HEADER METAL BINDING PROTEIN 15-JUL-09 2KM0 TITLE CU(I)-BOUND COPK COMPND MOL_ID: 1; COMPND 2 MOLECULE: COPPER RESISTANCE PROTEIN K; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RALSTONIA METALLIDURANS; SOURCE 3 ORGANISM_TAXID: 266264; SOURCE 4 STRAIN: CH34; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PET30 KEYWDS HEAVY METAL RESISTANCE, PERIPLASMIC COPPER BINDING PROTEIN, COPPER, KEYWDS 2 PERIPLASM, PLASMID, METAL BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR B.BERSCH REVDAT 2 26-FEB-20 2KM0 1 REMARK REVDAT 1 16-MAR-10 2KM0 0 JRNL AUTH G.SARRET,A.FAVIER,J.L.HAZEMANN,M.MERGEAY,B.BERSCH JRNL TITL COPK FROM CUPRIAVIDUS METALLIDURANS CH34 BINDS CU(I) IN A JRNL TITL 2 TETRATHIOETHER SITE: CHARACTERIZATION BY X-RAY ABSORPTION JRNL TITL 3 AND NMR SPECTROSCOPY JRNL REF J.AM.CHEM.SOC. 2010 JRNL REFN ESSN 1520-5126 JRNL PMID 20192263 JRNL DOI 10.1021/JA9083896 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH B.BERSCH,A.FAVIER,P.SCHANDA,S.VAN AELST,T.VALLAEYS,J.COVES, REMARK 1 AUTH 2 M.MERGEAY,R.WATTIEZ REMARK 1 TITL MOLECULAR STRUCTURE AND METAL-BINDING PROPERTIES OF THE REMARK 1 TITL 2 PERIPLASMIC COPK PROTEIN EXPRESSED IN CUPRIAVIDUS REMARK 1 TITL 3 METALLIDURANS CH34 DURING COPPER CHALLENGE REMARK 1 REF J.MOL.BIOL. V. 380 386 2008 REMARK 1 REFN ISSN 0022-2836 REMARK 1 PMID 18533181 REMARK 1 DOI 10.1016/J.JMB.2008.05.017 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NMRPIPE, ARIA 1.2 REMARK 3 AUTHORS : DELAGLIO, GRZESIEK, VUISTER, ZHU, PFEIFER AND BAX REMARK 3 (NMRPIPE), LINGE, O'DONOGHUE AND NILGES (ARIA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2KM0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 22-JUL-09. REMARK 100 THE DEPOSITION ID IS D_1000101287. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.8 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1 MM [U-100% 15N] COPK-1, 0.95 REMARK 210 MM COPPER(I) ION-2, 50 MM REMARK 210 AMMONIUM ACETATE-3, 10 MM SODIUM REMARK 210 ASCORBATE-4, 90% H2O/10% D2O; REMARK 210 1.6 MM [U-100% 13C; U-100% 15N] REMARK 210 COPK-5, 1.5 MM COPPER(I) ION-6, REMARK 210 50 MM AMMONIUM ACETATE-7, 16 MM REMARK 210 SODIUM ASCORBATE-8, 90% H2O/10% REMARK 210 D2O; 1.5 MM COPK-9, 1.4 MM REMARK 210 COPPER(I) ION-10, 50 MM AMMONIUM REMARK 210 ACETATE-11, 14 MM SODIUM REMARK 210 ASCORBATE-12, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D 1H-15N NOESY; REMARK 210 3D 1H-13C NOESY; 2D 1H-1H NOESY; REMARK 210 3D HNCO; 3D HNCACB; 3D HN(COCA) REMARK 210 CB; 3D C(CO)NH; 3D HCCH-TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : DIRECT DRIVE REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRVIEW, ATNOSCANDID, ARIA 1.2 REMARK 210 METHOD USED : SIMULATED ANNEALING, MOLECULAR REMARK 210 DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 1000 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY 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 HE2 MET A 3 HG11 VAL A 6 1.31 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 2 TYR A 10 CE1 TYR A 10 CZ 0.096 REMARK 500 2 TYR A 10 CZ TYR A 10 CE2 -0.096 REMARK 500 9 TYR A 10 CZ TYR A 10 CE2 -0.082 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 ARG A 61 88.36 -69.14 REMARK 500 1 LEU A 62 -52.22 -178.94 REMARK 500 1 LYS A 68 -146.23 -157.75 REMARK 500 1 HIS A 70 -81.57 -159.39 REMARK 500 1 SER A 71 -78.89 -87.81 REMARK 500 1 GLU A 72 83.80 57.56 REMARK 500 2 SER A 35 95.53 -42.64 REMARK 500 2 ARG A 61 -170.47 59.24 REMARK 500 2 ARG A 67 -76.18 -77.95 REMARK 500 2 LYS A 68 22.42 -144.23 REMARK 500 3 PRO A 39 -156.94 -83.53 REMARK 500 3 ILE A 59 178.14 67.12 REMARK 500 3 ARG A 61 16.70 55.15 REMARK 500 3 LEU A 66 -60.74 -102.03 REMARK 500 4 VAL A 43 99.83 -68.36 REMARK 500 4 ARG A 61 -126.94 70.74 REMARK 500 4 LEU A 62 -139.24 -97.88 REMARK 500 4 LYS A 68 -104.36 58.30 REMARK 500 5 SER A 35 104.75 -56.56 REMARK 500 5 GLU A 58 101.12 -167.25 REMARK 500 5 ARG A 61 -149.22 65.14 REMARK 500 5 LEU A 62 -115.25 -77.08 REMARK 500 5 ASP A 63 -71.51 -166.46 REMARK 500 5 LYS A 68 93.84 62.23 REMARK 500 6 ASN A 5 16.61 -147.33 REMARK 500 6 LYS A 31 -9.33 -56.45 REMARK 500 6 LYS A 55 -92.86 -138.50 REMARK 500 6 ARG A 61 174.89 64.80 REMARK 500 6 LEU A 62 -95.52 -116.59 REMARK 500 7 PRO A 39 -166.87 -75.81 REMARK 500 7 ILE A 59 169.73 55.36 REMARK 500 7 ARG A 61 75.74 36.62 REMARK 500 7 LEU A 62 -97.55 -121.53 REMARK 500 7 ASP A 63 -72.55 -151.25 REMARK 500 8 ARG A 61 -85.68 70.91 REMARK 500 8 LEU A 62 -53.15 -148.81 REMARK 500 8 ASP A 63 -29.35 73.68 REMARK 500 9 SER A 35 92.54 -33.06 REMARK 500 9 ARG A 61 -84.85 55.08 REMARK 500 9 LEU A 62 -74.42 70.91 REMARK 500 9 ASP A 63 -32.98 179.96 REMARK 500 9 LYS A 68 -72.32 -84.28 REMARK 500 9 HIS A 70 -68.82 -155.32 REMARK 500 9 SER A 71 -69.32 -140.74 REMARK 500 10 MET A 54 35.46 -81.70 REMARK 500 10 ARG A 61 -167.29 63.42 REMARK 500 10 ARG A 67 -73.06 -106.13 REMARK 500 10 HIS A 70 93.12 67.21 REMARK 500 10 SER A 71 -74.27 -95.50 REMARK 500 11 SER A 35 99.40 -58.89 REMARK 500 REMARK 500 THIS ENTRY HAS 110 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 CU1 A 75 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 MET A 44 SD REMARK 620 2 MET A 38 SD 106.1 REMARK 620 3 MET A 54 SD 106.2 111.0 REMARK 620 4 MET A 28 SD 109.4 108.4 115.3 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 CU1 A 75 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2K0Q RELATED DB: PDB REMARK 900 APO-COPK PROTEIN, SOLUTION STRUCTURE REMARK 900 RELATED ID: 16408 RELATED DB: BMRB DBREF 2KM0 A 1 74 UNP Q58AD3 COPK_RALME 21 94 SEQRES 1 A 74 VAL ASP MET SER ASN VAL VAL LYS THR TYR ASP LEU GLN SEQRES 2 A 74 ASP GLY SER LYS VAL HIS VAL PHE LYS ASP GLY LYS MET SEQRES 3 A 74 GLY MET GLU ASN LYS PHE GLY LYS SER MET ASN MET PRO SEQRES 4 A 74 GLU GLY LYS VAL MET GLU THR ARG ASP GLY THR LYS ILE SEQRES 5 A 74 ILE MET LYS GLY ASN GLU ILE PHE ARG LEU ASP GLU ALA SEQRES 6 A 74 LEU ARG LYS GLY HIS SER GLU GLY GLY HET CU1 A 75 1 HETNAM CU1 COPPER (I) ION FORMUL 2 CU1 CU 1+ HELIX 1 1 LEU A 62 ARG A 67 1 6 SHEET 1 A 3 VAL A 6 ASP A 11 0 SHEET 2 A 3 SER A 16 PHE A 21 -1 O VAL A 20 N LYS A 8 SHEET 3 A 3 MET A 26 ASN A 30 -1 O GLY A 27 N HIS A 19 SHEET 1 B 2 VAL A 43 GLU A 45 0 SHEET 2 B 2 LYS A 51 ILE A 53 -1 O ILE A 52 N MET A 44 LINK SD MET A 44 CU CU1 A 75 1555 1555 2.29 LINK SD MET A 38 CU CU1 A 75 1555 1555 2.30 LINK SD MET A 54 CU CU1 A 75 1555 1555 2.31 LINK SD MET A 28 CU CU1 A 75 1555 1555 2.31 SITE 1 AC1 4 MET A 28 MET A 38 MET A 44 MET A 54 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