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
(ATOM LINES ARE NOT SHOWN.)
END
