HEADER ELECTRON TRANSPORT 10-JAN-03 1NMI TITLE SOLUTION STRUCTURE OF THE IMIDAZOLE COMPLEX OF ISO-1 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 5 12-AUG-26 1NMI 1 COMPND FORMUL REVDAT 4 20-NOV-24 1NMI 1 REMARK REVDAT 3 23-FEB-22 1NMI 1 REMARK SEQADV LINK 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 ISO-1 JRNL TITL 2 CYTOCHROME C JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 2.6, DYANA 1.5 REMARK 3 AUTHORS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1NMI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 14-JAN-03. REMARK 100 THE DEPOSITION ID IS D_1000018004. 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 ISO- REMARK 210 1 CYTOCHROME C, 120MM 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 : 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 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 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 HIS A 18 NE2 REMARK 620 2 HEC A1018 NA 91.0 REMARK 620 3 HEC A1018 NB 88.9 90.7 REMARK 620 4 HEC A1018 NC 88.5 179.3 89.9 REMARK 620 5 HEC A1018 ND 87.5 89.9 176.4 89.5 REMARK 620 6 IMD A 104 N1 176.7 91.7 92.9 88.7 90.6 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 IMD A 104 REMARK 800 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 H36 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 SG CYS A 14 CAB HEC A1018 1555 1555 1.83 LINK SG CYS A 17 CAC HEC A1018 1555 1555 1.84 LINK NE2 HIS A 18 FE HEC A1018 1555 1555 1.94 LINK N1 IMD A 104 FE HEC A1018 1555 1555 1.99 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 CONECT 291 1732 CONECT 337 1740 CONECT 351 1710 CONECT 1701 1702 1705 1710 CONECT 1702 1701 1703 1706 CONECT 1703 1702 1704 1707 CONECT 1704 1703 1705 1708 CONECT 1705 1701 1704 1709 CONECT 1706 1702 CONECT 1707 1703 CONECT 1708 1704 CONECT 1709 1705 CONECT 1710 351 1701 1715 1726 CONECT 1710 1734 1742 CONECT 1711 1716 1746 1753 CONECT 1712 1719 1727 1754 CONECT 1713 1730 1735 1755 CONECT 1714 1738 1743 1756 CONECT 1715 1710 1716 1719 CONECT 1716 1711 1715 1717 CONECT 1717 1716 1718 1721 CONECT 1718 1717 1719 1720 CONECT 1719 1712 1715 1718 CONECT 1720 1718 1757 1758 1759 CONECT 1721 1717 1722 1760 1761 CONECT 1722 1721 1723 1762 1763 CONECT 1723 1722 1724 1725 CONECT 1724 1723 CONECT 1725 1723 CONECT 1726 1710 1727 1730 CONECT 1727 1712 1726 1728 CONECT 1728 1727 1729 1731 CONECT 1729 1728 1730 1732 CONECT 1730 1713 1726 1729 CONECT 1731 1728 1764 1765 1766 CONECT 1732 291 1729 1733 1767 CONECT 1733 1732 1768 1769 1770 CONECT 1734 1710 1735 1738 CONECT 1735 1713 1734 1736 CONECT 1736 1735 1737 1739 CONECT 1737 1736 1738 1740 CONECT 1738 1714 1734 1737 CONECT 1739 1736 1771 1772 1773 CONECT 1740 337 1737 1741 1774 CONECT 1741 1740 1775 1776 1777 CONECT 1742 1710 1743 1746 CONECT 1743 1714 1742 1744 CONECT 1744 1743 1745 1747 CONECT 1745 1744 1746 1748 CONECT 1746 1711 1742 1745 CONECT 1747 1744 1778 1779 1780 CONECT 1748 1745 1749 1781 1782 CONECT 1749 1748 1750 1783 1784 CONECT 1750 1749 1751 1752 CONECT 1751 1750 CONECT 1752 1750 CONECT 1753 1711 CONECT 1754 1712 CONECT 1755 1713 CONECT 1756 1714 CONECT 1757 1720 CONECT 1758 1720 CONECT 1759 1720 CONECT 1760 1721 CONECT 1761 1721 CONECT 1762 1722 CONECT 1763 1722 CONECT 1764 1731 CONECT 1765 1731 CONECT 1766 1731 CONECT 1767 1732 CONECT 1768 1733 CONECT 1769 1733 CONECT 1770 1733 CONECT 1771 1739 CONECT 1772 1739 CONECT 1773 1739 CONECT 1774 1740 CONECT 1775 1741 CONECT 1776 1741 CONECT 1777 1741 CONECT 1778 1747 CONECT 1779 1747 CONECT 1780 1747 CONECT 1781 1748 CONECT 1782 1748 CONECT 1783 1749 CONECT 1784 1749 MASTER 168 0 2 4 0 0 7 6 896 1 88 9 END