HEADER OXIDOREDUCTASE(CYTOCHROME) 20-SEP-00 1E8E TITLE SOLUTION STRUCTURE OF METHYLOPHILUS METHYLOTROPHUS CYTOCHROME C''. TITLE 2 INSIGHTS INTO THE STRUCTURAL BASIS OF HAEM-LIGAND DETACHMENT COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOCHROME C''; COMPND 3 CHAIN: A; COMPND 4 OTHER_DETAILS: C-TYPE CYTOCHROME, FULLY OXIDISED FORM SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHYLOPHILUS METHYLOTROPHUS; SOURCE 3 ORGANISM_COMMON: BACTERIUM W3A1; SOURCE 4 ORGANISM_TAXID: 17 KEYWDS OXIDOREDUCTASE(CYTOCHROME), CYTOCHROME C'', LIGAND DETACHMENT, REDOX- KEYWDS 2 BOHR EFFECT, PARAMAGNETIC EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR L.BRENNAN,D.L.TURNER,P.FARELEIRA,H.SANTOS REVDAT 3 15-JAN-20 1E8E 1 LINK REVDAT 2 24-FEB-09 1E8E 1 VERSN REVDAT 1 20-SEP-01 1E8E 0 JRNL AUTH L.BRENNAN,D.L.TURNER,P.FARELEIRA,H.SANTOS JRNL TITL SOLUTION STRUCTURE OF METHYLOPHILUS METHYLOTROPHUS JRNL TITL 2 CYTOCHROME C": INSIGHTS INTO THE STRUCTURAL BASIS OF JRNL TITL 3 HAEM-LIGAND DETACHMENT JRNL REF J.MOL.BIOL. V. 308 353 2001 JRNL REFN ISSN 0022-2836 JRNL PMID 11327772 JRNL DOI 10.1006/JMBI.2001.4600 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH H.S.COSTA,H.SANTOS,D.L.TURNER REMARK 1 TITL CHARACTERIZATION OF THE HAEM ENVIRONMENT IN METHYLOPHILUS REMARK 1 TITL 2 METHYLOTROPHUS FERRICYTOCHROME C'' BY 1H-NMR REMARK 1 REF EUR.J.BIOCHEM. V. 215 817 1993 REMARK 1 REFN ISSN 0014-2956 REMARK 1 PMID 8394812 REMARK 1 DOI 10.1111/J.1432-1033.1993.TB18097.X REMARK 1 REFERENCE 2 REMARK 1 AUTH H.S.COSTA,H.SANTOS,D.L.TURNER,A.V.XAVIER REMARK 1 TITL INVOLVEMENT OF A LABILE AXIAL HISTIDINE IN COUPLING ELECTRON REMARK 1 TITL 2 AND PROTON TRANSFER IN METHYLOPHILUS METHYLOTROPHUS REMARK 1 TITL 3 CYTOCHROME C'' REMARK 1 REF EUR.J.BIOCHEM. V. 208 427 1992 REMARK 1 REFN ISSN 0014-2956 REMARK 1 PMID 1325909 REMARK 1 DOI 10.1111/J.1432-1033.1992.TB17204.X REMARK 1 REFERENCE 3 REMARK 1 AUTH H.SANTOS,D.L.TURNER REMARK 1 TITL CHARACTERIZATION AND NMR STUDIES OF A NOVEL CYTOCHROME C REMARK 1 TITL 2 ISOLATED FROM METHYLOPHILUS METHYLOTROPHUS WHICH SHOWS A REMARK 1 TITL 3 REDOX-LINKED CHANGE OS SPIN-STATE REMARK 1 REF BIOCHIM.BIOPHYS.ACTA V. 954 277 1988 REMARK 1 REFN ISSN 0006-3002 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PARADYANA REMARK 3 AUTHORS : D.L.TURNER,L.BRENNAN,S.G.CHAMBERLIN, R.O.LOURO, REMARK 3 A.V.XAVIER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: DIPOLAR SHIFTS WERE USED AS RESTRAINTS REMARK 3 IN AN EXTENDED VERSION OF DYANA CALLED PARADYANA. D.L.TURNER,L, REMARK 3 BRENNAN,S.G.CHAMBERLIN, R.O.LOURO,A.V.XAVIER (1998)DETERMINATION REMARK 3 OF SOLUTION STRUCTURES OF PARAMAGNETIC PROTEINS BY REMARK 3 NMR.EUR.BIOPHYS.J.27,367-375. REMARK 4 REMARK 4 1E8E COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 20-SEP-00. REMARK 100 THE DEPOSITION ID IS D_1290005380. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 5.6 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : 10 MM PHOSPATE BUFFER REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D-1H-NOESY; 2D-1H-TOCSY; 2D-1H REMARK 210 -COSY; 3D(15N; 1H)-TOCSY-HSQC; REMARK 210 1H)-NOESY-HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 750 MHZ REMARK 210 SPECTROMETER MODEL : UNITYPLUS REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : PARADYANA REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS WITH REMARK 210 SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 400 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : LEAST RESTRAINT VIOLATION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 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 O ALA A 16 H ASN A 20 1.51 REMARK 500 O VAL A 2 H GLU A 6 1.52 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 VAL A 2 -41.47 87.08 REMARK 500 1 LYS A 11 -71.76 -96.28 REMARK 500 1 LYS A 32 -66.55 -141.21 REMARK 500 1 ASN A 36 22.62 -140.21 REMARK 500 1 LYS A 38 96.24 -56.42 REMARK 500 1 LYS A 45 124.79 172.49 REMARK 500 1 THR A 54 172.02 50.27 REMARK 500 1 LYS A 68 -94.44 -81.97 REMARK 500 1 GLU A 69 123.13 -177.99 REMARK 500 1 PRO A 71 167.83 -48.94 REMARK 500 1 PRO A 72 131.46 -37.76 REMARK 500 1 ALA A 74 98.42 -37.89 REMARK 500 1 LYS A 80 43.72 -107.82 REMARK 500 1 PHE A 82 64.76 36.44 REMARK 500 1 THR A 83 -64.26 -101.51 REMARK 500 1 ASP A 90 -50.35 178.39 REMARK 500 1 ILE A 99 -51.63 -121.71 REMARK 500 1 THR A 118 -67.61 -127.49 REMARK 500 2 VAL A 2 49.10 -145.91 REMARK 500 2 LYS A 11 -72.79 -100.20 REMARK 500 2 ILE A 28 38.16 -92.60 REMARK 500 2 THR A 29 34.68 -148.47 REMARK 500 2 ASP A 30 -49.94 -137.23 REMARK 500 2 LYS A 32 -72.16 -51.98 REMARK 500 2 LYS A 38 94.27 -51.66 REMARK 500 2 LYS A 45 112.34 178.68 REMARK 500 2 THR A 54 170.61 50.26 REMARK 500 2 LYS A 68 -94.54 -79.08 REMARK 500 2 GLU A 69 123.94 -179.47 REMARK 500 2 PRO A 71 167.08 -49.00 REMARK 500 2 PRO A 72 132.05 -37.18 REMARK 500 2 ALA A 74 113.41 -39.28 REMARK 500 2 PHE A 82 62.78 36.60 REMARK 500 2 ASP A 84 79.70 -174.86 REMARK 500 2 ASP A 90 -66.94 176.69 REMARK 500 2 LEU A 117 33.32 -91.98 REMARK 500 2 THR A 118 -68.02 -141.62 REMARK 500 3 VAL A 2 -21.65 87.35 REMARK 500 3 LYS A 11 -72.72 -97.90 REMARK 500 3 PRO A 26 -167.45 -75.25 REMARK 500 3 THR A 29 35.82 -162.21 REMARK 500 3 ASP A 30 -49.46 -143.99 REMARK 500 3 LYS A 32 -74.02 -46.44 REMARK 500 3 ASN A 36 28.37 -140.99 REMARK 500 3 LYS A 38 95.69 -44.50 REMARK 500 3 LYS A 45 123.13 -175.22 REMARK 500 3 THR A 54 170.39 50.25 REMARK 500 3 LYS A 62 131.75 176.10 REMARK 500 3 ALA A 74 97.80 -37.73 REMARK 500 3 LYS A 80 43.82 -104.93 REMARK 500 REMARK 500 THIS ENTRY HAS 426 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 125 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 53 NE2 REMARK 620 2 HEC A 125 NA 91.6 REMARK 620 3 HEC A 125 NB 90.3 90.1 REMARK 620 4 HEC A 125 NC 91.0 177.4 90.5 REMARK 620 5 HEC A 125 ND 87.1 89.5 177.4 90.0 REMARK 620 6 HIS A 95 NE2 178.8 88.4 90.9 89.0 91.7 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 125 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4837 RELATED DB: BMRB DBREF 1E8E A 1 124 UNP Q9RQB9 Q9RQB9 21 144 SEQRES 1 A 124 ASP VAL THR ASN ALA GLU LYS LEU VAL TYR LYS TYR THR SEQRES 2 A 124 ASN ILE ALA HIS SER ALA ASN PRO MET TYR GLU ALA PRO SEQRES 3 A 124 SER ILE THR ASP GLY LYS ILE PHE PHE ASN ARG LYS PHE SEQRES 4 A 124 LYS THR PRO SER GLY LYS GLU ALA ALA CYS ALA SER CYS SEQRES 5 A 124 HIS THR ASN ASN PRO ALA ASN VAL GLY LYS ASN ILE VAL SEQRES 6 A 124 THR GLY LYS GLU ILE PRO PRO LEU ALA PRO ARG VAL ASN SEQRES 7 A 124 THR LYS ARG PHE THR ASP ILE ASP LYS VAL GLU ASP GLU SEQRES 8 A 124 PHE THR LYS HIS CYS ASN ASP ILE LEU GLY ALA ASP CYS SEQRES 9 A 124 SER PRO SER GLU LYS ALA ASN PHE ILE ALA TYR LEU LEU SEQRES 10 A 124 THR GLU THR LYS PRO THR LYS HET HEC A 125 75 HETNAM HEC HEME C FORMUL 2 HEC C34 H34 FE N4 O4 HELIX 1 1 VAL A 2 ASN A 20 1 19 HELIX 2 2 LYS A 32 ASN A 36 5 5 HELIX 3 3 LYS A 87 LEU A 100 1 14 HELIX 4 4 SER A 105 LEU A 117 1 13 SHEET 1 A 2 PHE A 39 THR A 41 0 SHEET 2 A 2 LYS A 45 ALA A 47 -1 N ALA A 47 O PHE A 39 SSBOND 1 CYS A 96 CYS A 104 1555 1555 1.99 LINK SG CYS A 49 CAB HEC A 125 1555 1555 1.88 LINK SG CYS A 52 CAC HEC A 125 1555 1555 1.81 LINK NE2 HIS A 53 FE HEC A 125 1555 1555 1.94 LINK NE2 HIS A 95 FE HEC A 125 1555 1555 1.95 SITE 1 AC1 11 ALA A 48 CYS A 49 SER A 51 CYS A 52 SITE 2 AC1 11 HIS A 53 ASN A 63 ILE A 70 LEU A 73 SITE 3 AC1 11 PHE A 92 HIS A 95 PHE A 112 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