HEADER ELECTRON TRANSPORT 24-FEB-95 1DVH TITLE STRUCTURE AND DYNAMICS OF FERROCYTOCHROME C553 FROM DESULFOVIBRIO TITLE 2 VULGARIS STUDIED BY NMR SPECTROSCOPY AND RESTRAINED MOLECULAR TITLE 3 DYNAMICS COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOCHROME C553; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DESULFOVIBRIO VULGARIS; SOURCE 3 ORGANISM_TAXID: 881 KEYWDS ELECTRON TRANSPORT EXPDTA SOLUTION NMR NUMMDL 36 AUTHOR M.J.BLACKLEDGE,S.MEDVEDEVA,M.PONCIN,F.GUERLESQUIN,M.BRUSCHI,D.MARION REVDAT 5 30-OCT-24 1DVH 1 REMARK REVDAT 4 03-MAR-21 1DVH 1 COMPND REMARK HET HETNAM REVDAT 4 2 1 HETSYN FORMUL LINK ATOM REVDAT 3 29-NOV-17 1DVH 1 REMARK HELIX REVDAT 2 24-FEB-09 1DVH 1 VERSN REVDAT 1 03-JUN-95 1DVH 0 JRNL AUTH M.J.BLACKLEDGE,S.MEDVEDEVA,M.PONCIN,F.GUERLESQUIN,M.BRUSCHI, JRNL AUTH 2 D.MARION JRNL TITL STRUCTURE AND DYNAMICS OF FERROCYTOCHROME C553 FROM JRNL TITL 2 DESULFOVIBRIO VULGARIS STUDIED BY NMR SPECTROSCOPY AND JRNL TITL 3 RESTRAINED MOLECULAR DYNAMICS. JRNL REF J.MOL.BIOL. V. 245 661 1995 JRNL REFN ISSN 0022-2836 JRNL PMID 7844834 JRNL DOI 10.1006/JMBI.1994.0054 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.J.BLACKLEDGE,F.GUERLESQUIN,D.MARION REMARK 1 TITL CYTOCHROME C553 FROM DESULFOVIBRIO VULGARIS IN COMPARISON TO REMARK 1 TITL 2 CLASS I CYTOCHROME FAMILY REMARK 1 REF TO BE PUBLISHED REMARK 1 REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DISCOVER REMARK 3 AUTHORS : MOLECULAR SIMULATIONS INC. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1DVH COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000172948. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : NULL REMARK 210 PH : NULL REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NULL REMARK 210 SPECTROMETER FIELD STRENGTH : NULL REMARK 210 SPECTROMETER MODEL : NULL REMARK 210 SPECTROMETER MANUFACTURER : NULL REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : NULL REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL REMARK 210 CONFORMERS, NUMBER SUBMITTED : 36 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL 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: 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 7 TYR A 75 CB - CG - CD1 ANGL. DEV. = -3.7 DEGREES REMARK 500 9 GLY A 51 C - N - CA ANGL. DEV. = 13.0 DEGREES REMARK 500 14 GLY A 3 N - CA - C ANGL. DEV. = -17.5 DEGREES REMARK 500 14 TYR A 75 CB - CG - CD1 ANGL. DEV. = -4.0 DEGREES REMARK 500 15 TYR A 75 CB - CG - CD1 ANGL. DEV. = -3.9 DEGREES REMARK 500 28 TYR A 38 CB - CG - CD2 ANGL. DEV. = -4.2 DEGREES REMARK 500 31 TYR A 38 CB - CG - CD2 ANGL. DEV. = -3.6 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 ALA A 21 86.09 -67.04 REMARK 500 1 MET A 23 -74.54 22.81 REMARK 500 1 SER A 25 55.59 131.39 REMARK 500 1 PRO A 28 112.02 -37.82 REMARK 500 1 LYS A 30 105.95 -48.37 REMARK 500 1 ASP A 66 -51.88 -22.60 REMARK 500 2 ALA A 16 -65.68 59.23 REMARK 500 2 ASP A 17 63.26 -165.04 REMARK 500 2 ALA A 22 68.31 -40.52 REMARK 500 2 MET A 23 -66.09 60.41 REMARK 500 2 SER A 25 61.50 112.00 REMARK 500 2 PRO A 28 102.13 -20.51 REMARK 500 2 LYS A 30 93.76 -62.31 REMARK 500 3 ALA A 4 -38.46 118.82 REMARK 500 3 ALA A 16 -18.85 -42.72 REMARK 500 3 ASP A 17 40.37 -153.28 REMARK 500 3 ALA A 21 85.20 -69.16 REMARK 500 3 MET A 23 -78.90 22.01 REMARK 500 3 SER A 25 59.95 119.13 REMARK 500 3 PRO A 28 106.62 -33.58 REMARK 500 3 LYS A 30 92.52 -40.23 REMARK 500 4 ALA A 16 -70.37 61.76 REMARK 500 4 ALA A 22 133.28 -39.61 REMARK 500 4 MET A 23 -77.67 19.50 REMARK 500 4 SER A 25 59.48 126.90 REMARK 500 4 LYS A 30 104.41 -44.67 REMARK 500 5 ALA A 16 -48.72 66.13 REMARK 500 5 ASP A 17 -65.10 -146.56 REMARK 500 5 ALA A 22 128.82 -33.82 REMARK 500 5 MET A 23 -77.60 20.09 REMARK 500 5 PRO A 28 109.15 -37.12 REMARK 500 5 LYS A 30 89.23 -66.21 REMARK 500 5 ASP A 46 25.20 -144.05 REMARK 500 5 SER A 48 42.59 39.20 REMARK 500 6 ALA A 4 -26.70 119.29 REMARK 500 6 ALA A 22 126.85 -33.39 REMARK 500 6 MET A 23 -83.35 27.47 REMARK 500 6 PRO A 28 111.95 -37.00 REMARK 500 6 LYS A 30 105.74 -49.59 REMARK 500 6 TYR A 75 -70.67 -64.92 REMARK 500 7 ASP A 2 94.17 -33.55 REMARK 500 7 ALA A 16 -92.83 45.99 REMARK 500 7 ASP A 17 47.71 -83.14 REMARK 500 7 MET A 23 -65.45 27.83 REMARK 500 7 SER A 25 56.83 117.14 REMARK 500 7 PRO A 28 107.01 -26.52 REMARK 500 7 ALA A 34 -59.51 178.86 REMARK 500 7 LYS A 78 40.62 -107.04 REMARK 500 8 ASP A 2 95.66 -32.50 REMARK 500 8 ALA A 16 -67.29 56.76 REMARK 500 REMARK 500 THIS ENTRY HAS 242 RAMACHANDRAN OUTLIERS. 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 TYR A 7 0.11 SIDE CHAIN REMARK 500 1 TYR A 64 0.07 SIDE CHAIN REMARK 500 1 TYR A 75 0.13 SIDE CHAIN REMARK 500 2 TYR A 7 0.10 SIDE CHAIN REMARK 500 2 TYR A 64 0.24 SIDE CHAIN REMARK 500 3 TYR A 7 0.09 SIDE CHAIN REMARK 500 3 TYR A 38 0.07 SIDE CHAIN REMARK 500 3 TYR A 49 0.08 SIDE CHAIN REMARK 500 4 TYR A 7 0.10 SIDE CHAIN REMARK 500 4 TYR A 49 0.08 SIDE CHAIN REMARK 500 5 TYR A 7 0.12 SIDE CHAIN REMARK 500 5 TYR A 38 0.08 SIDE CHAIN REMARK 500 5 TYR A 49 0.07 SIDE CHAIN REMARK 500 5 TYR A 75 0.10 SIDE CHAIN REMARK 500 6 TYR A 7 0.21 SIDE CHAIN REMARK 500 6 TYR A 38 0.08 SIDE CHAIN REMARK 500 6 TYR A 75 0.06 SIDE CHAIN REMARK 500 7 TYR A 7 0.09 SIDE CHAIN REMARK 500 7 TYR A 75 0.26 SIDE CHAIN REMARK 500 8 TYR A 7 0.15 SIDE CHAIN REMARK 500 8 TYR A 75 0.13 SIDE CHAIN REMARK 500 9 TYR A 7 0.11 SIDE CHAIN REMARK 500 9 TYR A 38 0.10 SIDE CHAIN REMARK 500 9 TYR A 44 0.11 SIDE CHAIN REMARK 500 10 TYR A 7 0.08 SIDE CHAIN REMARK 500 11 TYR A 7 0.10 SIDE CHAIN REMARK 500 11 TYR A 75 0.08 SIDE CHAIN REMARK 500 12 TYR A 38 0.08 SIDE CHAIN REMARK 500 12 TYR A 44 0.09 SIDE CHAIN REMARK 500 12 TYR A 75 0.12 SIDE CHAIN REMARK 500 13 TYR A 38 0.08 SIDE CHAIN REMARK 500 13 TYR A 49 0.08 SIDE CHAIN REMARK 500 13 TYR A 64 0.11 SIDE CHAIN REMARK 500 13 TYR A 75 0.10 SIDE CHAIN REMARK 500 14 TYR A 7 0.11 SIDE CHAIN REMARK 500 14 TYR A 49 0.08 SIDE CHAIN REMARK 500 14 TYR A 64 0.16 SIDE CHAIN REMARK 500 14 TYR A 75 0.27 SIDE CHAIN REMARK 500 15 TYR A 75 0.26 SIDE CHAIN REMARK 500 16 TYR A 7 0.13 SIDE CHAIN REMARK 500 16 TYR A 38 0.07 SIDE CHAIN REMARK 500 16 TYR A 75 0.12 SIDE CHAIN REMARK 500 17 TYR A 7 0.11 SIDE CHAIN REMARK 500 17 TYR A 44 0.08 SIDE CHAIN REMARK 500 17 TYR A 75 0.09 SIDE CHAIN REMARK 500 18 TYR A 64 0.23 SIDE CHAIN REMARK 500 18 TYR A 75 0.09 SIDE CHAIN REMARK 500 19 TYR A 7 0.09 SIDE CHAIN REMARK 500 19 TYR A 64 0.08 SIDE CHAIN REMARK 500 19 TYR A 75 0.06 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 86 PLANE DEVIATIONS. 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 80 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 14 NE2 REMARK 620 2 HEC A 80 NA 92.2 REMARK 620 3 HEC A 80 NB 103.6 89.0 REMARK 620 4 HEC A 80 NC 90.1 177.7 90.4 REMARK 620 5 HEC A 80 ND 86.0 91.3 170.3 88.9 REMARK 620 6 MET A 57 SD 174.3 83.3 79.8 94.5 90.6 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 80 DBREF 1DVH A 1 79 UNP P04032 CY553_DESVH 25 103 SEQRES 1 A 79 ALA ASP GLY ALA ALA LEU TYR LYS SER CYS ILE GLY CYS SEQRES 2 A 79 HIS GLY ALA ASP GLY SER LYS ALA ALA MET GLY SER ALA SEQRES 3 A 79 LYS PRO VAL LYS GLY GLN GLY ALA GLU GLU LEU TYR LYS SEQRES 4 A 79 LYS MET LYS GLY TYR ALA ASP GLY SER TYR GLY GLY GLU SEQRES 5 A 79 ARG LYS ALA MET MET THR ASN ALA VAL LYS LYS TYR SER SEQRES 6 A 79 ASP GLU GLU LEU LYS ALA LEU ALA ASP TYR MET SER LYS SEQRES 7 A 79 LEU HET HEC A 80 43 HETNAM HEC HEME C FORMUL 2 HEC C34 H34 FE N4 O4 HELIX 1 N ASP A 2 CYS A 10 1 9 HELIX 2 30 ALA A 34 ALA A 45 1 12 HELIX 3 50 ALA A 55 VAL A 61 1 7 HELIX 4 C ASP A 66 LEU A 79 1 14 LINK SG CYS A 10 CAB HEC A 80 1555 1555 1.81 LINK SG CYS A 13 CAC HEC A 80 1555 1555 1.83 LINK NE2 HIS A 14 FE HEC A 80 1555 1555 2.02 LINK SD MET A 57 FE HEC A 80 1555 1555 2.35 SITE 1 AC1 20 TYR A 7 CYS A 10 CYS A 13 HIS A 14 SITE 2 AC1 20 ALA A 22 MET A 23 ALA A 26 LYS A 27 SITE 3 AC1 20 VAL A 29 GLN A 32 LYS A 40 TYR A 44 SITE 4 AC1 20 TYR A 49 GLY A 51 GLU A 52 ARG A 53 SITE 5 AC1 20 MET A 57 ALA A 60 TYR A 64 MET A 76 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