HEADER ELECTRON TRANSPORT 30-DEC-03 1S05 TITLE NMR-VALIDATED STRUCTURAL MODEL FOR OXIDIZED R.PALUSTRIS CYTOCHROME TITLE 2 C556 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOCHROME C-556; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: C556; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RHODOPSEUDOMONAS PALUSTRIS; SOURCE 3 ORGANISM_TAXID: 1076; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PEE-PET, PEC86 KEYWDS THIS IS A MODEL OBTAINED BY NMR-RESTRAINED MODELING AND KEYWDS 2 MINIMIZATION., ELECTRON TRANSPORT EXPDTA SOLUTION NMR MDLTYP MINIMIZED AVERAGE AUTHOR I.BERTINI,J.FARAONE-MENNELLA,H.B.GRAY,C.LUCHINAT,G.PARIGI,J.R.WINKLER REVDAT 5 09-OCT-24 1S05 1 REMARK REVDAT 4 03-MAR-21 1S05 1 COMPND REMARK HET HETNAM REVDAT 4 2 1 HETSYN FORMUL LINK ATOM REVDAT 3 24-FEB-09 1S05 1 VERSN REVDAT 2 09-MAR-04 1S05 1 JRNL REVDAT 1 20-JAN-04 1S05 0 JRNL AUTH I.BERTINI,J.FARAONE-MENNELLA,H.B.GRAY,C.LUCHINAT,G.PARIGI, JRNL AUTH 2 J.R.WINKLER JRNL TITL NMR-VALIDATED STRUCTURAL MODEL FOR OXIDIZED RHODOPSEUDOMONAS JRNL TITL 2 PALUSTRIS CYTOCHROME C(556). JRNL REF J.BIOL.INORG.CHEM. V. 9 224 2004 JRNL REFN ISSN 0949-8257 JRNL PMID 14735333 JRNL DOI 10.1007/S00775-003-0511-2 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PARAMAGNETIC DYANA REMARK 3 AUTHORS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1S05 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-DEC-03. REMARK 100 THE DEPOSITION ID IS D_1000021199. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 294 REMARK 210 PH : NULL REMARK 210 IONIC STRENGTH : 0.5 M PHOSPHATE REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 3 MM CYTTOCROME C556 15N, 0.5M REMARK 210 PHOSPHATE BUFFER, REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 3D 15N HSQC TOCSY; 3D REMARK 210 15N HSQC NOESY; 1D NOE; 1J REMARK 210 MODULATED HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 400 MHZ; 700 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : MODELLER 4.0, PARAMAGNETIC DYANA REMARK 210 METHOD USED : NULL REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THIS IS A MODEL STRUCTURE VALIDATED BY NMR CONSTRAINTS 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 GLU A 78 H PHE A 82 1.38 REMARK 500 O ALA A 24 H GLY A 28 1.54 REMARK 500 O PRO A 112 H LYS A 115 1.58 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 LEU A 4 -50.59 -124.12 REMARK 500 LYS A 30 145.43 55.92 REMARK 500 PRO A 31 49.78 -75.06 REMARK 500 TYR A 32 163.38 54.70 REMARK 500 ASP A 33 -59.53 -131.00 REMARK 500 GLN A 34 -52.95 89.76 REMARK 500 LYS A 53 -40.82 -166.99 REMARK 500 VAL A 59 56.81 -141.10 REMARK 500 LYS A 60 -84.40 -122.18 REMARK 500 LEU A 62 9.83 93.33 REMARK 500 LYS A 63 -51.06 162.08 REMARK 500 LYS A 68 -52.44 -165.56 REMARK 500 TYR A 69 166.29 -49.26 REMARK 500 ARG A 79 -39.46 -36.53 REMARK 500 ILE A 100 147.26 -39.27 REMARK 500 LYS A 101 -40.25 -171.50 REMARK 500 ARG A 125 87.09 177.91 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 130 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 MET A 12 SD REMARK 620 2 HEC A 130 NA 103.3 REMARK 620 3 HEC A 130 NB 102.1 93.1 REMARK 620 4 HEC A 130 NC 81.3 172.6 91.5 REMARK 620 5 HEC A 130 ND 79.7 85.8 178.0 89.5 REMARK 620 6 HIS A 121 NE2 171.3 68.1 77.5 107.4 100.6 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 130 DBREF 1S05 A 1 129 UNP P00150 C556_RHOPA 1 129 SEQRES 1 A 129 GLN GLN ASP LEU VAL ASP LYS THR GLN LYS LEU MET LYS SEQRES 2 A 129 ASP ASN GLY ARG ASN MET MET VAL LEU GLY ALA ILE ALA SEQRES 3 A 129 LYS GLY GLU LYS PRO TYR ASP GLN ALA ALA VAL ASP ALA SEQRES 4 A 129 ALA LEU LYS GLN PHE ASP GLU THR ALA LYS ASP LEU PRO SEQRES 5 A 129 LYS LEU PHE PRO ASP SER VAL LYS GLY LEU LYS PRO PHE SEQRES 6 A 129 ASP SER LYS TYR SER SER SER PRO LYS ILE TRP ALA GLU SEQRES 7 A 129 ARG ALA LYS PHE ASP THR GLU ILE ALA ASP PHE ALA LYS SEQRES 8 A 129 ALA VAL ASP GLY ALA LYS GLY LYS ILE LYS ASP VAL ASP SEQRES 9 A 129 THR LEU LYS ALA ALA MET GLN PRO ILE GLY LYS ALA CYS SEQRES 10 A 129 GLY ASN CYS HIS GLU ASN PHE ARG ASP LYS GLU GLY HET HEC A 130 55 HETNAM HEC HEME C FORMUL 2 HEC C34 H34 FE N4 O4 HELIX 1 1 LEU A 4 GLY A 28 1 25 HELIX 2 2 GLN A 34 THR A 47 1 14 HELIX 3 3 ALA A 48 ASP A 50 5 3 HELIX 4 4 PRO A 73 GLU A 78 1 6 HELIX 5 5 GLU A 78 ILE A 100 1 23 HELIX 6 6 ASP A 102 MET A 110 1 9 HELIX 7 7 GLY A 114 PHE A 124 1 11 LINK SG CYS A 117 CAB HEC A 130 1555 1555 1.92 LINK SG CYS A 120 CAC HEC A 130 1555 1555 1.92 LINK SD MET A 12 FE HEC A 130 1555 1555 2.43 LINK NE2 HIS A 121 FE HEC A 130 1555 1555 2.44 SITE 1 AC1 12 MET A 12 PHE A 44 SER A 70 SER A 71 SITE 2 AC1 12 ILE A 86 PHE A 89 ALA A 116 CYS A 117 SITE 3 AC1 12 CYS A 120 HIS A 121 PHE A 124 ARG A 125 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