HEADER ELECTRON TRANSPORT 12-OCT-12 2LZZ TITLE SOLUTION STRUCTURE OF A MUTANT OF THE TRIHEME CYTOCHROME PPCA FROM TITLE 2 GEOBACTER SULFURREDUCENS SHEDS LIGHT ON THE ROLE OF THE CONSERVED TITLE 3 AROMATIC RESIDUE F15 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOCHROME C, 3 HEME-BINDING SITES; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GEOBACTER SULFURREDUCENS; SOURCE 3 ORGANISM_TAXID: 663917; SOURCE 4 STRAIN: DL-1 / KN400; SOURCE 5 GENE: GSU0612, KN400_0591, PPCA; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PCK32 KEYWDS GEOBACTER, TRIHEME CYTOCHROME, SITE-DIRECTED MUTAGENESIS, ELECTRON KEYWDS 2 TRANSPORT EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR J.M.DANTAS,L.MORGADO,D.L.TURNER,C.A.SALGUEIRO REVDAT 2 13-MAR-13 2LZZ 1 JRNL REVDAT 1 30-JAN-13 2LZZ 0 JRNL AUTH J.M.DANTAS,L.MORGADO,P.R.POKKULURI,D.L.TURNER,C.A.SALGUEIRO JRNL TITL SOLUTION STRUCTURE OF A MUTANT OF THE TRIHEME CYTOCHROME JRNL TITL 2 PPCA FROM GEOBACTER SULFURREDUCENS SHEDS LIGHT ON THE ROLE JRNL TITL 3 OF THE CONSERVED AROMATIC RESIDUE F15. JRNL REF BIOCHIM.BIOPHYS.ACTA V.1827 484 2013 JRNL REFN ISSN 0006-3002 JRNL PMID 23313804 JRNL DOI 10.1016/J.BBABIO.2012.12.008 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PARADYANA REMARK 3 AUTHORS : TURNER, D. L. BRENNAN, L. CHAMBERLIN, S. G. LOURO, REMARK 3 R. O. XAVIER, A. V. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2LZZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-OCT-12. REMARK 100 THE RCSB ID CODE IS RCSB103035. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298; 298 REMARK 210 PH : 7.1; 7.1 REMARK 210 IONIC STRENGTH : 100; 45 REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 1 MM F15L POLYPEPTIDE, 3 MM REMARK 210 PROTOPORPHYRIN IX CONTAINING FE, REMARK 210 45 MM SODIUM PHOSPHATE, 0.04 % REMARK 210 SODIUM AZIDE, 93% H2O/7% D2O; 0.4 REMARK 210 MM [U-100% 15N] F15L POLYPEPTIDE, REMARK 210 3 MM PROTOPORPHYRIN IX CONTAINING REMARK 210 FE, 45 MM SODIUM PHOSPHATE, 0.04 REMARK 210 % SODIUM AZIDE, 93% H2O/7% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-1H TOCSY; REMARK 210 2D 1H-1H COSY; 2D 1H-1H NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 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, CING 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 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 LYS A 52 H GLU A 56 1.39 REMARK 500 O PRO A 16 H HIS A 20 1.49 REMARK 500 O CYS A 54 H MET A 58 1.51 REMARK 500 O MET A 45 H GLY A 48 1.59 REMARK 500 O LEU A 15 H HIS A 17 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 3 117.18 -38.15 REMARK 500 1 ALA A 8 103.73 174.84 REMARK 500 1 ASP A 12 151.39 -43.26 REMARK 500 1 PRO A 16 64.86 -59.03 REMARK 500 1 LYS A 28 -49.23 -136.98 REMARK 500 1 GLU A 32 -98.89 -77.00 REMARK 500 1 LYS A 33 -30.16 -39.10 REMARK 500 1 LYS A 43 -78.61 -79.95 REMARK 500 1 LYS A 49 83.43 -58.72 REMARK 500 1 CYS A 51 -55.31 -139.69 REMARK 500 1 LYS A 59 48.31 79.01 REMARK 500 1 LYS A 60 -44.48 -130.93 REMARK 500 1 THR A 63 29.52 -140.03 REMARK 500 1 CYS A 68 -62.02 -133.41 REMARK 500 2 ASP A 3 121.81 -39.12 REMARK 500 2 ALA A 8 103.93 -174.21 REMARK 500 2 ASP A 12 156.37 -46.58 REMARK 500 2 ASP A 26 94.09 -168.69 REMARK 500 2 LYS A 28 -63.67 -134.79 REMARK 500 2 GLU A 32 -100.75 -68.89 REMARK 500 2 LYS A 33 -30.61 -38.57 REMARK 500 2 LYS A 43 -82.72 -161.06 REMARK 500 2 LYS A 49 85.53 -56.98 REMARK 500 2 CYS A 51 -57.04 -142.66 REMARK 500 2 LYS A 59 49.01 79.57 REMARK 500 2 LYS A 60 -45.63 -134.14 REMARK 500 2 THR A 63 31.41 -140.41 REMARK 500 2 CYS A 68 -63.53 -135.47 REMARK 500 3 ASP A 3 114.41 -39.63 REMARK 500 3 ALA A 8 107.51 -167.32 REMARK 500 3 PRO A 16 65.15 -59.23 REMARK 500 3 LYS A 28 -47.14 -140.20 REMARK 500 3 GLU A 32 -100.75 -68.58 REMARK 500 3 LYS A 33 -29.76 -39.37 REMARK 500 3 LYS A 43 -79.73 -166.77 REMARK 500 3 LYS A 49 83.57 -59.40 REMARK 500 3 CYS A 51 -55.43 -137.89 REMARK 500 3 LYS A 59 48.43 78.26 REMARK 500 3 LYS A 60 -44.88 -130.95 REMARK 500 3 CYS A 68 -61.21 -131.19 REMARK 500 4 ASP A 3 109.48 -41.08 REMARK 500 4 ALA A 8 108.57 -164.02 REMARK 500 4 ASP A 12 154.61 -43.10 REMARK 500 4 PRO A 16 64.53 -58.70 REMARK 500 4 PRO A 25 49.84 -75.56 REMARK 500 4 ASP A 26 84.79 -168.28 REMARK 500 4 LYS A 28 -51.91 -142.61 REMARK 500 4 GLU A 32 -100.85 -71.93 REMARK 500 4 LYS A 33 -31.52 -37.74 REMARK 500 4 LYS A 43 -80.30 -157.65 REMARK 500 REMARK 500 THIS ENTRY HAS 259 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 1 HEM A 103 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 69 NE2 REMARK 620 2 HEM A 103 NA 92.0 REMARK 620 3 HEM A 103 NB 94.8 89.3 REMARK 620 4 HEM A 103 NC 95.8 171.3 93.9 REMARK 620 5 HEM A 103 ND 85.9 86.9 176.2 89.7 REMARK 620 6 HIS A 47 NE2 175.0 87.0 90.2 84.9 89.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 1 HEM A 102 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 55 NE2 REMARK 620 2 HEM A 102 NA 90.6 REMARK 620 3 HEM A 102 NB 86.0 85.5 REMARK 620 4 HEM A 102 NC 93.8 173.7 90.3 REMARK 620 5 HEM A 102 ND 96.0 90.2 175.3 93.9 REMARK 620 6 HIS A 20 NE2 171.2 84.5 86.4 90.6 91.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 1 HEM A 101 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 31 NE2 REMARK 620 2 HEM A 101 NA 85.9 REMARK 620 3 HEM A 101 NB 92.5 86.1 REMARK 620 4 HEM A 101 NC 98.3 175.2 96.1 REMARK 620 5 HEM A 101 ND 88.0 85.1 171.1 92.6 REMARK 620 6 HIS A 17 NE2 169.8 84.3 89.5 91.5 88.5 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 HEM A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM A 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM A 103 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 18787 RELATED DB: BMRB DBREF 2LZZ A 1 71 UNP D7AFU0 D7AFU0_GEOSK 21 91 SEQADV 2LZZ LEU A 15 UNP D7AFU0 PHE 35 ENGINEERED MUTATION SEQRES 1 A 71 ALA ASP ASP ILE VAL LEU LYS ALA LYS ASN GLY ASP VAL SEQRES 2 A 71 LYS LEU 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 HEM A 101 43 HET HEM A 102 43 HET HEM A 103 43 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETSYN HEM HEME FORMUL 2 HEM 3(C34 H32 FE N4 O4) HELIX 1 1 PRO A 16 VAL A 24 1 9 HELIX 2 2 GLY A 42 HIS A 47 1 6 HELIX 3 3 CYS A 51 LYS A 59 1 9 HELIX 4 4 LYS A 64 CYS A 68 5 5 LINK NE2 HIS A 69 FE HEM A 103 1555 1555 1.84 LINK NE2 HIS A 55 FE HEM A 102 1555 1555 1.87 LINK NE2 HIS A 31 FE HEM A 101 1555 1555 1.88 LINK NE2 HIS A 47 FE HEM A 103 1555 1555 1.99 LINK NE2 HIS A 20 FE HEM A 102 1555 1555 1.99 LINK NE2 HIS A 17 FE HEM A 101 1555 1555 1.99 LINK CAB HEM A 101 SG CYS A 27 1555 1555 1.85 LINK CAC HEM A 101 SG CYS A 30 1555 1555 1.81 LINK CAB HEM A 102 SG CYS A 51 1555 1555 1.82 LINK CAC HEM A 102 SG CYS A 54 1555 1555 1.81 LINK CAB HEM A 103 SG CYS A 65 1555 1555 1.86 LINK CAC HEM A 103 SG CYS A 68 1555 1555 1.81 SITE 1 AC1 11 LEU A 6 HIS A 17 HIS A 20 GLN A 21 SITE 2 AC1 11 VAL A 24 CYS A 27 CYS A 30 HIS A 31 SITE 3 AC1 11 GLY A 36 PHE A 41 HEM A 102 SITE 1 AC2 16 VAL A 13 LYS A 14 LEU A 15 PRO A 16 SITE 2 AC2 16 HIS A 20 ALA A 23 LYS A 29 CYS A 30 SITE 3 AC2 16 GLY A 50 CYS A 51 CYS A 54 HIS A 55 SITE 4 AC2 16 LYS A 60 GLY A 61 PRO A 62 HEM A 101 SITE 1 AC3 15 LEU A 6 LYS A 7 LYS A 9 ASN A 10 SITE 2 AC3 15 PHE A 41 GLY A 42 LYS A 43 ALA A 46 SITE 3 AC3 15 HIS A 47 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