HEADER ELECTRON TRANSPORT 08-FEB-15 2MZ9 TITLE SOLUTION STRUCTURE OF OXIDIZED TRIHEME CYTOCHROME PPCA FROM GEOBACTER TITLE 2 SULFURREDUCENS COMPND MOL_ID: 1; COMPND 2 MOLECULE: PPCA; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 21-91; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GEOBACTER SULFURREDUCENS; SOURCE 3 ORGANISM_TAXID: 35554; SOURCE 4 GENE: PPCA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PCK32 KEYWDS CYTOCHROME, PARAMAGNETIC, ELECTRON TRANSPORT EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR L.MORGADO,M.BRUIX,R.POKKULURI,C.A.SALGUEIRO,D.L.TURNER REVDAT 3 01-MAY-24 2MZ9 1 REMARK LINK REVDAT 2 15-MAR-17 2MZ9 1 JRNL REVDAT 1 10-FEB-16 2MZ9 0 JRNL AUTH L.MORGADO,M.BRUIX,P.R.POKKULURI,C.A.SALGUEIRO,D.L.TURNER JRNL TITL REDOX- AND PH-LINKED CONFORMATIONAL CHANGES IN TRIHEME JRNL TITL 2 CYTOCHROME PPCA FROM GEOBACTER SULFURREDUCENS. JRNL REF BIOCHEM. J. V. 474 231 2017 JRNL REFN ESSN 1470-8728 JRNL PMID 28062839 JRNL DOI 10.1042/BCJ20160932 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 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2MZ9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-FEB-15. REMARK 100 THE DEPOSITION ID IS D_1000104222. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 5.5 REMARK 210 IONIC STRENGTH : 100 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 2 MM PROTEIN_1, 92 % H2O, 8 % REMARK 210 D2O, 45 MM SODIUM PHOSPHATE, REMARK 210 0.04 % SODIUM AZIDE, 93% H2O/7% REMARK 210 D2O; 2 MM [U-100% 15N] PROTEIN_1, REMARK 210 92 % H2O, 8 % D2O, 45 MM SODIUM REMARK 210 PHOSPHATE, 0.04 % SODIUM AZIDE, REMARK 210 93% H2O/7% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H TOCSY; 2D 1H-1H NOESY; REMARK 210 2D 1H-15N HSQC 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 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 500 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 CYS A 54 H MET A 58 1.45 REMARK 500 O CYS A 54 H GLU A 57 1.58 REMARK 500 O CYS A 65 H HIS A 69 1.60 REMARK 500 SG CYS A 68 CAC HEC A 103 1.81 REMARK 500 SG CYS A 54 CAC HEC A 102 1.81 REMARK 500 SG CYS A 30 CAC HEC A 101 1.81 REMARK 500 SG CYS A 65 CAB HEC A 103 1.84 REMARK 500 SG CYS A 51 CAB HEC A 102 1.91 REMARK 500 SG CYS A 27 CAB HEC A 101 1.97 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 -42.69 85.89 REMARK 500 1 LEU A 6 78.91 -105.24 REMARK 500 1 LYS A 7 119.19 -36.84 REMARK 500 1 LYS A 22 -159.27 -121.04 REMARK 500 1 PRO A 25 -67.91 -29.59 REMARK 500 1 ASP A 26 44.87 -161.52 REMARK 500 1 CYS A 27 172.59 54.14 REMARK 500 1 LYS A 28 19.42 83.31 REMARK 500 1 GLU A 32 32.11 85.62 REMARK 500 1 LYS A 33 82.79 81.19 REMARK 500 1 PRO A 35 -160.50 -73.68 REMARK 500 1 GLU A 39 -141.46 34.27 REMARK 500 1 PHE A 41 101.95 -36.26 REMARK 500 1 LYS A 49 48.28 -106.76 REMARK 500 1 CYS A 51 -71.64 177.74 REMARK 500 1 CYS A 54 -74.49 -53.44 REMARK 500 2 ASP A 2 -54.87 66.56 REMARK 500 2 LYS A 7 113.07 -35.46 REMARK 500 2 LYS A 22 45.04 -157.60 REMARK 500 2 ALA A 23 39.40 -155.55 REMARK 500 2 PRO A 25 21.12 -79.74 REMARK 500 2 ASP A 26 82.17 174.44 REMARK 500 2 PRO A 35 -158.58 -59.87 REMARK 500 2 GLU A 39 92.53 -32.67 REMARK 500 2 CYS A 51 -70.08 -179.86 REMARK 500 2 CYS A 54 -77.33 -54.84 REMARK 500 3 ASP A 2 -65.63 68.47 REMARK 500 3 LYS A 7 122.12 -36.44 REMARK 500 3 LYS A 22 23.12 -155.14 REMARK 500 3 PRO A 25 -69.44 -29.18 REMARK 500 3 ASP A 26 43.04 -152.73 REMARK 500 3 CYS A 27 -168.09 45.00 REMARK 500 3 HIS A 31 49.46 -79.18 REMARK 500 3 LYS A 33 -72.47 -73.38 REMARK 500 3 PHE A 41 145.07 -34.30 REMARK 500 3 CYS A 51 -66.40 178.39 REMARK 500 4 ASP A 2 -68.86 -171.62 REMARK 500 4 ASP A 12 171.74 -59.95 REMARK 500 4 PRO A 25 -38.46 -30.02 REMARK 500 4 CYS A 27 -167.08 -48.60 REMARK 500 4 LYS A 28 -11.09 102.14 REMARK 500 4 HIS A 31 47.06 -86.77 REMARK 500 4 GLU A 32 69.62 -62.98 REMARK 500 4 LYS A 33 -59.76 163.46 REMARK 500 4 PRO A 35 -158.23 -57.06 REMARK 500 4 GLU A 39 96.09 -26.47 REMARK 500 4 CYS A 51 -66.77 -179.85 REMARK 500 5 LYS A 7 114.50 -33.25 REMARK 500 5 ASN A 10 51.97 -153.31 REMARK 500 5 PRO A 25 -70.04 -40.52 REMARK 500 REMARK 500 THIS ENTRY HAS 245 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 101 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 17 NE2 REMARK 620 2 HEC A 101 NA 91.1 REMARK 620 3 HEC A 101 NB 91.8 90.5 REMARK 620 4 HEC A 101 NC 91.6 176.3 91.9 REMARK 620 5 HEC A 101 ND 90.6 88.5 177.4 89.0 REMARK 620 6 HIS A 31 NE2 178.5 88.3 89.6 88.9 88.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEC A 102 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 20 NE2 REMARK 620 2 HEC A 102 NA 89.3 REMARK 620 3 HEC A 102 NB 91.4 86.5 REMARK 620 4 HEC A 102 NC 91.9 175.1 88.8 REMARK 620 5 HEC A 102 ND 95.9 91.9 172.5 92.7 REMARK 620 6 HIS A 55 NE2 177.1 89.6 85.8 89.0 86.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEC A 103 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 47 NE2 REMARK 620 2 HEC A 103 NA 90.4 REMARK 620 3 HEC A 103 NB 91.9 89.1 REMARK 620 4 HEC A 103 NC 91.3 177.7 89.3 REMARK 620 5 HEC A 103 ND 94.4 91.1 173.7 90.2 REMARK 620 6 HIS A 69 NE2 179.5 89.1 88.3 89.2 85.4 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 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEC A 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEC A 103 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 25477 RELATED DB: BMRB DBREF 2MZ9 A 1 71 UNP Q8GGK7 Q8GGK7_GEOSN 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 101 43 HET HEC A 102 43 HET HEC A 103 43 HETNAM HEC HEME C FORMUL 2 HEC 3(C34 H34 FE N4 O4) HELIX 1 1 HIS A 17 GLN A 21 1 5 HELIX 2 2 GLY A 42 GLY A 48 1 7 HELIX 3 3 CYS A 51 LYS A 59 1 9 HELIX 4 4 LYS A 64 CYS A 68 1 5 SHEET 1 A 3 ASP A 3 VAL A 5 0 SHEET 2 A 3 ASP A 12 PRO A 16 -1 O PHE A 15 N ILE A 4 SHEET 3 A 3 HIS A 69 LYS A 70 -1 O LYS A 70 N ASP A 12 LINK NE2 HIS A 17 FE HEC A 101 1555 1555 1.91 LINK NE2 HIS A 20 FE HEC A 102 1555 1555 1.87 LINK NE2 HIS A 31 FE HEC A 101 1555 1555 2.00 LINK NE2 HIS A 47 FE HEC A 103 1555 1555 1.89 LINK NE2 HIS A 55 FE HEC A 102 1555 1555 2.00 LINK NE2 HIS A 69 FE HEC A 103 1555 1555 2.00 SITE 1 AC1 10 ILE A 4 LEU A 6 HIS A 17 GLN A 21 SITE 2 AC1 10 CYS A 27 CYS A 30 HIS A 31 LYS A 37 SITE 3 AC1 10 ILE A 38 HEC A 102 SITE 1 AC2 15 LEU A 6 VAL A 13 PHE A 15 PRO A 16 SITE 2 AC2 15 HIS A 20 ALA A 23 LYS A 29 CYS A 51 SITE 3 AC2 15 CYS A 54 HIS A 55 MET A 58 LYS A 60 SITE 4 AC2 15 PRO A 62 CYS A 68 HEC A 101 SITE 1 AC3 13 LEU A 6 LYS A 7 LYS A 9 ASN A 10 SITE 2 AC3 13 PHE A 41 LYS A 43 ALA A 46 HIS A 47 SITE 3 AC3 13 THR A 63 LYS A 64 CYS A 65 CYS A 68 SITE 4 AC3 13 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