10 20 30 40 50 60 70 80 1NMI - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER ELECTRON TRANSPORT 10-JAN-03 1NMI
TITLE SOLUTION STRUCTURE OF THE IMIDAZOLE COMPLEX OF ISO-1 TITLE 2 CYTOCHROME C
COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOCHROME C, ISO-1; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562
KEYWDS LIGAND-PROTEIN COMPLEX, ELECTRON TRANSPORT
EXPDTA SOLUTION NMR
MDLTYP MINIMIZED AVERAGE
AUTHOR Y.YAO,Y.TONG,G.LIU,J.WANG,J.ZHENG,W.TANG
REVDAT 2 24-FEB-09 1NMI 1 VERSN REVDAT 1 04-FEB-03 1NMI 0
JRNL AUTH Y.YAO,Y.TONG,G.LIU,J.WANG,J.ZHENG,W.TANG JRNL TITL SOLUTION STRUCTURE OF THE IMIDAZOLE COMPLEX OF JRNL TITL 2 ISO-1 CYTOCHROME C JRNL REF TO BE PUBLISHED JRNL REFN
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DYANA 1.5 REMARK 3 AUTHORS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 1NMI COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 16-JAN-03. REMARK 100 THE RCSB ID CODE IS RCSB018004.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : 1MM ISO-1 CYTOCHROME C, 120MM REMARK 210 D5IMIDAZOLE; 1MM 15N LABELED REMARK 210 ISO-1 CYTOCHROME C, 120MM REMARK 210 D5IMIDAZOLE REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D TOCSY, 2D NOESY, DQF-COSY, REMARK 210 3D_15N-SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ, 500 MHZ REMARK 210 SPECTROMETER MODEL : DMX, DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XWINNMR 2.6, DYANA 1.5 REMARK 210 METHOD USED : RESTRAINED ENERGY MINIMIZATION REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH ACCEPTABLE REMARK 210 COVALENT GEOMETRY 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 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 ARG A 13 NE - CZ - NH2 ANGL. DEV. = -3.2 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 SER A 2 -62.60 -104.78 REMARK 500 ARG A 13 -60.76 -133.47 REMARK 500 LYS A 22 96.07 -65.39 REMARK 500 VAL A 28 -51.40 -121.52 REMARK 500 ARG A 38 -102.99 -142.16 REMARK 500 HIS A 39 -177.59 -179.40 REMARK 500 SER A 40 82.18 -66.10 REMARK 500 GLN A 42 46.17 -92.84 REMARK 500 LYS A 54 -77.70 -53.76 REMARK 500 LYS A 55 46.01 26.71 REMARK 500 ASN A 56 68.63 15.23 REMARK 500 THR A 69 -65.00 -104.80 REMARK 500 LYS A 72 -137.47 51.92 REMARK 500 LYS A 73 -33.36 70.57 REMARK 500 ILE A 75 56.92 20.12 REMARK 500 THR A 78 -66.22 -21.77 REMARK 500 LYS A 79 -71.40 -167.78 REMARK 500 LYS A 86 -49.56 -162.00 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 ARG A 13 0.14 SIDE_CHAIN REMARK 500 HIS A 18 0.11 SIDE_CHAIN REMARK 500 ARG A 38 0.09 SIDE_CHAIN REMARK 500 TYR A 48 0.11 SIDE_CHAIN REMARK 500 TYR A 74 0.07 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 A1018 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 IMD A 104 N1 REMARK 620 2 HIS A 18 NE2 176.7 REMARK 620 N 1
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IMD A 104 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEC A 1018
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1YIC RELATED DB: PDB
DBREF 1NMI A -5 103 UNP P00044 CYC1_YEAST 1 108
SEQADV 1NMI THR A 102 UNP P00044 CYS 107 CONFLICT
SEQRES 1 A 108 THR GLU PHE LYS ALA GLY SER ALA LYS LYS GLY ALA THR SEQRES 2 A 108 LEU PHE LYS THR ARG CYS LEU GLN CYS HIS THR VAL GLU SEQRES 3 A 108 LYS GLY GLY PRO HIS LYS VAL GLY PRO ASN LEU HIS GLY SEQRES 4 A 108 ILE PHE GLY ARG HIS SER GLY GLN ALA GLU GLY TYR SER SEQRES 5 A 108 TYR THR ASP ALA ASN ILE LYS LYS ASN VAL LEU TRP ASP SEQRES 6 A 108 GLU ASN ASN MET SER GLU TYR LEU THR ASN PRO LYS LYS SEQRES 7 A 108 TYR ILE PRO GLY THR LYS MET ALA PHE GLY GLY LEU LYS SEQRES 8 A 108 LYS GLU LYS ASP ARG ASN ASP LEU ILE THR TYR LEU LYS SEQRES 9 A 108 LYS ALA THR GLU
HET IMD A 104 9 HET HEC A1018 75
HETNAM IMD IMIDAZOLE HETNAM HEC HEME C
FORMUL 2 IMD C3 H5 N2 1+ FORMUL 3 HEC C34 H34 FE N4 O4
HELIX 1 1 LYS A 5 THR A 12 1 8 HELIX 2 2 ASP A 50 LYS A 55 1 6 HELIX 3 3 ASP A 60 LEU A 68 1 9 HELIX 4 4 LYS A 87 GLU A 103 1 17
LINK N1 IMD A 104 FE HEC A1018 1555 1555 1.99 LINK FE HEC A1018 NE2 HIS A 18 1555 1555 1.94 LINK SG CYS A 14 CAB HEC A1018 1555 1555 1.83 LINK SG CYS A 17 CAC HEC A1018 1555 1555 1.84
SITE 1 AC1 3 TYR A 67 ALA A 81 HEC A1018 SITE 1 AC2 21 ARG A 13 CYS A 14 CYS A 17 HIS A 18 SITE 2 AC2 21 PRO A 30 LEU A 32 ILE A 35 TYR A 48 SITE 3 AC2 21 ASP A 50 TRP A 59 MET A 64 LEU A 68 SITE 4 AC2 21 PRO A 76 THR A 78 LYS A 79 MET A 80 SITE 5 AC2 21 ALA A 81 PHE A 82 LEU A 94 LEU A 98 SITE 6 AC2 21 IMD A 104
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