HEADER OXIDOREDUCTASE 27-DEC-06 2ODX TITLE SOLUTION STRUCTURE OF ZN(II)COX4 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOCHROME C OXIDASE POLYPEPTIDE IV; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: COX4 SUBUNIT; COMPND 5 EC: 1.9.3.1; COMPND 6 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 GENE: COX4; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET20B+ KEYWDS ALL BETA-PROTEIN, METALLO-PROTEIN, OXIDOREDUCTASE EXPDTA SOLUTION NMR NUMMDL 21 MDLTYP MINIMIZED AVERAGE AUTHOR J.H.COYNE III,S.CIOFI-BAFFONI REVDAT 5 27-DEC-23 2ODX 1 REMARK REVDAT 4 16-MAR-22 2ODX 1 REMARK SEQADV LINK REVDAT 3 24-FEB-09 2ODX 1 VERSN REVDAT 2 03-APR-07 2ODX 1 JRNL REVDAT 1 09-JAN-07 2ODX 0 JRNL AUTH H.J.COYNE,S.CIOFI-BAFFONI,L.BANCI,I.BERTINI,L.ZHANG, JRNL AUTH 2 G.N.GEORGE,D.R.WINGE JRNL TITL THE CHARACTERIZATION AND ROLE OF ZINC BINDING IN YEAST COX4. JRNL REF J.BIOL.CHEM. V. 282 8926 2007 JRNL REFN ISSN 0021-9258 JRNL PMID 17215247 JRNL DOI 10.1074/JBC.M610303200 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR, AMBER 8.0 REMARK 3 AUTHORS : REMARK 3 PEARLMAN,CASE,CALDWELL,ROSS,CHEATHAM,FERGUSON,SEIBEL,SINGH, REMARK 3 WEINER,KOLLMAN (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 STRUCTURE CALCULATIONS WERE PERFORMED WITH THE SOFTWARE PACKAGE REMARK 3 ATNOS/CANDID/CYANA. REMARK 3 THE STRUCTURES ARE BASED ON A TOTAL OF 1218 RESTRAINTS, 1172 ARE REMARK 3 NOE-DERIVED DISTANCE CONSTRAINTS, 46 ARE DIHEDRAL ANGLE RESTRAINTS. REMARK 4 REMARK 4 2ODX COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-DEC-06. REMARK 100 THE DEPOSITION ID IS D_1000041013. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.9 REMARK 210 IONIC STRENGTH : 50 MM PHOSPHATE, 200 MM NACL REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 1 MM ZN(II)COX4 U-15N, 50MM REMARK 210 PHOSPHATE BUFFER NA, 200 MM NACL, REMARK 210 90% H2O, 10% D2O; 1 MM ZN(II) REMARK 210 COX4 U-15N,13C, 50MM PHOSPHATE REMARK 210 BUFFER NA, 200 MM NACL, 90% H2O, REMARK 210 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 2D TOCSY; HNHA; 3D_13C REMARK 210 -SEPARATED_NOESY; 3D_15N- REMARK 210 SEPARATED_NOESY; CBCA(CO)NH; REMARK 210 CBCANH; HNCO; HN(CA)CO; (H)CCH- REMARK 210 TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 500 MHZ; 700 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XWINNMR, CARA, CYANA REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 21 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR REMARK 210 SPECTROSCOPY 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-21 REMARK 465 RES C SSSEQI REMARK 465 MET A 76 REMARK 465 MET A 77 REMARK 465 ALA A 78 REMARK 465 ASP A 79 REMARK 465 VAL A 80 REMARK 465 PHE A 81 REMARK 465 ASP A 82 REMARK 465 THR A 83 REMARK 465 LYS A 84 REMARK 465 PRO A 85 REMARK 465 LEU A 86 REMARK 465 ASP A 87 REMARK 465 SER A 88 REMARK 465 SER A 89 REMARK 465 ARG A 90 REMARK 465 LYS A 91 REMARK 465 GLY A 92 REMARK 465 THR A 93 REMARK 465 VAL A 148 REMARK 465 PRO A 149 REMARK 465 ASN A 150 REMARK 465 ASP A 151 REMARK 465 ASP A 152 REMARK 465 HIS A 153 REMARK 465 HIS A 154 REMARK 465 HIS A 155 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 HG SER A 102 O ASP A 104 1.55 REMARK 500 HG1 THR A 127 OE1 GLU A 130 1.57 REMARK 500 REMARK 500 REMARK: NULL 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 3 PRO A 97 C - N - CA ANGL. DEV. = 9.5 DEGREES REMARK 500 4 ARG A 107 NE - CZ - NH1 ANGL. DEV. = 5.1 DEGREES REMARK 500 6 ARG A 107 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 8 ARG A 133 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 11 PRO A 97 C - N - CA ANGL. DEV. = 9.3 DEGREES REMARK 500 11 ARG A 107 NE - CZ - NH1 ANGL. DEV. = 4.4 DEGREES REMARK 500 11 ARG A 133 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 14 TYR A 141 CB - CG - CD1 ANGL. DEV. = -3.6 DEGREES REMARK 500 16 ARG A 133 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 18 VAL A 146 CG1 - CB - CG2 ANGL. DEV. = -11.8 DEGREES REMARK 500 20 ARG A 107 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 20 ARG A 133 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 21 ARG A 107 NE - CZ - NH1 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 1 ASP A 96 74.52 167.65 REMARK 500 1 SER A 102 -67.83 -108.16 REMARK 500 1 TYR A 103 -3.90 75.79 REMARK 500 1 SER A 114 159.92 169.49 REMARK 500 1 ALA A 116 42.43 -91.69 REMARK 500 1 HIS A 119 -145.84 -104.88 REMARK 500 1 THR A 120 -158.40 -76.56 REMARK 500 1 GLU A 136 -60.82 -95.32 REMARK 500 1 VAL A 146 133.37 -36.83 REMARK 500 2 ASP A 96 73.77 164.88 REMARK 500 2 SER A 102 111.94 -163.63 REMARK 500 2 ASP A 105 -16.73 59.55 REMARK 500 2 TYR A 106 14.63 -150.88 REMARK 500 2 SER A 114 154.51 175.44 REMARK 500 2 SER A 118 -43.43 -166.62 REMARK 500 2 HIS A 119 -158.08 -107.64 REMARK 500 2 THR A 120 -158.96 -69.64 REMARK 500 3 LYS A 95 -143.65 123.39 REMARK 500 3 ASP A 104 -101.56 -104.03 REMARK 500 3 ASP A 105 -38.33 -171.64 REMARK 500 3 SER A 114 178.50 71.08 REMARK 500 3 ALA A 116 33.48 -94.58 REMARK 500 3 HIS A 119 -144.34 -123.81 REMARK 500 3 THR A 120 -153.73 -78.39 REMARK 500 3 GLU A 136 -100.00 -96.87 REMARK 500 4 ASP A 96 70.89 161.68 REMARK 500 4 TYR A 103 35.33 -77.10 REMARK 500 4 SER A 118 -36.19 -177.82 REMARK 500 4 HIS A 119 -153.15 -118.57 REMARK 500 4 THR A 120 -155.39 -74.78 REMARK 500 4 GLU A 136 -94.18 -100.09 REMARK 500 5 LYS A 95 -122.41 -173.21 REMARK 500 5 PRO A 97 -81.83 -83.12 REMARK 500 5 ARG A 107 156.75 -48.20 REMARK 500 5 SER A 114 162.29 175.36 REMARK 500 5 HIS A 119 -148.73 -100.80 REMARK 500 5 THR A 120 -134.09 -77.67 REMARK 500 5 LYS A 125 76.22 -119.94 REMARK 500 5 PRO A 126 43.43 -92.15 REMARK 500 5 THR A 127 151.00 -28.61 REMARK 500 5 GLU A 136 -88.23 -81.41 REMARK 500 6 LYS A 95 -66.21 -4.00 REMARK 500 6 ASP A 96 77.77 176.69 REMARK 500 6 TYR A 103 40.02 -75.03 REMARK 500 6 ASP A 104 -2.18 -146.34 REMARK 500 6 ASP A 105 -16.46 63.25 REMARK 500 6 TYR A 106 27.47 -151.68 REMARK 500 6 HIS A 119 -151.37 -125.15 REMARK 500 6 THR A 120 -157.68 -73.02 REMARK 500 6 THR A 127 147.37 100.94 REMARK 500 REMARK 500 THIS ENTRY HAS 202 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ALA A 116 GLY A 117 2 -147.47 REMARK 500 GLY A 117 SER A 118 3 -148.52 REMARK 500 ASN A 129 GLU A 130 4 -149.20 REMARK 500 ASN A 129 GLU A 130 6 -143.14 REMARK 500 GLY A 113 SER A 114 7 -138.72 REMARK 500 VAL A 146 GLY A 147 7 132.03 REMARK 500 TYR A 103 ASP A 104 10 134.90 REMARK 500 GLY A 113 SER A 114 10 103.26 REMARK 500 GLY A 117 SER A 118 10 -144.60 REMARK 500 VAL A 146 GLY A 147 11 132.22 REMARK 500 ARG A 107 TYR A 108 12 149.18 REMARK 500 VAL A 146 GLY A 147 13 139.33 REMARK 500 GLY A 117 SER A 118 14 -140.37 REMARK 500 HIS A 119 THR A 120 14 -145.99 REMARK 500 GLY A 113 SER A 114 21 -120.82 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 106 0.12 SIDE CHAIN REMARK 500 2 TYR A 141 0.08 SIDE CHAIN REMARK 500 3 TYR A 106 0.10 SIDE CHAIN REMARK 500 3 ARG A 133 0.18 SIDE CHAIN REMARK 500 3 TYR A 141 0.09 SIDE CHAIN REMARK 500 4 TYR A 106 0.08 SIDE CHAIN REMARK 500 5 HIS A 119 0.09 SIDE CHAIN REMARK 500 6 TYR A 141 0.07 SIDE CHAIN REMARK 500 7 ARG A 133 0.08 SIDE CHAIN REMARK 500 8 TYR A 106 0.14 SIDE CHAIN REMARK 500 9 TYR A 141 0.07 SIDE CHAIN REMARK 500 10 TYR A 106 0.10 SIDE CHAIN REMARK 500 11 TYR A 103 0.10 SIDE CHAIN REMARK 500 11 TYR A 106 0.15 SIDE CHAIN REMARK 500 11 TYR A 108 0.06 SIDE CHAIN REMARK 500 13 TYR A 106 0.13 SIDE CHAIN REMARK 500 13 ARG A 107 0.09 SIDE CHAIN REMARK 500 14 TYR A 106 0.10 SIDE CHAIN REMARK 500 14 ARG A 133 0.12 SIDE CHAIN REMARK 500 17 TYR A 106 0.07 SIDE CHAIN REMARK 500 18 TYR A 103 0.08 SIDE CHAIN REMARK 500 20 TYR A 106 0.10 SIDE CHAIN REMARK 500 21 TYR A 106 0.08 SIDE CHAIN REMARK 500 21 TYR A 141 0.08 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 ZN A 156 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 111 SG REMARK 620 2 HIS A 119 NE2 121.8 REMARK 620 3 CYS A 134 SG 117.2 113.8 REMARK 620 4 CYS A 137 SG 110.6 106.9 76.2 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 156 DBREF 2ODX A 79 155 UNP P04037 COX4_YEAST 79 155 SEQADV 2ODX MET A 76 UNP P04037 CLONING ARTIFACT SEQADV 2ODX MET A 77 UNP P04037 CLONING ARTIFACT SEQADV 2ODX ALA A 78 UNP P04037 CLONING ARTIFACT SEQRES 1 A 80 MET MET ALA ASP VAL PHE ASP THR LYS PRO LEU ASP SER SEQRES 2 A 80 SER ARG LYS GLY THR MET LYS ASP PRO ILE ILE ILE GLU SEQRES 3 A 80 SER TYR ASP ASP TYR ARG TYR VAL GLY CYS THR GLY SER SEQRES 4 A 80 PRO ALA GLY SER HIS THR ILE MET TRP LEU LYS PRO THR SEQRES 5 A 80 VAL ASN GLU VAL ALA ARG CYS TRP GLU CYS GLY SER VAL SEQRES 6 A 80 TYR LYS LEU ASN PRO VAL GLY VAL PRO ASN ASP ASP HIS SEQRES 7 A 80 HIS HIS HET ZN A 156 1 HETNAM ZN ZINC ION FORMUL 2 ZN ZN 2+ SHEET 1 A 3 ILE A 99 ILE A 100 0 SHEET 2 A 3 VAL A 140 LEU A 143 1 O LYS A 142 N ILE A 100 SHEET 3 A 3 VAL A 131 ARG A 133 -1 N ALA A 132 O TYR A 141 SHEET 1 B 2 VAL A 109 CYS A 111 0 SHEET 2 B 2 MET A 122 LEU A 124 -1 O LEU A 124 N VAL A 109 LINK SG CYS A 111 ZN ZN A 156 1555 1555 2.42 LINK NE2 HIS A 119 ZN ZN A 156 1555 1555 2.11 LINK SG CYS A 134 ZN ZN A 156 1555 1555 2.43 LINK SG CYS A 137 ZN ZN A 156 1555 1555 2.36 SITE 1 AC1 5 CYS A 111 HIS A 119 MET A 122 CYS A 134 SITE 2 AC1 5 CYS A 137 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