Header list of 2dvh.pdb file
Complete list - v 3 2 Bytes
HEADER ELECTRON TRANSPORT 25-MAR-98 2DVH TITLE THE Y64A MUTANT OF CYTOCHROME C553 FROM DESULFOVIBRIO VULGARIS TITLE 2 HILDENBOROUGH, NMR, 39 STRUCTURES COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOCHROME C-553; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DESULFOVIBRIO VULGARIS SUBSP. VULGARIS STR. SOURCE 3 HILDENBOROUGH; SOURCE 4 ORGANISM_TAXID: 882; SOURCE 5 STRAIN: HILDENBOROUGH / ATCC 29579 / NCIMB 8303; SOURCE 6 CELLULAR_LOCATION: PERIPLASM; SOURCE 7 GENE: M13CYF; SOURCE 8 EXPRESSION_SYSTEM: DESULFOVIBRIO DESULFURICANS; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 876; SOURCE 10 EXPRESSION_SYSTEM_STRAIN: G200; SOURCE 11 EXPRESSION_SYSTEM_CELLULAR_LOCATION: PERIPLASM; SOURCE 12 EXPRESSION_SYSTEM_PLASMID: PRC41/TYR64ALA; SOURCE 13 EXPRESSION_SYSTEM_GENE: CYF KEYWDS ELECTRON TRANSPORT, CYTOCHROME C, HEME EXPDTA SOLUTION NMR NUMMDL 39 AUTHOR C.SEBBAN-KREUZER,M.J.BLACKLEDGE,A.DOLLA,D.MARION,F.GUERLESQUIN REVDAT 4 03-NOV-21 2DVH 1 REMARK SEQADV LINK REVDAT 3 29-NOV-17 2DVH 1 REMARK HELIX REVDAT 2 24-FEB-09 2DVH 1 VERSN REVDAT 1 17-JUN-98 2DVH 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 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER REMARK 3 AUTHORS : BIOSYM REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2DVH 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_1000178017. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 310 REMARK 210 PH : 5.9 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY; HOHAHA REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AMX600 REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : MSI DISCOVER DISCOVER REMARK 210 METHOD USED : SIMULATED ANNEALING AND REMARK 210 RESTRAINED MOLECULAR DYNAMICS REMARK 210 ENERGY REFINEMENT REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 40 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 39 REMARK 210 CONFORMERS, SELECTION CRITERIA : LEAST RESTRAINT VIOLATION 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 14 ARG A 53 NE - CZ - NH2 ANGL. DEV. = -3.4 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 16 -72.98 -64.37 REMARK 500 1 SER A 19 -4.57 -141.06 REMARK 500 1 ALA A 22 -139.38 -85.40 REMARK 500 1 LYS A 30 92.80 -20.08 REMARK 500 1 ASP A 66 -55.36 -157.67 REMARK 500 2 ASP A 2 -149.86 60.36 REMARK 500 2 LYS A 20 45.40 -78.70 REMARK 500 2 ALA A 21 -113.04 53.62 REMARK 500 2 ALA A 22 -159.32 -161.49 REMARK 500 2 LYS A 30 -96.91 39.12 REMARK 500 2 GLU A 52 -76.59 -60.40 REMARK 500 2 SER A 77 30.73 -73.93 REMARK 500 2 LYS A 78 34.66 -153.64 REMARK 500 3 ALA A 16 46.13 -76.72 REMARK 500 3 ASP A 17 -47.13 179.93 REMARK 500 3 LYS A 20 31.66 -66.71 REMARK 500 3 ALA A 21 21.93 45.57 REMARK 500 3 ALA A 22 -123.67 33.88 REMARK 500 3 MET A 23 79.68 -68.37 REMARK 500 3 SER A 25 46.30 -151.13 REMARK 500 3 LYS A 30 99.57 -37.95 REMARK 500 3 GLU A 52 -87.79 -77.78 REMARK 500 4 ASP A 2 84.09 -39.84 REMARK 500 4 ALA A 16 -70.19 64.67 REMARK 500 4 ASP A 17 31.02 -80.36 REMARK 500 4 ALA A 22 -131.11 -88.31 REMARK 500 4 LYS A 30 87.95 -29.88 REMARK 500 4 SER A 48 -71.40 -100.62 REMARK 500 4 LYS A 78 41.87 -106.74 REMARK 500 5 ASP A 2 -101.63 -155.33 REMARK 500 5 ASP A 17 36.93 -90.40 REMARK 500 5 ALA A 21 41.21 -76.50 REMARK 500 5 ALA A 22 -142.34 44.46 REMARK 500 5 LYS A 30 89.28 -27.80 REMARK 500 5 GLU A 52 -118.41 42.30 REMARK 500 6 ILE A 11 151.18 -47.52 REMARK 500 6 ALA A 16 -70.15 -111.97 REMARK 500 6 ASP A 17 49.91 -84.71 REMARK 500 6 ALA A 21 41.93 -80.24 REMARK 500 6 ALA A 22 -114.88 -27.12 REMARK 500 6 MET A 23 91.99 -61.69 REMARK 500 6 LYS A 30 99.28 -36.45 REMARK 500 6 SER A 48 -65.40 -93.33 REMARK 500 6 GLU A 52 -114.47 34.06 REMARK 500 7 ALA A 22 -122.82 -79.66 REMARK 500 7 MET A 23 83.42 -69.10 REMARK 500 7 SER A 25 57.81 -69.34 REMARK 500 8 ASP A 2 39.37 34.57 REMARK 500 8 SER A 25 -28.14 -163.73 REMARK 500 8 GLU A 52 -107.20 46.95 REMARK 500 REMARK 500 THIS ENTRY HAS 281 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 0.08 SIDE CHAIN REMARK 500 1 TYR A 75 0.07 SIDE CHAIN REMARK 500 2 TYR A 7 0.08 SIDE CHAIN REMARK 500 3 TYR A 7 0.11 SIDE CHAIN REMARK 500 5 TYR A 7 0.10 SIDE CHAIN REMARK 500 7 TYR A 7 0.12 SIDE CHAIN REMARK 500 8 TYR A 7 0.12 SIDE CHAIN REMARK 500 8 TYR A 38 0.06 SIDE CHAIN REMARK 500 8 TYR A 44 0.10 SIDE CHAIN REMARK 500 9 TYR A 49 0.07 SIDE CHAIN REMARK 500 10 TYR A 7 0.07 SIDE CHAIN REMARK 500 10 TYR A 49 0.07 SIDE CHAIN REMARK 500 11 TYR A 7 0.08 SIDE CHAIN REMARK 500 14 TYR A 7 0.08 SIDE CHAIN REMARK 500 14 TYR A 44 0.08 SIDE CHAIN REMARK 500 14 ARG A 53 0.08 SIDE CHAIN REMARK 500 15 TYR A 7 0.11 SIDE CHAIN REMARK 500 16 TYR A 7 0.09 SIDE CHAIN REMARK 500 17 TYR A 44 0.07 SIDE CHAIN REMARK 500 19 TYR A 7 0.10 SIDE CHAIN REMARK 500 20 TYR A 7 0.11 SIDE CHAIN REMARK 500 20 TYR A 75 0.08 SIDE CHAIN REMARK 500 22 TYR A 7 0.13 SIDE CHAIN REMARK 500 22 TYR A 75 0.06 SIDE CHAIN REMARK 500 23 TYR A 7 0.07 SIDE CHAIN REMARK 500 23 TYR A 38 0.09 SIDE CHAIN REMARK 500 24 TYR A 7 0.09 SIDE CHAIN REMARK 500 25 TYR A 38 0.06 SIDE CHAIN REMARK 500 28 TYR A 7 0.09 SIDE CHAIN REMARK 500 29 TYR A 44 0.10 SIDE CHAIN REMARK 500 30 TYR A 7 0.10 SIDE CHAIN REMARK 500 30 TYR A 44 0.11 SIDE CHAIN REMARK 500 30 TYR A 49 0.07 SIDE CHAIN REMARK 500 31 TYR A 7 0.08 SIDE CHAIN REMARK 500 31 TYR A 38 0.08 SIDE CHAIN REMARK 500 31 TYR A 44 0.10 SIDE CHAIN REMARK 500 31 ARG A 53 0.15 SIDE CHAIN REMARK 500 32 TYR A 44 0.14 SIDE CHAIN REMARK 500 32 TYR A 49 0.18 SIDE CHAIN REMARK 500 33 TYR A 7 0.10 SIDE CHAIN REMARK 500 33 TYR A 44 0.17 SIDE CHAIN REMARK 500 33 TYR A 49 0.15 SIDE CHAIN REMARK 500 34 TYR A 7 0.12 SIDE CHAIN REMARK 500 35 TYR A 44 0.13 SIDE CHAIN REMARK 500 37 TYR A 7 0.10 SIDE CHAIN REMARK 500 39 TYR A 7 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 80 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 14 NE2 REMARK 620 2 HEC A 80 NA 93.7 REMARK 620 3 HEC A 80 NB 92.2 88.7 REMARK 620 4 HEC A 80 NC 86.3 179.7 91.1 REMARK 620 5 HEC A 80 ND 93.1 89.2 174.3 91.0 REMARK 620 6 MET A 57 SD 173.6 92.8 88.1 87.3 86.8 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: HEC REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: HEM BINDING SITE. REMARK 800 REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEC A 80 DBREF 2DVH A 1 79 UNP P04032 CY553_DESVH 25 103 SEQADV 2DVH ALA A 64 UNP P04032 TYR 88 ENGINEERED MUTATION 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 ALA 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 75 HETNAM HEC HEME C FORMUL 2 HEC C34 H34 FE N4 O4 HELIX 1 H1 ASP A 2 CYS A 10 1 9 HELIX 2 H2 ALA A 34 ALA A 45 1 12 HELIX 3 H3 ALA A 55 VAL A 61 1 7 HELIX 4 H4 ASP A 66 LEU A 79 1 14 LINK SG CYS A 10 CAB HEC A 80 1555 1555 1.84 LINK SG CYS A 13 CAC HEC A 80 1555 1555 1.82 LINK NE2 HIS A 14 FE HEC A 80 1555 1555 2.04 LINK SD MET A 57 FE HEC A 80 1555 1555 2.34 SITE 1 HEC 4 CYS A 10 CYS A 13 HIS A 14 MET A 57 SITE 1 AC1 17 CYS A 10 CYS A 13 HIS A 14 ALA A 22 SITE 2 AC1 17 ALA A 26 LYS A 27 VAL A 29 GLN A 32 SITE 3 AC1 17 LEU A 37 LYS A 40 TYR A 44 TYR A 49 SITE 4 AC1 17 ARG A 53 MET A 56 MET A 57 VAL A 61 SITE 5 AC1 17 LEU A 72 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
Complete list - v 3 2 Bytes