY ASP VAL SEQRES 2 A 71 LYS PHE PRO HIS LYS ALA HIS GLN LYS ALA VAL PRO ASP SEQRES 3 A 71 CYS LYS LYS CYS HIS GLU LYS GLY PRO GLY LYS ILE GLU SEQRES 4 A 71 GLY PHE GLY LYS GLU MET ALA HIS GLY LYS GLY CYS LYS SEQRES 5 A 71 GLY CYS HIS GLU GLU MET LYS LYS GLY PRO THR LYS CYS SEQRES 6 A 71 GLY GLU CYS HIS LYS LYS HET HEC A 130 43 HET HEC A 154 43 HET HEC A 168 43 HETNAM HEC HEME C FORMUL 2 HEC 3(C34 H34 FE N4 O4) HELIX 1 1 LYS A 18 ALA A 23 1 6 HELIX 2 2 GLY A 42 GLY A 48 1 7 HELIX 3 3 CYS A 51 LYS A 59 1 9 SHEET 1 A 2 ASP A 3 LEU A 6 0 SHEET 2 A 2 VAL A 13 PRO A 16 -1 O VAL A 13 N LEU A 6 LINK SG CYS A 27 CAB HEC A 130 1555 1555 1.85 LINK SG CYS A 30 CAC HEC A 130 1555 1555 1.81 LINK SG CYS A 51 CAB HEC A 154 1555 1555 1.84 LINK SG CYS A 54 CAC HEC A 154 1555 1555 1.81 LINK SG CYS A 65 CAB HEC A 168 1555 1555 1.87 LINK SG CYS A 68 CAC HEC A 168 1555 1555 1.81 LINK NE2 HIS A 17 FE HEC A 130 1555 1555 1.89 LINK NE2 HIS A 20 FE HEC A 154 1555 1555 1.92 LINK NE2 HIS A 31 FE HEC A 130 1555 1555 1.99 LINK NE2 HIS A 47 FE HEC A 168 1555 1555 1.89 LINK NE2 HIS A 55 FE HEC A 154 1555 1555 1.99 LINK NE2 HIS A 69 FE HEC A 168 1555 1555 1.99 SITE 1 AC1 9 LEU A 6 HIS A 17 ASP A 26 CYS A 27 SITE 2 AC1 9 CYS A 30 HIS A 31 PRO A 35 ILE A 38 SITE 3 AC1 9 PHE A 41 SITE 1 AC2 8 PHE A 15 HIS A 20 ALA A 23 GLY A 50 SITE 2 AC2 8 CYS A 51 CYS A 54 HIS A 55 PRO A 62 SITE 1 AC3 15 LEU A 6 LYS A 7 LYS A 9 VAL A 13 SITE 2 AC3 15 PHE A 41 LYS A 43 ALA A 46 HIS A 47 SITE 3 AC3 15 LYS A 52 HIS A 55 PRO A 62 LYS A 64 SITE 4 AC3 15 CYS A 65 CYS A 68 HIS A 69 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