10 20 30 40 50 60 70 80 2KM0 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER 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, KEYWDS 2 COPPER, PERIPLASM, PLASMID, METAL BINDING PROTEIN
EXPDTA SOLUTION NMR
NUMMDL 20
AUTHOR B.BERSCH
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 JRNL TITL 2 CU(I) IN A TETRATHIOETHER SITE: CHARACTERIZATION BY JRNL TITL 3 X-RAY ABSORPTION 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, REMARK 1 AUTH 2 J.COVES,M.MERGEAY,R.WATTIEZ REMARK 1 TITL MOLECULAR STRUCTURE AND METAL-BINDING PROPERTIES OF REMARK 1 TITL 2 THE PERIPLASMIC COPK PROTEIN EXPRESSED IN REMARK 1 TITL 3 CUPRIAVIDUS METALLIDURANS CH34 DURING COPPER REMARK 1 TITL 4 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 : ARIA 1.2 REMARK 3 AUTHORS : LINGE, O'DONOGHUE AND NILGES REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 2KM0 COMPLIES WITH FORMAT V. 3.20, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 22-JUL-09. REMARK 100 THE RCSB ID CODE IS RCSB101287.
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, REMARK 210 0.95 MM COPPER(I) ION-2, 50 MM REMARK 210 AMMONIUM ACETATE-3, 10 MM REMARK 210 SODIUM ASCORBATE-4, 90% H2O/ REMARK 210 10% D2O; 1.6 MM [U-100% 13C; U REMARK 210 -100% 15N] COPK-5, 1.5 MM REMARK 210 COPPER(I) ION-6, 50 MM REMARK 210 AMMONIUM ACETATE-7, 16 MM REMARK 210 SODIUM ASCORBATE-8, 90% H2O/ REMARK 210 10% D2O; 1.5 MM COPK-9, 1.4 MM REMARK 210 COPPER(I) ION-10, 50 MM REMARK 210 AMMONIUM ACETATE-11, 14 MM REMARK 210 SODIUM ASCORBATE-12, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D 1H-15N REMARK 210 NOESY; 3D 1H-13C NOESY; 2D 1H- REMARK 210 1H NOESY; 3D HNCO; 3D HNCACB; REMARK 210 3D HN(COCA)CB; 3D C(CO)NH; 3D REMARK 210 HCCH-TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : DIRECTDRIVE REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE, NMRVIEW, REMARK 210 ATNOSCANDID, ARIA 1.2 REMARK 210 METHOD USED : SIMULATED ANNEALING, REMARK 210 MOLECULAR 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 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 HG13 VAL A 20 HG2 MET A 26 1.35 REMARK 500 HB2 MET A 28 HE2 MET A 54 1.39 REMARK 500 HA VAL A 6 HA PHE A 21 1.48 REMARK 500 HG3 GLU A 40 HA LYS A 55 1.56 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 1 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