HEADER ELECTRON TRANSPORT 29-DEC-01 1IT1 TITLE SOLUTION STRUCTURES OF FERROCYTOCHROME C3 FROM DESULFOVIBRIO VULGARIS TITLE 2 MIYAZAKI F COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOCHROME C3; COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DESULFOVIBRIO VULGARIS STR. 'MIYAZAKI F'; SOURCE 3 ORGANISM_TAXID: 883; SOURCE 4 STRAIN: MIYAZAKI F KEYWDS ELECTRON TRANSFER, TETRAHEME PROTEIN, ELECTRON TRANSPORT EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR E.HARADA,Y.FUKUOKA,T.OHMURA,A.FUKUNISHI,G.KAWAI,T.FUJIWARA,H.AKUTSU REVDAT 5 27-DEC-23 1IT1 1 REMARK REVDAT 4 23-FEB-22 1IT1 1 REMARK LINK REVDAT 3 24-FEB-09 1IT1 1 VERSN REVDAT 2 07-JAN-03 1IT1 1 REMARK REVDAT 1 10-JUL-02 1IT1 0 JRNL AUTH E.HARADA,Y.FUKUOKA,T.OHMURA,A.FUKUNISHI,G.KAWAI,T.FUJIWARA, JRNL AUTH 2 H.AKUTSU JRNL TITL REDOX-COUPLED CONFORMATIONAL ALTERNATIONS IN CYTOCHROME C(3) JRNL TITL 2 FROM D. VULGARIS MIYAZAKI F ON THE BASIS OF ITS REDUCED JRNL TITL 3 SOLUTION STRUCTURE. JRNL REF J.MOL.BIOL. V. 319 767 2002 JRNL REFN ISSN 0022-2836 JRNL PMID 12054869 JRNL DOI 10.1016/S0022-2836(02)00367-4 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.8.5.1, X-PLOR 3.8.5.1 REMARK 3 AUTHORS : BRUNGER, A.T. (X-PLOR), BRUNGER, A.T. (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1IT1 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 15-JAN-02. REMARK 100 THE DEPOSITION ID IS D_1000005250. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 56MM REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : U-15N CYTOCHROME C3 IN THE FULLY REMARK 210 REDUCED STATE; 30MM SODIUM REMARK 210 PHOSPHATE BUFFER; CYTOCHROME C3 REMARK 210 IN THE FULLY REDUCED STATE; 30MM REMARK 210 SODIUM PHOSPHATE BUFFER REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 2D REMARK 210 NOESY; DQF-COSY; E-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 500 MHZ; 400 MHZ REMARK 210 SPECTROMETER MODEL : DRX; AMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 300 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL 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 SG CYS A 30 HAB HEC A 201 1.03 REMARK 500 SG CYS A 79 HAB HEC A 203 1.04 REMARK 500 SG CYS A 105 HAC HEC A 204 1.07 REMARK 500 SG CYS A 51 HAC HEC A 202 1.08 REMARK 500 SG CYS A 100 HAB HEC A 204 1.30 REMARK 500 SG CYS A 46 HAB HEC A 202 1.32 REMARK 500 O ASP A 71 HG SER A 78 1.40 REMARK 500 O LEU A 9 H PHE A 20 1.42 REMARK 500 O LYS A 29 H ASP A 32 1.43 REMARK 500 HD1 HIS A 83 O LEU A 97 1.44 REMARK 500 H MET A 11 O VAL A 18 1.44 REMARK 500 O VAL A 37 H LYS A 40 1.45 REMARK 500 O HIS A 25 H VAL A 28 1.50 REMARK 500 O LYS A 72 H THR A 74 1.55 REMARK 500 O HIS A 22 H HIS A 25 1.58 REMARK 500 O THR A 48 H GLY A 50 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 ALA A 4 137.55 -39.86 REMARK 500 1 HIS A 34 46.00 -88.20 REMARK 500 1 HIS A 35 163.83 -35.01 REMARK 500 1 ASN A 38 21.76 47.79 REMARK 500 1 ALA A 47 48.69 -89.64 REMARK 500 1 THR A 48 168.66 -45.36 REMARK 500 1 ALA A 49 63.83 -65.72 REMARK 500 1 CYS A 51 -80.67 -120.98 REMARK 500 1 LYS A 57 24.02 44.49 REMARK 500 1 ASP A 59 103.50 -51.06 REMARK 500 1 LYS A 60 31.61 -87.15 REMARK 500 1 SER A 61 -160.11 -110.96 REMARK 500 1 HIS A 67 -80.28 -39.17 REMARK 500 1 LYS A 75 -32.04 -38.86 REMARK 500 1 ALA A 89 57.28 39.70 REMARK 500 1 ALA A 91 -28.35 -38.06 REMARK 500 1 SER A 103 -148.82 -127.57 REMARK 500 2 ALA A 6 173.96 -58.42 REMARK 500 2 HIS A 34 38.88 -88.34 REMARK 500 2 HIS A 35 157.79 -31.36 REMARK 500 2 PRO A 36 99.10 -64.74 REMARK 500 2 ASN A 38 -85.59 58.39 REMARK 500 2 ALA A 47 52.97 -106.51 REMARK 500 2 THR A 48 -165.83 -51.43 REMARK 500 2 CYS A 51 -132.09 -104.04 REMARK 500 2 MET A 55 20.50 -79.47 REMARK 500 2 LYS A 57 23.36 45.53 REMARK 500 2 SER A 61 -156.49 -80.51 REMARK 500 2 HIS A 67 -72.37 -86.31 REMARK 500 2 ALA A 68 -19.37 -49.11 REMARK 500 2 LYS A 72 -167.18 -102.75 REMARK 500 2 LYS A 75 -34.47 -38.84 REMARK 500 2 ALA A 89 48.06 -95.09 REMARK 500 2 ALA A 91 -26.55 -38.87 REMARK 500 2 SER A 103 -149.51 -124.34 REMARK 500 3 ALA A 6 -179.56 -58.65 REMARK 500 3 HIS A 34 37.67 -90.26 REMARK 500 3 HIS A 35 165.18 -33.39 REMARK 500 3 ASN A 38 -84.47 174.89 REMARK 500 3 ALA A 47 52.22 -108.76 REMARK 500 3 THR A 48 -168.43 -50.22 REMARK 500 3 CYS A 51 -132.34 -106.03 REMARK 500 3 HIS A 52 49.51 -79.14 REMARK 500 3 LYS A 57 17.40 54.07 REMARK 500 3 SER A 61 -156.56 -103.93 REMARK 500 3 HIS A 67 -79.77 -39.35 REMARK 500 3 LYS A 75 -33.96 -38.87 REMARK 500 3 ALA A 89 49.28 -92.85 REMARK 500 3 ALA A 91 -27.14 -38.81 REMARK 500 3 SER A 103 -152.31 -82.15 REMARK 500 REMARK 500 THIS ENTRY HAS 306 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 201 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 22 NE2 REMARK 620 2 HEC A 201 NA 89.8 REMARK 620 3 HEC A 201 NB 90.0 89.9 REMARK 620 4 HEC A 201 NC 89.4 179.1 89.7 REMARK 620 5 HEC A 201 ND 89.3 89.3 178.9 91.1 REMARK 620 6 HIS A 34 NE2 178.8 91.2 90.6 89.6 90.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEC A 203 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 25 NE2 REMARK 620 2 HEC A 203 NA 88.5 REMARK 620 3 HEC A 203 NB 87.9 89.7 REMARK 620 4 HEC A 203 NC 88.6 177.1 89.8 REMARK 620 5 HEC A 203 ND 86.7 90.4 174.6 89.8 REMARK 620 6 HIS A 83 NE2 177.4 89.3 90.8 93.6 94.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEC A 202 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 35 NE2 REMARK 620 2 HEC A 202 NA 91.5 REMARK 620 3 HEC A 202 NB 92.2 89.6 REMARK 620 4 HEC A 202 NC 89.8 178.7 90.5 REMARK 620 5 HEC A 202 ND 87.1 89.0 178.5 90.9 REMARK 620 6 HIS A 52 NE2 176.7 89.4 91.1 89.3 89.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEC A 204 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 70 NE2 REMARK 620 2 HEC A 204 NA 90.6 REMARK 620 3 HEC A 204 NB 87.2 90.8 REMARK 620 4 HEC A 204 NC 90.3 178.8 89.9 REMARK 620 5 HEC A 204 ND 89.9 89.7 177.1 89.6 REMARK 620 6 HIS A 106 NE2 177.1 92.2 92.1 86.9 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 HEC A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEC A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEC A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEC A 204 DBREF 1IT1 A 1 107 UNP P00132 CYC3_DESVM 24 130 SEQRES 1 A 107 ALA PRO LYS ALA PRO ALA ASP GLY LEU LYS MET ASP LYS SEQRES 2 A 107 THR LYS GLN PRO VAL VAL PHE ASN HIS SER THR HIS LYS SEQRES 3 A 107 ALA VAL LYS CYS GLY ASP CYS HIS HIS PRO VAL ASN GLY SEQRES 4 A 107 LYS GLU ASP TYR GLN LYS CYS ALA THR ALA GLY CYS HIS SEQRES 5 A 107 ASP ASN MET ASP LYS LYS ASP LYS SER ALA LYS GLY TYR SEQRES 6 A 107 TYR HIS ALA MET HIS ASP LYS GLY THR LYS PHE LYS SER SEQRES 7 A 107 CYS VAL GLY CYS HIS LEU GLU THR ALA GLY ALA ASP ALA SEQRES 8 A 107 ALA LYS LYS LYS GLU LEU THR GLY CYS LYS GLY SER LYS SEQRES 9 A 107 CYS HIS SER HET HEC A 201 75 HET HEC A 202 75 HET HEC A 203 75 HET HEC A 204 75 HETNAM HEC HEME C FORMUL 2 HEC 4(C34 H34 FE N4 O4) HELIX 1 1 ASN A 21 HIS A 25 5 5 HELIX 2 2 LYS A 29 HIS A 34 1 6 HELIX 3 3 GLY A 64 ASP A 71 1 8 HELIX 4 4 SER A 78 ALA A 87 1 10 HELIX 5 5 ASP A 90 LEU A 97 1 8 SHEET 1 A 2 LEU A 9 MET A 11 0 SHEET 2 A 2 VAL A 18 PHE A 20 -1 O VAL A 18 N MET A 11 SHEET 1 B 2 PRO A 36 VAL A 37 0 SHEET 2 B 2 LYS A 40 GLU A 41 -1 O LYS A 40 N VAL A 37 LINK SG CYS A 30 CAB HEC A 201 1555 1555 1.81 LINK SG CYS A 33 CAC HEC A 201 1555 1555 1.81 LINK SG CYS A 46 CAB HEC A 202 1555 1555 1.81 LINK SG CYS A 51 CAC HEC A 202 1555 1555 1.81 LINK SG CYS A 79 CAB HEC A 203 1555 1555 1.81 LINK SG CYS A 82 CAC HEC A 203 1555 1555 1.81 LINK SG CYS A 100 CAB HEC A 204 1555 1555 1.81 LINK SG CYS A 105 CAC HEC A 204 1555 1555 1.81 LINK NE2 HIS A 22 FE HEC A 201 1555 1555 2.20 LINK NE2 HIS A 25 FE HEC A 203 1555 1555 2.23 LINK NE2 HIS A 34 FE HEC A 201 1555 1555 2.18 LINK NE2 HIS A 35 FE HEC A 202 1555 1555 2.19 LINK NE2 HIS A 52 FE HEC A 202 1555 1555 2.21 LINK NE2 HIS A 70 FE HEC A 204 1555 1555 2.19 LINK NE2 HIS A 83 FE HEC A 203 1555 1555 2.27 LINK NE2 HIS A 106 FE HEC A 204 1555 1555 2.16 SITE 1 AC1 19 PRO A 2 ALA A 4 PRO A 5 LEU A 9 SITE 2 AC1 19 LYS A 10 MET A 11 PHE A 20 HIS A 22 SITE 3 AC1 19 HIS A 25 VAL A 28 CYS A 30 CYS A 33 SITE 4 AC1 19 HIS A 34 TYR A 43 GLN A 44 LYS A 45 SITE 5 AC1 19 CYS A 46 HEC A 202 HEC A 203 SITE 1 AC2 18 CYS A 33 HIS A 34 HIS A 35 ASP A 42 SITE 2 AC2 18 GLN A 44 LYS A 45 CYS A 46 THR A 48 SITE 3 AC2 18 CYS A 51 HIS A 52 SER A 61 ALA A 62 SITE 4 AC2 18 HIS A 67 ALA A 68 THR A 74 LYS A 75 SITE 5 AC2 18 SER A 78 HEC A 201 SITE 1 AC3 16 VAL A 18 PHE A 20 THR A 24 HIS A 25 SITE 2 AC3 16 VAL A 28 CYS A 33 LYS A 77 SER A 78 SITE 3 AC3 16 CYS A 79 CYS A 82 HIS A 83 THR A 86 SITE 4 AC3 16 GLU A 96 LYS A 104 CYS A 105 HEC A 201 SITE 1 AC4 22 MET A 11 ASP A 12 LYS A 13 THR A 14 SITE 2 AC4 22 LYS A 15 GLN A 16 PRO A 17 VAL A 18 SITE 3 AC4 22 LYS A 57 TYR A 65 TYR A 66 MET A 69 SITE 4 AC4 22 HIS A 70 CYS A 79 VAL A 80 HIS A 83 SITE 5 AC4 22 LEU A 97 THR A 98 GLY A 99 CYS A 100 SITE 6 AC4 22 CYS A 105 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