HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 21-MAY-10 2KY9 TITLE SOLUTION NMR STRUCTURE OF YDHK C-TERMINAL DOMAIN FROM B.SUBTILIS, TITLE 2 NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET TARGET SR518 COMPND MOL_ID: 1; COMPND 2 MOLECULE: UNCHARACTERIZED PROTEIN YDHK; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SEQUENCE DATABASE RESIDUES 83-205; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS; SOURCE 3 ORGANISM_TAXID: 1423; SOURCE 4 STRAIN: 168; SOURCE 5 GENE: BSU05790, YDHK; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)PMGK; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET21-23C KEYWDS TANDEM TUDOR, STRUCTURAL GENOMICS, NORTHEAST STRUCTURAL GENOMICS KEYWDS 2 CONSORTIUM (NESG), PSI-2, PROTEIN STRUCTURE INITIATIVE, UNKNOWN KEYWDS 3 FUNCTION EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR A.ELETSKY,D.K.SUKUMARAN,H.LEE,D.LEE,C.CICCOSANTI,H.JANJUA,J.LIU, AUTHOR 2 B.ROST,T.B.ACTON,R.XIAO,J.K.EVERETT,J.H.PRESTEGARD,G.T.MONTELIONE, AUTHOR 3 T.SZYPERSKI,NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) REVDAT 4 22-MAY-24 2KY9 1 JRNL REVDAT 3 15-MAY-24 2KY9 1 REMARK REVDAT 2 16-MAR-22 2KY9 1 REMARK SEQADV REVDAT 1 21-JUL-10 2KY9 0 JRNL AUTH Z.ROSARIO-CRUZ,A.ELETSKY,N.S.DAIGHAM,H.AL-TAMEEMI, JRNL AUTH 2 G.V.T.SWAPNA,P.C.KAHN,T.SZYPERSKI,G.T.MONTELIONE,J.M.BOYD JRNL TITL THE COPBL OPERON PROTECTS STAPHYLOCOCCUS AUREUS FROM COPPER JRNL TITL 2 TOXICITY: COPL IS AN EXTRACELLULAR MEMBRANE-ASSOCIATED JRNL TITL 3 COPPER-BINDING PROTEIN. JRNL REF J.BIOL.CHEM. V. 294 4027 2019 JRNL REFN ESSN 1083-351X JRNL PMID 30655293 JRNL DOI 10.1074/JBC.RA118.004723 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.2, CYANA 3.0 REMARK 3 AUTHORS : BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ REMARK 3 (CNS), GUNTERT, MUMENTHALER AND WUTHRICH (CYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: STRUCTURE DETERMINATION WAS PERFORMED REMARK 3 BY RUNNING CYANA AND AUTOSTRUCTURE IN PARALLEL USING NOE-BASED REMARK 3 CONSTRAINTS AND PHI AND PSI DIHEDRAL ANGLE CONSTRAINTS FROM REMARK 3 TALOS+. CONSENSUS PEAK ASSIGNMENTS WERE SELECTED AND USED IN REMARK 3 ITERATIVE REFINEMENT WITH CYANA, WITH RDC CONSTRAINTS ADDED AT REMARK 3 LATER STAGES. THE 20 CONFORMERS OUT OF 100 WITH THE LOWEST REMARK 3 TARGET FUNCTION WERE FURTHER REFINED BY SIMULATED ANNEALING IN REMARK 3 EXPLICIT WATER BATH USING THE PROGRAM CNS WITH PARAM19 FORCE REMARK 3 FIELD AND UPPER LIMIT CONSTRAINTS RELAXED BY 5% REMARK 4 REMARK 4 2KY9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-JUN-10. REMARK 100 THE DEPOSITION ID IS D_1000101723. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298; 298 REMARK 210 PH : 7.5; 7.5 REMARK 210 IONIC STRENGTH : 100; 180 REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 0.4 MM [U-100% 13C; U-100% 15N] REMARK 210 SR518, 100 MM SODIUM CHLORIDE, 5 REMARK 210 MM DTT, 10 MM TRIS, 0.02 % REMARK 210 SODIUM AZIDE, 20 UM DSS, 95% H2O/ REMARK 210 5% D2O; 0.7 MM [U-5% 13C; U-100% REMARK 210 15N] SR518, 100 MM SODIUM REMARK 210 CHLORIDE, 5 MM DTT, 10 MM TRIS, REMARK 210 0.02 % SODIUM AZIDE, 20 UM DSS, REMARK 210 95% H2O/5% D2O; 0.5 MM [U-5% 13C; REMARK 210 U-100% 15N] SR518, 100 MM REMARK 210 SODIUM CHLORIDE, 5 MM DTT, 10 MM REMARK 210 TRIS, 0.02 % SODIUM AZIDE, 20 UM REMARK 210 DSS, 3.5 % PEG, 88% H2O/12% D2O; REMARK 210 0.5 MM [U-5% 13C; U-100% 15N] REMARK 210 SR518, 180 MM SODIUM CHLORIDE, REMARK 210 3.5 MM DTT, 7 MM TRIS, 0.014 % REMARK 210 SODIUM AZIDE, 14 UM DSS, 10.5 G/ REMARK 210 L PF1 PHAGE, 88% H2O/12% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC REMARK 210 ALIPHATIC; 3D HNCO; 3D CBCA(CO) REMARK 210 NH; 3D HNCACB; 3D HN(CA)CO; 3D REMARK 210 SIMUTANEOUS 13C-AROMATIC,13C- REMARK 210 ALIPHATIC,15N EDITED 1H-1H NOESY; REMARK 210 3D HBHA(CO)NH; 2D 1H-13C CT- REMARK 210 HSQC ALIPHATIC; 2D 1H-13C CT- REMARK 210 HSQC AROMATIC; 3D (H)CCH-COSY REMARK 210 ALIPHATIC; 3D (H)CCH-TOCSY REMARK 210 ALIPHATIC; 3D (H)CCH-COSY REMARK 210 AROMATIC; 2D 1H-13C CT-HSQC REMARK 210 METHYL; 2D 1H-15N LR-HSQC FOR REMARK 210 HISTIDINE; 2D 1H-15N J-MODULATED REMARK 210 HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 900 MHZ; 600 MHZ; 750 MHZ; 700 REMARK 210 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE; INOVA REMARK 210 SPECTROMETER MANUFACTURER : BRUKER; VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CNS 1.2, CYANA 3.0, REMARK 210 AUTOSTRUCTURE 2.2.1, AUTOASSIGN REMARK 210 2.3.0, NMRPIPE, XEASY, TOPSPIN REMARK 210 2.1, VNMRJ, CARA 1.8.4, PROSA REMARK 210 6.4, MOLMOL 2K.2, TALOS+ REMARK 210 1.2009.0721.18, PSVS 1.3 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION 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: 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 SER A 103 95.98 -56.84 REMARK 500 1 HIS A 128 -21.65 75.49 REMARK 500 2 ASN A 10 -60.06 -95.11 REMARK 500 2 THR A 40 2.06 -68.83 REMARK 500 2 ASP A 62 -2.94 68.84 REMARK 500 2 HIS A 130 -2.46 -147.35 REMARK 500 3 PRO A 67 106.78 -44.71 REMARK 500 3 SER A 103 109.30 -56.85 REMARK 500 4 ASP A 62 -10.58 73.76 REMARK 500 4 LYS A 124 87.39 -64.37 REMARK 500 5 SER A 106 -40.19 -134.74 REMARK 500 6 ASN A 10 -63.05 -96.80 REMARK 500 6 PRO A 39 152.82 -47.59 REMARK 500 7 ASP A 29 78.87 -106.18 REMARK 500 8 ASP A 29 79.67 -103.98 REMARK 500 9 ARG A 45 105.67 -57.29 REMARK 500 9 LYS A 79 95.91 -66.78 REMARK 500 9 ILE A 88 98.87 -60.10 REMARK 500 10 ILE A 88 94.46 -64.35 REMARK 500 10 HIS A 128 -70.52 -56.26 REMARK 500 11 ASP A 62 -2.63 72.54 REMARK 500 11 SER A 103 103.48 -55.54 REMARK 500 11 LYS A 124 85.84 -61.16 REMARK 500 11 HIS A 127 61.20 -154.92 REMARK 500 11 HIS A 129 105.25 -167.83 REMARK 500 12 ASP A 62 28.28 44.60 REMARK 500 12 HIS A 77 -42.85 -141.50 REMARK 500 12 ILE A 88 96.23 -69.09 REMARK 500 12 LYS A 124 98.72 -54.79 REMARK 500 12 HIS A 128 113.81 48.05 REMARK 500 12 HIS A 130 106.74 -163.53 REMARK 500 13 SER A 103 106.06 -57.54 REMARK 500 13 SER A 106 -42.55 -142.63 REMARK 500 13 LYS A 124 99.88 -54.39 REMARK 500 14 LYS A 124 93.31 -62.47 REMARK 500 15 PRO A 67 109.60 -44.10 REMARK 500 15 SER A 103 109.24 -59.61 REMARK 500 15 ALA A 123 105.60 -59.77 REMARK 500 15 LYS A 124 74.40 33.94 REMARK 500 15 HIS A 131 97.58 -65.97 REMARK 500 16 ASP A 29 79.49 -107.31 REMARK 500 17 HIS A 48 79.11 57.70 REMARK 500 17 LYS A 124 -59.49 64.62 REMARK 500 17 HIS A 128 4.44 80.94 REMARK 500 17 HIS A 129 95.74 -66.09 REMARK 500 18 LYS A 79 108.97 -58.69 REMARK 500 19 SER A 103 96.82 -57.21 REMARK 500 19 HIS A 131 -164.60 -75.36 REMARK 500 20 ASP A 62 -3.08 71.81 REMARK 500 20 HIS A 129 74.10 -107.40 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: SR518 RELATED DB: TARGETDB REMARK 900 RELATED ID: 16942 RELATED DB: BMRB DBREF 2KY9 A 2 124 UNP O05503 YDHK_BACSU 83 205 SEQADV 2KY9 MET A 1 UNP O05503 INITIATING METHIONINE SEQADV 2KY9 LEU A 125 UNP O05503 EXPRESSION TAG SEQADV 2KY9 GLU A 126 UNP O05503 EXPRESSION TAG SEQADV 2KY9 HIS A 127 UNP O05503 EXPRESSION TAG SEQADV 2KY9 HIS A 128 UNP O05503 EXPRESSION TAG SEQADV 2KY9 HIS A 129 UNP O05503 EXPRESSION TAG SEQADV 2KY9 HIS A 130 UNP O05503 EXPRESSION TAG SEQADV 2KY9 HIS A 131 UNP O05503 EXPRESSION TAG SEQADV 2KY9 HIS A 132 UNP O05503 EXPRESSION TAG SEQRES 1 A 132 MET LYS VAL GLY SER GLN VAL ILE ILE ASN THR SER HIS SEQRES 2 A 132 MET LYS GLY MET LYS GLY ALA GLU ALA THR VAL THR GLY SEQRES 3 A 132 ALA TYR ASP THR THR ALA TYR VAL VAL SER TYR THR PRO SEQRES 4 A 132 THR ASN GLY GLY GLN ARG VAL ASP HIS HIS LYS TRP VAL SEQRES 5 A 132 ILE GLN GLU GLU ILE LYS ASP ALA GLY ASP LYS THR LEU SEQRES 6 A 132 GLN PRO GLY ASP GLN VAL ILE LEU GLU ALA SER HIS MET SEQRES 7 A 132 LYS GLY MET LYS GLY ALA THR ALA GLU ILE ASP SER ALA SEQRES 8 A 132 GLU LYS THR THR VAL TYR MET VAL ASP TYR THR SER THR SEQRES 9 A 132 THR SER GLY GLU LYS VAL LYS ASN HIS LYS TRP VAL THR SEQRES 10 A 132 GLU ASP GLU LEU SER ALA LYS LEU GLU HIS HIS HIS HIS SEQRES 11 A 132 HIS HIS HELIX 1 1 MET A 14 LYS A 18 5 5 HELIX 2 2 GLU A 55 ILE A 57 5 3 SHEET 1 A 4 VAL A 46 ILE A 53 0 SHEET 2 A 4 GLU A 21 TYR A 37 -1 N VAL A 35 O HIS A 49 SHEET 3 A 4 THR A 85 THR A 102 -1 O ASP A 89 N VAL A 34 SHEET 4 A 4 LYS A 109 THR A 117 -1 O VAL A 116 N TYR A 97 SHEET 1 B 5 GLN A 70 ILE A 72 0 SHEET 2 B 5 THR A 85 THR A 102 -1 O ALA A 86 N VAL A 71 SHEET 3 B 5 GLU A 21 TYR A 37 -1 N VAL A 34 O ASP A 89 SHEET 4 B 5 GLN A 6 ILE A 9 -1 N VAL A 7 O ALA A 22 SHEET 5 B 5 LEU A 121 ALA A 123 -1 O SER A 122 N ILE A 8 CISPEP 1 LYS A 50 TRP A 51 1 -2.33 CISPEP 2 LYS A 114 TRP A 115 1 -11.46 CISPEP 3 LYS A 50 TRP A 51 2 -11.20 CISPEP 4 LYS A 114 TRP A 115 2 -4.83 CISPEP 5 LYS A 50 TRP A 51 3 -0.63 CISPEP 6 LYS A 114 TRP A 115 3 -10.29 CISPEP 7 LYS A 50 TRP A 51 4 -9.37 CISPEP 8 LYS A 114 TRP A 115 4 1.08 CISPEP 9 LYS A 50 TRP A 51 5 0.43 CISPEP 10 LYS A 114 TRP A 115 5 -15.88 CISPEP 11 LYS A 50 TRP A 51 6 -14.12 CISPEP 12 LYS A 114 TRP A 115 6 -4.77 CISPEP 13 LYS A 50 TRP A 51 7 -7.95 CISPEP 14 LYS A 114 TRP A 115 7 -10.67 CISPEP 15 LYS A 50 TRP A 51 8 -0.83 CISPEP 16 LYS A 114 TRP A 115 8 -12.41 CISPEP 17 LYS A 50 TRP A 51 9 -4.13 CISPEP 18 LYS A 114 TRP A 115 9 -9.75 CISPEP 19 LYS A 50 TRP A 51 10 -5.87 CISPEP 20 LYS A 114 TRP A 115 10 -4.95 CISPEP 21 LYS A 50 TRP A 51 11 -11.50 CISPEP 22 LYS A 114 TRP A 115 11 -12.10 CISPEP 23 LYS A 50 TRP A 51 12 -10.18 CISPEP 24 LYS A 114 TRP A 115 12 0.68 CISPEP 25 LYS A 50 TRP A 51 13 -10.03 CISPEP 26 LYS A 114 TRP A 115 13 -13.53 CISPEP 27 LYS A 50 TRP A 51 14 -3.47 CISPEP 28 LYS A 114 TRP A 115 14 -11.23 CISPEP 29 LYS A 50 TRP A 51 15 4.86 CISPEP 30 LYS A 114 TRP A 115 15 -12.49 CISPEP 31 LYS A 50 TRP A 51 16 0.38 CISPEP 32 LYS A 114 TRP A 115 16 -8.13 CISPEP 33 LYS A 50 TRP A 51 17 2.26 CISPEP 34 LYS A 114 TRP A 115 17 -15.33 CISPEP 35 LYS A 50 TRP A 51 18 -7.39 CISPEP 36 LYS A 114 TRP A 115 18 -11.61 CISPEP 37 LYS A 50 TRP A 51 19 -4.47 CISPEP 38 LYS A 114 TRP A 115 19 -9.05 CISPEP 39 LYS A 50 TRP A 51 20 -9.44 CISPEP 40 LYS A 114 TRP A 115 20 4.22 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