HEADER ELECTRON TRANSPORT 23-MAY-00 1F22 TITLE A PROTON-NMR INVESTIGATION OF THE FULLY REDUCED CYTOCHROME C7 FROM TITLE 2 DESULFUROMONAS ACETOXIDANS. COMPARISON BETWEEN THE REDUCED AND THE TITLE 3 OXIDIZED FORMS. COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOCHROME C7; COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DESULFUROMONAS ACETOXIDANS; SOURCE 3 ORGANISM_TAXID: 891 KEYWDS TRIHEME, ELECTRON TRANSPORT EXPDTA SOLUTION NMR NUMMDL 35 AUTHOR M.ASSFALG,L.BANCI,I.BERTINI,M.BRUSCHI,M.T.GIUDICI-ORTICONI REVDAT 4 16-FEB-22 1F22 1 REMARK LINK REVDAT 3 24-FEB-09 1F22 1 VERSN REVDAT 2 06-SEP-05 1F22 1 JRNL REMARK LINK HETATM REVDAT 1 21-JUN-00 1F22 0 JRNL AUTH M.ASSFALG,L.BANCI,I.BERTINI,M.BRUSCHI,M.T.GIUDICI-ORTICONI JRNL TITL A PROTON-NMR INVESTIGATION OF THE FULLY REDUCED CYTOCHROME JRNL TITL 2 C7 FROM DESULFUROMONAS ACETOXIDANS. COMPARISON BETWEEN THE JRNL TITL 3 REDUCED AND THE OXIDIZED FORMS. JRNL REF EUR.J.BIOCHEM. V. 266 634 1999 JRNL REFN ISSN 0014-2956 JRNL PMID 10561607 JRNL DOI 10.1046/J.1432-1327.1999.00904.X REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DYANA 1.5 REMARK 3 AUTHORS : WUTHRICH REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1F22 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-JUN-00. REMARK 100 THE DEPOSITION ID IS D_1000011148. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 292 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 0.1 MM REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 2-3MM CYTOCHROME C7; 10MM REMARK 210 PHOSPHATE BUFFER; CATALYTIC REMARK 210 AMOUNTS OF D. VULGARIS REMARK 210 HYDROGENASE REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : AMX; AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : SIMULATED ANNEALING AND ENERGY REMARK 210 MINIMIZATION REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 35 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 35 REMARK 210 CONFORMERS, SELECTION CRITERIA : ALL CALCULATED STRUCTURES REMARK 210 SUBMITTED REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D REMARK 210 HOMONUCLEAR TECHNIQUES. 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 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 5 HIS A 30 CB - CG - CD2 ANGL. DEV. = -9.7 DEGREES REMARK 500 26 ASP A 47 CB - CG - OD2 ANGL. DEV. = -6.6 DEGREES REMARK 500 33 ASP A 40 CB - CG - OD2 ANGL. DEV. = -6.3 DEGREES 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 ASN A 12 121.94 -38.26 REMARK 500 1 ASP A 16 131.12 -37.10 REMARK 500 1 HIS A 17 -63.99 -120.60 REMARK 500 1 CYS A 26 -50.85 177.09 REMARK 500 1 ALA A 35 -33.37 -172.35 REMARK 500 1 LYS A 36 175.07 161.53 REMARK 500 1 ILE A 37 -62.20 -133.95 REMARK 500 1 ALA A 38 82.14 72.96 REMARK 500 1 LYS A 42 -83.17 -45.35 REMARK 500 1 LYS A 46 -70.18 -99.56 REMARK 500 1 ALA A 48 -89.64 -98.82 REMARK 500 1 HIS A 53 43.69 -73.98 REMARK 500 1 ASN A 57 -175.75 60.49 REMARK 500 1 THR A 60 39.78 -157.22 REMARK 500 1 LYS A 61 -73.88 55.62 REMARK 500 1 CYS A 62 -151.91 -121.39 REMARK 500 1 CYS A 65 -52.43 -133.28 REMARK 500 2 ASP A 2 -11.32 -144.48 REMARK 500 2 GLU A 7 131.35 74.53 REMARK 500 2 ASN A 12 -168.17 57.64 REMARK 500 2 HIS A 17 -71.36 -109.78 REMARK 500 2 CYS A 26 -50.59 174.76 REMARK 500 2 GLU A 31 -114.62 -85.34 REMARK 500 2 ALA A 35 44.41 38.22 REMARK 500 2 LYS A 36 125.94 59.64 REMARK 500 2 ILE A 37 -133.59 -87.85 REMARK 500 2 ALA A 38 50.36 164.28 REMARK 500 2 LYS A 46 -73.52 -80.82 REMARK 500 2 ASP A 47 86.28 -159.79 REMARK 500 2 ALA A 48 -75.52 -147.37 REMARK 500 2 THR A 51 -36.68 -161.12 REMARK 500 2 SER A 55 62.24 -158.22 REMARK 500 2 ASN A 56 -39.47 173.00 REMARK 500 2 THR A 60 -53.70 -145.52 REMARK 500 2 LYS A 61 74.23 -164.44 REMARK 500 2 CYS A 62 -133.91 55.72 REMARK 500 3 ASP A 2 54.16 -44.43 REMARK 500 3 VAL A 3 138.56 172.61 REMARK 500 3 GLU A 7 85.86 58.32 REMARK 500 3 HIS A 17 -65.53 -130.56 REMARK 500 3 CYS A 26 -43.43 172.68 REMARK 500 3 ALA A 28 -51.17 -29.09 REMARK 500 3 ALA A 35 43.79 -178.38 REMARK 500 3 LYS A 36 116.57 62.82 REMARK 500 3 ALA A 38 75.65 60.95 REMARK 500 3 HIS A 45 32.63 -92.73 REMARK 500 3 LYS A 46 -74.21 -133.47 REMARK 500 3 ALA A 48 -80.37 -153.25 REMARK 500 3 HIS A 53 45.02 -74.24 REMARK 500 3 ASN A 57 178.76 60.12 REMARK 500 REMARK 500 THIS ENTRY HAS 608 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 PRO A 59 THR A 60 2 -140.69 REMARK 500 ALA A 1 ASP A 2 3 140.59 REMARK 500 PRO A 59 THR A 60 4 -137.48 REMARK 500 ASP A 47 ALA A 48 5 -145.61 REMARK 500 ALA A 1 ASP A 2 10 -144.65 REMARK 500 ALA A 1 ASP A 2 11 140.59 REMARK 500 PRO A 59 THR A 60 13 -135.00 REMARK 500 PRO A 59 THR A 60 15 -134.02 REMARK 500 ALA A 1 ASP A 2 16 143.41 REMARK 500 LYS A 61 CYS A 62 17 144.00 REMARK 500 ALA A 1 ASP A 2 18 142.56 REMARK 500 ALA A 1 ASP A 2 20 144.88 REMARK 500 PHE A 15 ASP A 16 25 144.41 REMARK 500 PRO A 59 THR A 60 25 -141.48 REMARK 500 PRO A 59 THR A 60 30 -129.04 REMARK 500 PRO A 59 THR A 60 33 -136.16 REMARK 500 PRO A 59 THR A 60 35 -129.76 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 HIS A 30 0.09 SIDE CHAIN REMARK 500 2 TYR A 6 0.12 SIDE CHAIN REMARK 500 2 HIS A 30 0.09 SIDE CHAIN REMARK 500 4 TYR A 6 0.14 SIDE CHAIN REMARK 500 5 PHE A 15 0.10 SIDE CHAIN REMARK 500 5 HIS A 30 0.13 SIDE CHAIN REMARK 500 6 HIS A 30 0.10 SIDE CHAIN REMARK 500 7 TYR A 6 0.11 SIDE CHAIN REMARK 500 8 TYR A 6 0.11 SIDE CHAIN REMARK 500 9 HIS A 30 0.09 SIDE CHAIN REMARK 500 10 TYR A 6 0.08 SIDE CHAIN REMARK 500 10 HIS A 30 0.10 SIDE CHAIN REMARK 500 11 TYR A 6 0.10 SIDE CHAIN REMARK 500 11 HIS A 30 0.11 SIDE CHAIN REMARK 500 13 HIS A 30 0.09 SIDE CHAIN REMARK 500 14 HIS A 30 0.12 SIDE CHAIN REMARK 500 15 HIS A 30 0.11 SIDE CHAIN REMARK 500 18 TYR A 6 0.09 SIDE CHAIN REMARK 500 18 HIS A 30 0.11 SIDE CHAIN REMARK 500 19 PHE A 15 0.08 SIDE CHAIN REMARK 500 20 HIS A 30 0.12 SIDE CHAIN REMARK 500 21 TYR A 6 0.14 SIDE CHAIN REMARK 500 22 TYR A 6 0.12 SIDE CHAIN REMARK 500 23 TYR A 6 0.16 SIDE CHAIN REMARK 500 24 HIS A 30 0.12 SIDE CHAIN REMARK 500 26 TYR A 6 0.11 SIDE CHAIN REMARK 500 26 HIS A 30 0.11 SIDE CHAIN REMARK 500 28 HIS A 30 0.09 SIDE CHAIN REMARK 500 29 HIS A 30 0.10 SIDE CHAIN REMARK 500 30 TYR A 6 0.06 SIDE CHAIN REMARK 500 33 TYR A 6 0.07 SIDE CHAIN REMARK 500 34 PHE A 15 0.14 SIDE CHAIN REMARK 500 35 HIS A 30 0.09 SIDE CHAIN 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 69 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 17 NE2 REMARK 620 2 HEC A 69 NA 93.5 REMARK 620 3 HEC A 69 NB 90.7 90.2 REMARK 620 4 HEC A 69 NC 85.2 178.2 91.1 REMARK 620 5 HEC A 69 ND 89.7 88.7 178.8 90.1 REMARK 620 6 HIS A 30 NE2 172.9 93.6 89.4 87.8 90.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEC A 70 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 20 NE2 REMARK 620 2 HEC A 70 NA 91.1 REMARK 620 3 HEC A 70 NB 94.9 90.8 REMARK 620 4 HEC A 70 NC 87.6 178.6 89.7 REMARK 620 5 HEC A 70 ND 86.0 90.5 178.4 88.9 REMARK 620 6 HIS A 53 NE2 175.8 90.7 88.9 90.5 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 71 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 45 NE2 REMARK 620 2 HEC A 71 NA 91.6 REMARK 620 3 HEC A 71 NB 92.2 91.0 REMARK 620 4 HEC A 71 NC 89.9 178.5 88.7 REMARK 620 5 HEC A 71 ND 92.4 91.4 174.7 88.8 REMARK 620 6 HIS A 66 NE2 178.0 89.3 89.6 89.2 85.7 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 69 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEC A 70 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEC A 71 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1EHJ RELATED DB: PDB REMARK 900 MINIMIZED AVERAGE STRUCTURE DBREF 1F22 A 1 68 UNP P00137 CYC3_DESAC 1 68 SEQRES 1 A 68 ALA ASP VAL VAL THR TYR GLU ASN LYS LYS GLY ASN VAL SEQRES 2 A 68 THR PHE ASP HIS LYS ALA HIS ALA GLU LYS LEU GLY CYS SEQRES 3 A 68 ASP ALA CYS HIS GLU GLY THR PRO ALA LYS ILE ALA ILE SEQRES 4 A 68 ASP LYS LYS SER ALA HIS LYS ASP ALA CYS LYS THR CYS SEQRES 5 A 68 HIS LYS SER ASN ASN GLY PRO THR LYS CYS GLY GLY CYS SEQRES 6 A 68 HIS ILE LYS HET HEC A 69 75 HET HEC A 70 75 HET HEC A 71 75 HETNAM HEC HEME C FORMUL 2 HEC 3(C34 H34 FE N4 O4) HELIX 1 1 HIS A 17 GLY A 25 1 9 HELIX 2 2 ASP A 40 ASP A 47 1 8 HELIX 3 3 ALA A 48 HIS A 53 1 6 SHEET 1 A 2 VAL A 3 TYR A 6 0 SHEET 2 A 2 VAL A 13 ASP A 16 -1 N VAL A 13 O TYR A 6 LINK SG CYS A 26 CAB HEC A 69 1555 1555 1.82 LINK SG CYS A 29 CAC HEC A 69 1555 1555 1.81 LINK SG CYS A 49 CAB HEC A 70 1555 1555 1.82 LINK SG CYS A 52 CAC HEC A 70 1555 1555 1.81 LINK SG CYS A 62 CAB HEC A 71 1555 1555 1.81 LINK SG CYS A 65 CAC HEC A 71 1555 1555 1.81 LINK NE2 HIS A 17 FE HEC A 69 1555 1555 1.91 LINK NE2 HIS A 20 FE HEC A 70 1555 1555 1.99 LINK NE2 HIS A 30 FE HEC A 69 1555 1555 1.93 LINK NE2 HIS A 45 FE HEC A 71 1555 1555 1.96 LINK NE2 HIS A 53 FE HEC A 70 1555 1555 2.00 LINK NE2 HIS A 66 FE HEC A 71 1555 1555 1.90 SITE 1 AC1 13 ALA A 1 TYR A 6 HIS A 17 HIS A 20 SITE 2 AC1 13 GLY A 25 CYS A 26 CYS A 29 HIS A 30 SITE 3 AC1 13 PRO A 34 ALA A 35 LYS A 36 ILE A 37 SITE 4 AC1 13 ALA A 38 SITE 1 AC2 11 VAL A 13 PHE A 15 ASP A 16 HIS A 20 SITE 2 AC2 11 LYS A 23 LEU A 24 CYS A 49 CYS A 52 SITE 3 AC2 11 HIS A 53 ASN A 57 GLY A 64 SITE 1 AC3 15 TYR A 6 ASN A 8 LYS A 10 VAL A 13 SITE 2 AC3 15 ILE A 39 ASP A 40 LYS A 41 ALA A 44 SITE 3 AC3 15 HIS A 45 CYS A 49 HIS A 53 LYS A 61 SITE 4 AC3 15 CYS A 62 CYS A 65 HIS A 66 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