HEADER ELECTRON TRANSPORT 05-AUG-09 2KMY TITLE NMR SOLUTION STRUCTURES OF FULLY OXIDISED CYTOCHROME C3 FROM TITLE 2 DESULFOVIBRIO DESULFURICANS ATCC 27774 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOCHROME C3; COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DESULFOVIBRIO DESULFURICANS; SOURCE 3 ORGANISM_TAXID: 876; SOURCE 4 STRAIN: ATCC 27774; SOURCE 5 OTHER_DETAILS: FULLY OXIDIZED PROTEIN SAMPLE KEYWDS DESULFOVIBRIO DESULFURICANS, ATCC 27774, MULTIHAEM CYTOCHROME, KEYWDS 2 DIPOLAR SHIFTS, FULLY OXIDISED, ELECTRON TRANSPORT EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR D.L.TURNER,V.B.PAIXAO,H.VIS REVDAT 3 02-OCT-19 2KMY 1 COMPND REMARK HET HETNAM REVDAT 3 2 1 HETSYN FORMUL LINK SITE REVDAT 3 3 1 ATOM REVDAT 2 14-AUG-13 2KMY 1 JRNL VERSN REVDAT 1 11-AUG-10 2KMY 0 JRNL AUTH V.B.PAIXAO,H.VIS,D.L.TURNER JRNL TITL REDOX LINKED CONFORMATIONAL CHANGES IN CYTOCHROME C3 FROM JRNL TITL 2 DESULFOVIBRIO DESULFURICANS ATCC 27774 JRNL REF BIOCHEMISTRY V. 49 9620 2010 JRNL REFN ISSN 0006-2960 JRNL PMID 20886839 JRNL DOI 10.1021/BI101237W REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR, PARADYANA REMARK 3 AUTHORS : BRUKER BIOSPIN (XWINNMR), (INDYANA) TURNER ET AL. REMARK 3 (PARADYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2KMY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-AUG-09. REMARK 100 THE DEPOSITION ID IS D_1000101320. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 4.2 REMARK 210 IONIC STRENGTH : 0,1 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.8-2.0 MM CYTOCHROME C3-1, 90% REMARK 210 H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D DQF-COSY; 2D 1H-1H TOCSY; 2D REMARK 210 1H-1H NOESY 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 : XEASY, PARADYANA, MOLMOL, REMARK 210 PROCHECKNMR REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS, REMARK 210 SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 600 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (RES=RESIDUE NAME; REMARK 470 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 470 MODELS 1-20 REMARK 470 RES CSSEQI ATOMS REMARK 470 ALA A 1 N 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 51 H ASP A 53 1.59 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 PRO A 2 174.10 -46.76 REMARK 500 1 ASP A 6 -65.28 -102.02 REMARK 500 1 VAL A 11 56.71 -107.92 REMARK 500 1 GLN A 15 25.88 -158.36 REMARK 500 1 HIS A 25 43.13 -100.68 REMARK 500 1 TYR A 43 34.35 -160.68 REMARK 500 1 SER A 49 114.10 -39.10 REMARK 500 1 CYS A 51 -142.53 -85.89 REMARK 500 1 HIS A 52 58.83 -66.22 REMARK 500 1 THR A 56 -60.37 -98.41 REMARK 500 1 VAL A 67 46.06 -109.82 REMARK 500 1 VAL A 68 -49.34 -161.79 REMARK 500 1 LEU A 97 50.25 -103.99 REMARK 500 1 THR A 98 -27.04 161.99 REMARK 500 1 CYS A 105 -70.70 -93.86 REMARK 500 2 PRO A 2 168.90 -49.00 REMARK 500 2 ASP A 6 -65.14 -97.52 REMARK 500 2 VAL A 11 64.48 -104.77 REMARK 500 2 GLN A 15 29.45 -154.33 REMARK 500 2 HIS A 25 45.02 -96.10 REMARK 500 2 GLU A 29 165.24 -42.29 REMARK 500 2 TYR A 43 33.88 -160.86 REMARK 500 2 SER A 49 119.38 -38.10 REMARK 500 2 CYS A 51 -143.35 -84.27 REMARK 500 2 HIS A 52 57.62 -65.71 REMARK 500 2 THR A 56 -63.49 -98.88 REMARK 500 2 ALA A 57 155.48 -44.52 REMARK 500 2 VAL A 67 40.84 -107.65 REMARK 500 2 VAL A 68 -50.75 -154.09 REMARK 500 2 CYS A 79 -72.57 -70.96 REMARK 500 2 LEU A 80 -31.40 -39.90 REMARK 500 2 LEU A 97 45.54 -101.33 REMARK 500 2 THR A 98 -28.94 165.15 REMARK 500 2 CYS A 105 -70.19 -93.67 REMARK 500 3 PRO A 2 170.76 -50.52 REMARK 500 3 VAL A 11 63.86 -114.63 REMARK 500 3 GLN A 15 27.11 -161.45 REMARK 500 3 ALA A 23 -71.43 -42.24 REMARK 500 3 HIS A 25 47.22 -95.64 REMARK 500 3 GLU A 29 165.10 -47.97 REMARK 500 3 TYR A 43 33.16 -159.17 REMARK 500 3 SER A 49 112.73 -37.53 REMARK 500 3 CYS A 51 -142.55 -81.90 REMARK 500 3 HIS A 52 57.33 -66.41 REMARK 500 3 VAL A 68 -47.85 -158.11 REMARK 500 3 HIS A 76 -169.96 -118.45 REMARK 500 3 LEU A 97 44.55 -99.54 REMARK 500 3 THR A 98 -27.36 162.53 REMARK 500 3 CYS A 105 -72.95 -100.14 REMARK 500 4 PRO A 2 171.05 -51.74 REMARK 500 REMARK 500 THIS ENTRY HAS 376 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 233 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 22 NE2 REMARK 620 2 HEC A 233 NA 87.3 REMARK 620 3 HEC A 233 NB 92.2 91.3 REMARK 620 4 HEC A 233 NC 90.2 172.7 95.7 REMARK 620 5 HEC A 233 ND 85.5 85.0 175.7 88.0 REMARK 620 6 HIS A 34 NE2 172.2 89.1 94.7 92.6 87.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEC A 282 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 25 NE2 REMARK 620 2 HEC A 282 NA 85.4 REMARK 620 3 HEC A 282 NB 87.9 85.1 REMARK 620 4 HEC A 282 NC 92.9 177.7 93.3 REMARK 620 5 HEC A 282 ND 89.7 86.7 171.6 94.8 REMARK 620 6 HIS A 83 NE2 171.8 86.7 89.4 95.0 91.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEC A 251 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 35 NE2 REMARK 620 2 HEC A 251 NA 88.6 REMARK 620 3 HEC A 251 NB 91.3 92.0 REMARK 620 4 HEC A 251 NC 87.5 173.5 93.2 REMARK 620 5 HEC A 251 ND 87.2 87.8 178.5 86.8 REMARK 620 6 HIS A 52 NE2 174.0 91.8 94.7 91.5 86.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEC A 305 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 69 NE2 REMARK 620 2 HEC A 305 NA 87.9 REMARK 620 3 HEC A 305 NB 89.1 89.4 REMARK 620 4 HEC A 305 NC 88.8 176.5 91.8 REMARK 620 5 HEC A 305 ND 87.9 88.0 176.2 90.6 REMARK 620 6 HIS A 106 NE2 178.4 91.2 92.2 92.0 90.7 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 HEM A 233 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM A 251 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM A 282 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM A 305 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 16443 RELATED DB: BMRB REMARK 900 RELATED ID: 2KSU RELATED DB: PDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 RESIDUE 71 (UNP RESIDUE NUMBER 92) IN DATABASE UNIPROTKB/TREMBL REMARK 999 Q9L915 (Q9L915_DESDE) IS LYS IN CURRENT VERSION (32), BUT WAS ARG REMARK 999 WHEN FIRST RELEASED ON 2000-10-01. DBREF 2KMY A 1 107 UNP Q9L915 Q9L915_DESDE 22 128 SEQADV 2KMY ARG A 71 UNP Q9L915 LYS 92 SEE REMARK 999 SEQRES 1 A 107 ALA PRO ALA VAL PRO ASP LYS PRO VAL GLU VAL LYS GLY SEQRES 2 A 107 SER GLN LYS THR VAL MET PHE PRO HIS ALA PRO HIS GLU SEQRES 3 A 107 LYS VAL GLU CYS VAL THR CYS HIS HIS LEU VAL ASP GLY SEQRES 4 A 107 LYS GLU SER TYR ALA LYS CYS GLY SER SER GLY CYS HIS SEQRES 5 A 107 ASP ASP LEU THR ALA LYS LYS GLY GLU LYS SER LEU TYR SEQRES 6 A 107 TYR VAL VAL HIS ALA ARG GLY GLU LEU LYS HIS THR SER SEQRES 7 A 107 CYS LEU ALA CYS HIS SER LYS VAL VAL ALA GLU LYS PRO SEQRES 8 A 107 GLU LEU LYS LYS ASP LEU THR GLY CYS ALA LYS SER LYS SEQRES 9 A 107 CYS HIS PRO HET HEC A 233 43 HET HEC A 251 43 HET HEC A 282 43 HET HEC A 305 43 HETNAM HEC HEME C FORMUL 2 HEC 4(C34 H34 FE N4 O4) HELIX 1 1 HIS A 22 GLU A 26 5 5 HELIX 2 2 GLU A 29 HIS A 34 1 6 HELIX 3 3 SER A 78 ALA A 88 1 11 SHEET 1 A 2 VAL A 9 GLU A 10 0 SHEET 2 A 2 MET A 19 PHE A 20 -1 O PHE A 20 N VAL A 9 LINK NE2 HIS A 22 FE HEC A 233 1555 1555 2.00 LINK NE2 HIS A 25 FE HEC A 282 1555 1555 2.00 LINK NE2 HIS A 34 FE HEC A 233 1555 1555 1.92 LINK NE2 HIS A 35 FE HEC A 251 1555 1555 2.00 LINK NE2 HIS A 52 FE HEC A 251 1555 1555 1.90 LINK NE2 HIS A 69 FE HEC A 305 1555 1555 2.00 LINK NE2 HIS A 83 FE HEC A 282 1555 1555 1.94 LINK NE2 HIS A 106 FE HEC A 305 1555 1555 1.89 LINK SG CYS A 30 CAB HEC A 233 1555 1555 1.87 LINK SG CYS A 33 CAC HEC A 233 1555 1555 1.81 LINK SG CYS A 46 CAB HEC A 251 1555 1555 1.91 LINK SG CYS A 51 CAC HEC A 251 1555 1555 1.81 LINK SG CYS A 79 CAB HEC A 282 1555 1555 1.88 LINK SG CYS A 82 CAC HEC A 282 1555 1555 1.81 LINK SG CYS A 100 CAB HEC A 305 1555 1555 1.92 LINK SG CYS A 105 CAC HEC A 305 1555 1555 1.81 SITE 1 AC1 14 PRO A 5 GLU A 10 VAL A 11 PHE A 20 SITE 2 AC1 14 HIS A 22 HIS A 25 VAL A 28 GLU A 29 SITE 3 AC1 14 CYS A 30 CYS A 33 HIS A 34 LYS A 45 SITE 4 AC1 14 CYS A 46 HEC A 282 SITE 1 AC2 12 HIS A 34 HIS A 35 VAL A 37 LYS A 45 SITE 2 AC2 12 CYS A 46 CYS A 51 HIS A 52 GLU A 61 SITE 3 AC2 12 VAL A 67 LEU A 74 LYS A 75 HIS A 76 SITE 1 AC3 11 PHE A 20 PRO A 21 HIS A 25 THR A 77 SITE 2 AC3 11 SER A 78 CYS A 79 CYS A 82 HIS A 83 SITE 3 AC3 11 LEU A 97 LYS A 104 HEC A 233 SITE 1 AC4 13 GLY A 13 SER A 14 LEU A 55 LEU A 64 SITE 2 AC4 13 TYR A 65 VAL A 68 HIS A 69 LEU A 80 SITE 3 AC4 13 HIS A 83 THR A 98 CYS A 100 CYS A 105 SITE 4 AC4 13 HIS A 106 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