HEADER TRANSPORT PROTEIN 12-JAN-15 4XKN TITLE CRYSTAL STRUCTURE OF NIKA FROM STAPHYLOCOCCUS AUREUS IN COMPLEX WITH TITLE 2 NI(L-HIS)2 (CO-CRYSTALLIZATION WITH NI(II) AND L-HISTIDINE) COMPND MOL_ID: 1; COMPND 2 MOLECULE: NICKEL ABC TRANSPORTER SUBSTRATE-BINDING PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 19-491; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS USA300-ISMMS1; SOURCE 3 ORGANISM_TAXID: 1458279; SOURCE 4 GENE: AZ30_01190; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS EXTRACYTOPLASMIC NICKEL-BINDING PROTEIN, NICKEL IMPORT, ABC-TYPE KEYWDS 2 IMPORTER, TRANSPORT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR H.LEBRETTE,C.CAVAZZA REVDAT 4 10-JAN-24 4XKN 1 LINK REVDAT 3 15-APR-15 4XKN 1 JRNL REVDAT 2 18-FEB-15 4XKN 1 JRNL REVDAT 1 11-FEB-15 4XKN 0 JRNL AUTH H.LEBRETTE,E.BOREZEE-DURANT,L.MARTIN,P.RICHAUD,E.BOERI ERBA, JRNL AUTH 2 C.CAVAZZA JRNL TITL NOVEL INSIGHTS INTO NICKEL IMPORT IN STAPHYLOCOCCUS AUREUS: JRNL TITL 2 THE POSITIVE ROLE OF FREE HISTIDINE AND STRUCTURAL JRNL TITL 3 CHARACTERIZATION OF A NEW THIAZOLIDINE-TYPE NICKEL CHELATOR. JRNL REF METALLOMICS V. 7 613 2015 JRNL REFN ESSN 1756-591X JRNL PMID 25611161 JRNL DOI 10.1039/C4MT00295D REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.9_1692) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.76 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 42158 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.152 REMARK 3 R VALUE (WORKING SET) : 0.150 REMARK 3 FREE R VALUE : 0.192 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2109 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 45.7757 - 4.5612 0.99 2849 150 0.1597 0.2098 REMARK 3 2 4.5612 - 3.6208 1.00 2733 144 0.1203 0.1529 REMARK 3 3 3.6208 - 3.1633 1.00 2706 143 0.1285 0.1611 REMARK 3 4 3.1633 - 2.8741 1.00 2699 142 0.1388 0.1749 REMARK 3 5 2.8741 - 2.6681 1.00 2678 141 0.1491 0.1848 REMARK 3 6 2.6681 - 2.5108 1.00 2659 139 0.1452 0.2033 REMARK 3 7 2.5108 - 2.3851 1.00 2671 141 0.1507 0.1928 REMARK 3 8 2.3851 - 2.2813 1.00 2653 140 0.1415 0.1978 REMARK 3 9 2.2813 - 2.1934 1.00 2656 139 0.1423 0.1941 REMARK 3 10 2.1934 - 2.1178 1.00 2640 139 0.1473 0.1715 REMARK 3 11 2.1178 - 2.0515 0.99 2609 138 0.1886 0.2479 REMARK 3 12 2.0515 - 1.9929 1.00 2615 138 0.1771 0.2192 REMARK 3 13 1.9929 - 1.9404 1.00 2649 139 0.1873 0.2337 REMARK 3 14 1.9404 - 1.8931 1.00 2624 138 0.1908 0.2719 REMARK 3 15 1.8931 - 1.8501 0.99 2608 138 0.2288 0.2600 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.420 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.90 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.008 3957 REMARK 3 ANGLE : 1.106 5325 REMARK 3 CHIRALITY : 0.047 582 REMARK 3 PLANARITY : 0.005 680 REMARK 3 DIHEDRAL : 14.119 1534 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 8 THROUGH 145 ) REMARK 3 ORIGIN FOR THE GROUP (A): 43.3263 43.2234 12.0013 REMARK 3 T TENSOR REMARK 3 T11: 0.0908 T22: 0.1020 REMARK 3 T33: 0.1089 T12: 0.0087 REMARK 3 T13: 0.0201 T23: 0.0125 REMARK 3 L TENSOR REMARK 3 L11: 0.5405 L22: 1.1399 REMARK 3 L33: 1.1640 L12: -0.2191 REMARK 3 L13: -0.0455 L23: 0.5038 REMARK 3 S TENSOR REMARK 3 S11: -0.0366 S12: 0.0120 S13: -0.0343 REMARK 3 S21: 0.0297 S22: 0.0019 S23: 0.0551 REMARK 3 S31: 0.0567 S32: -0.0114 S33: 0.0280 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 146 THROUGH 230 ) REMARK 3 ORIGIN FOR THE GROUP (A): 48.8834 57.4968 28.9888 REMARK 3 T TENSOR REMARK 3 T11: 0.1323 T22: 0.1693 REMARK 3 T33: 0.1065 T12: 0.0123 REMARK 3 T13: -0.0201 T23: 0.0056 REMARK 3 L TENSOR REMARK 3 L11: 0.7785 L22: 1.5161 REMARK 3 L33: 1.0230 L12: 0.0756 REMARK 3 L13: 0.2036 L23: 0.1729 REMARK 3 S TENSOR REMARK 3 S11: -0.0761 S12: -0.0989 S13: 0.0688 REMARK 3 S21: 0.2011 S22: 0.0426 S23: -0.1109 REMARK 3 S31: -0.0498 S32: 0.2100 S33: 0.0355 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 231 THROUGH 472 ) REMARK 3 ORIGIN FOR THE GROUP (A): 38.5300 70.1383 7.6562 REMARK 3 T TENSOR REMARK 3 T11: 0.0919 T22: 0.1010 REMARK 3 T33: 0.1054 T12: -0.0147 REMARK 3 T13: 0.0047 T23: 0.0039 REMARK 3 L TENSOR REMARK 3 L11: 0.5221 L22: 0.9559 REMARK 3 L33: 0.8256 L12: -0.0920 REMARK 3 L13: 0.0769 L23: 0.0433 REMARK 3 S TENSOR REMARK 3 S11: -0.0040 S12: 0.0213 S13: 0.0685 REMARK 3 S21: -0.0784 S22: 0.0025 S23: -0.0599 REMARK 3 S31: -0.1045 S32: 0.0509 S33: 0.0069 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4XKN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 12-JAN-15. REMARK 100 THE DEPOSITION ID IS D_1000205836. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-DEC-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM30A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979621 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 42182 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 45.760 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.11000 REMARK 200 FOR THE DATA SET : 16.8900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.2 REMARK 200 DATA REDUNDANCY IN SHELL : 6.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.66900 REMARK 200 FOR SHELL : 2.940 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 4OFJ REMARK 200 REMARK 200 REMARK: PLATE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.27 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 27% PEG 3350, 0.1 M HEPES PH 7.0 - REMARK 280 PROTEIN PRE-INCUBATED WITH 2 AND 4 MOLAR EQUIVALENTS OF NICL2 REMARK 280 AND L-HISTIDINE, RESPECTIVELY., VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 31.24500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 57.76500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.60000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 57.76500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 31.24500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.60000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4390 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18870 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 1.0 KCAL/MOL 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. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 CYS A 1 REMARK 465 GLY A 2 REMARK 465 SER A 3 REMARK 465 MET A 4 REMARK 465 HIS A 5 REMARK 465 SER A 6 REMARK 465 SER A 7 REMARK 465 ARG A 473 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 LYS A 9 40.71 -105.46 REMARK 500 LEU A 17 64.70 69.49 REMARK 500 LYS A 20 -94.79 -101.40 REMARK 500 ALA A 51 -72.65 -121.68 REMARK 500 ARG A 165 -55.80 -136.02 REMARK 500 PHE A 233 38.90 -140.65 REMARK 500 THR A 277 -61.81 -126.26 REMARK 500 ILE A 374 69.31 -156.91 REMARK 500 LEU A 464 -58.09 -151.17 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 NI A 501 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 502 ND1 REMARK 620 2 HIS A 502 N 87.7 REMARK 620 3 HIS A 502 O 86.1 79.6 REMARK 620 4 HIS A 503 ND1 97.2 97.6 175.6 REMARK 620 5 HIS A 503 N 99.6 172.1 97.9 84.5 REMARK 620 6 HIS A 503 OXT 171.7 92.3 85.8 91.0 80.0 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 NI A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue HIS A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue HIS A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EPE A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 507 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 508 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 509 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 510 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 511 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 512 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 513 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 514 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 515 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 516 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 517 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 518 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 519 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 520 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 521 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4OFJ RELATED DB: PDB REMARK 900 THE SAME PROTEIN CO-PURIFIED WITH NI(L-HIS)2 REMARK 900 RELATED ID: 4XKP RELATED DB: PDB REMARK 900 THE SAME PROTEIN, CO-CRYSTALLIZATION WITH NI(II) AND BHI MEDIUM REMARK 900 SUPERNATANT REMARK 900 RELATED ID: 4XKQ RELATED DB: PDB REMARK 900 THE SAME PROTEIN, CO-CRYSTALLIZATION WITH NI(II) AND CD MEDIUM REMARK 900 SUPERNATANT REMARK 900 RELATED ID: 4XKR RELATED DB: PDB REMARK 900 THE SAME PROTEIN, CO-CRYSTALLIZATION WITH NI(II) AND CDDELTAHIS REMARK 900 MEDIUM SUPERNATANT DBREF 4XKN A 1 473 UNP W6DY02 W6DY02_STAAU 19 491 SEQRES 1 A 473 CYS GLY SER MET HIS SER SER GLY LYS ASP LEU ASN ILE SEQRES 2 A 473 SER LEU PRO LEU LYS THR LYS SER ILE ALA PRO TYR GLU SEQRES 3 A 473 THR ASP VAL PRO VAL LYS ILE GLY ALA ALA GLU SER LEU SEQRES 4 A 473 PHE LYS THR ASN ASP GLN GLY LYS ILE GLU LYS ALA LEU SEQRES 5 A 473 VAL LYS SER TYR HIS GLN PRO ASN ASP THR THR LEU ASP SEQRES 6 A 473 ILE GLU LEU LYS ASP ASN ILE LYS PHE GLN ASN GLY GLN SEQRES 7 A 473 LYS LEU THR ALA GLU LYS VAL LYS SER SER LEU GLU ASN SEQRES 8 A 473 SER MET LYS LYS SER ASP LEU VAL LYS TYR SER LEU PRO SEQRES 9 A 473 ILE SER SER ILE THR ALA LYS GLY GLN LYS LEU THR ILE SEQRES 10 A 473 LYS THR ASN SER ALA TYR PRO GLU LEU VAL SER GLU LEU SEQRES 11 A 473 ALA ASN PRO PHE MET ALA ILE TYR ASP THR ASP ALA LYS SEQRES 12 A 473 SER ASP VAL ASN GLN THR PRO VAL GLY THR GLY PRO TYR SEQRES 13 A 473 GLN ILE LYS ASP TYR LYS GLN SER ARG LYS ILE SER LEU SEQRES 14 A 473 SER ASN PHE LYS ASP TYR TRP GLN GLY LYS PRO LYS LEU SEQRES 15 A 473 ASP HIS ILE THR VAL THR TYR GLN GLU ASP GLY ASN ASN SEQRES 16 A 473 ARG VAL ARG ASN LEU GLU SER GLN LYS ASP ASP LEU ILE SEQRES 17 A 473 THR ASP VAL PRO VAL ASN LYS VAL GLN ASP ILE GLU ASN SEQRES 18 A 473 ASN GLN ASN LEU LYS VAL SER LYS GLU SER GLY PHE ARG SEQRES 19 A 473 THR SER LEU LEU MET TYR ASN HIS THR ASN LYS LYS MET SEQRES 20 A 473 THR LYS SER VAL ARG GLU ALA LEU ASP HIS ILE ILE ASP SEQRES 21 A 473 ARG GLN GLY ILE ALA ASP HIS ILE TYR GLN GLY TYR ALA SEQRES 22 A 473 LYS PRO ALA THR SER PRO PHE ASN ASP LYS ILE PRO TYR SEQRES 23 A 473 ILE LYS GLU PRO LYS LEU THR LYS GLN ASN ILE GLU GLN SEQRES 24 A 473 ALA LYS MET LEU LEU ALA LYS ASP GLY TYR THR LYS GLU SEQRES 25 A 473 HIS PRO LEU LYS ILE LYS LEU ILE THR TYR ASP GLY ARG SEQRES 26 A 473 PRO GLU LEU SER LYS ILE ALA GLN VAL LEU GLN SER ASP SEQRES 27 A 473 ALA LYS LYS ALA ASN ILE GLU ILE ASP ILE LYS SER VAL SEQRES 28 A 473 ASP ASP ILE GLU GLY TYR LEU LYS ASP ARG SER ALA TRP SEQRES 29 A 473 ASP ALA THR MET TYR SER PHE GLY THR ILE PRO ARG GLY SEQRES 30 A 473 ASP THR GLY TYR PHE PHE ASN GLN ALA TYR LYS LYS ASP SEQRES 31 A 473 GLY ALA ILE ASN LYS GLY ASP TYR ASN ASN SER ASN VAL SEQRES 32 A 473 ASP ASP LEU ILE ASN GLN LEU ASN HIS THR VAL ASP VAL SEQRES 33 A 473 LYS GLU ARG HIS ASN ILE SER ASN ASP ILE ILE LYS LEU SEQRES 34 A 473 SER SER ARG ASP VAL PRO ASN SER TYR ILE ALA TYR ASN SEQRES 35 A 473 ASP GLN ILE VAL ALA ALA ASN SER LYS VAL LYS ASN TYR SEQRES 36 A 473 LYS VAL THR PRO GLU GLY ILE TYR LEU ILE ASP TYR ARG SEQRES 37 A 473 THR THR ILE GLU ARG HET NI A 501 1 HET HIS A 502 11 HET HIS A 503 11 HET EPE A 504 15 HET GOL A 505 6 HET GOL A 506 6 HET GOL A 507 6 HET GOL A 508 6 HET GOL A 509 6 HET GOL A 510 6 HET GOL A 511 6 HET GOL A 512 6 HET GOL A 513 6 HET GOL A 514 6 HET GOL A 515 6 HET GOL A 516 6 HET GOL A 517 6 HET GOL A 518 6 HET GOL A 519 6 HET GOL A 520 6 HET GOL A 521 6 HETNAM NI NICKEL (II) ION HETNAM HIS HISTIDINE HETNAM EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID HETNAM GOL GLYCEROL HETSYN EPE HEPES HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 NI NI 2+ FORMUL 3 HIS 2(C6 H10 N3 O2 1+) FORMUL 5 EPE C8 H18 N2 O4 S FORMUL 6 GOL 17(C3 H8 O3) FORMUL 23 HOH *496(H2 O) HELIX 1 AA1 ASP A 28 ILE A 33 1 6 HELIX 2 AA2 THR A 81 SER A 96 1 16 HELIX 3 AA3 SER A 96 LEU A 103 1 8 HELIX 4 AA4 GLU A 125 LEU A 130 1 6 HELIX 5 AA5 ALA A 131 ALA A 136 5 6 HELIX 6 AA6 ASP A 192 SER A 202 1 11 HELIX 7 AA7 PRO A 212 ASN A 214 5 3 HELIX 8 AA8 LYS A 215 ASN A 222 1 8 HELIX 9 AA9 THR A 248 ILE A 259 1 12 HELIX 10 AB1 ASP A 260 ILE A 268 1 9 HELIX 11 AB2 ASN A 296 ASP A 307 1 12 HELIX 12 AB3 GLU A 327 LYS A 341 1 15 HELIX 13 AB4 ASP A 353 LYS A 359 1 7 HELIX 14 AB5 THR A 379 TYR A 387 1 9 HELIX 15 AB6 ASN A 400 HIS A 412 1 13 HELIX 16 AB7 ASP A 415 ARG A 432 1 18 SHEET 1 AA1 7 TYR A 156 LYS A 162 0 SHEET 2 AA1 7 LYS A 166 ASN A 171 -1 O LYS A 166 N LYS A 162 SHEET 3 AA1 7 HIS A 184 TYR A 189 -1 O VAL A 187 N ILE A 167 SHEET 4 AA1 7 ASP A 10 LEU A 15 1 N ILE A 13 O THR A 186 SHEET 5 AA1 7 LEU A 207 THR A 209 1 O LEU A 207 N SER A 14 SHEET 6 AA1 7 ASN A 436 ASN A 449 -1 O ALA A 447 N ILE A 208 SHEET 7 AA1 7 ALA A 273 PRO A 275 -1 N LYS A 274 O TYR A 441 SHEET 1 AA210 TYR A 156 LYS A 162 0 SHEET 2 AA210 LYS A 166 ASN A 171 -1 O LYS A 166 N LYS A 162 SHEET 3 AA210 HIS A 184 TYR A 189 -1 O VAL A 187 N ILE A 167 SHEET 4 AA210 ASP A 10 LEU A 15 1 N ILE A 13 O THR A 186 SHEET 5 AA210 LEU A 207 THR A 209 1 O LEU A 207 N SER A 14 SHEET 6 AA210 ASN A 436 ASN A 449 -1 O ALA A 447 N ILE A 208 SHEET 7 AA210 LEU A 225 TYR A 240 -1 N GLU A 230 O GLN A 444 SHEET 8 AA210 ALA A 366 GLY A 372 -1 O THR A 367 N MET A 239 SHEET 9 AA210 LEU A 315 THR A 321 1 N ILE A 320 O MET A 368 SHEET 10 AA210 ILE A 344 SER A 350 1 O GLU A 345 N LEU A 315 SHEET 1 AA3 2 PHE A 40 THR A 42 0 SHEET 2 AA3 2 ILE A 48 LYS A 50 -1 O GLU A 49 N LYS A 41 SHEET 1 AA4 4 VAL A 53 ASN A 60 0 SHEET 2 AA4 4 THR A 63 LEU A 68 -1 O GLU A 67 N LYS A 54 SHEET 3 AA4 4 LYS A 114 THR A 119 -1 O ILE A 117 N LEU A 64 SHEET 4 AA4 4 ILE A 105 LYS A 111 -1 N SER A 106 O LYS A 118 SHEET 1 AA5 2 VAL A 452 LYS A 453 0 SHEET 2 AA5 2 THR A 470 ILE A 471 -1 O THR A 470 N LYS A 453 LINK NI NI A 501 ND1 HIS A 502 1555 1555 2.06 LINK NI NI A 501 N HIS A 502 1555 1555 2.12 LINK NI NI A 501 O HIS A 502 1555 1555 2.15 LINK NI NI A 501 ND1 HIS A 503 1555 1555 2.10 LINK NI NI A 501 N HIS A 503 1555 1555 2.15 LINK NI NI A 501 OXT HIS A 503 1555 1555 2.15 SITE 1 AC1 2 HIS A 502 HIS A 503 SITE 1 AC2 11 LEU A 17 ARG A 234 TYR A 322 ARG A 325 SITE 2 AC2 11 ILE A 354 GLU A 355 TYR A 369 SER A 370 SITE 3 AC2 11 NI A 501 HIS A 503 HOH A 745 SITE 1 AC3 11 PHE A 134 ARG A 234 GLU A 355 TYR A 369 SITE 2 AC3 11 SER A 370 PHE A 371 GLY A 372 NI A 501 SITE 3 AC3 11 HIS A 502 HOH A 840 HOH A 851 SITE 1 AC4 11 ILE A 48 GLU A 49 LYS A 50 TYR A 56 SITE 2 AC4 11 TYR A 101 LYS A 389 ASP A 390 ASP A 404 SITE 3 AC4 11 GOL A 508 HOH A 613 HOH A 660 SITE 1 AC5 6 THR A 109 LYS A 114 LEU A 115 THR A 116 SITE 2 AC5 6 LYS A 245 HOH A 667 SITE 1 AC6 9 LYS A 32 LYS A 456 GLY A 461 ILE A 462 SITE 2 AC6 9 TYR A 463 HOH A 778 HOH A 919 HOH A 964 SITE 3 AC6 9 HOH A 969 SITE 1 AC7 8 GLU A 83 ALA A 110 GLN A 295 ASP A 338 SITE 2 AC7 8 LYS A 341 GOL A 520 HOH A 645 HOH A 688 SITE 1 AC8 6 TYR A 101 ASN A 384 LYS A 388 LYS A 389 SITE 2 AC8 6 EPE A 504 HOH A 781 SITE 1 AC9 8 ASP A 260 GLY A 263 ILE A 264 HIS A 267 SITE 2 AC9 8 ILE A 268 VAL A 334 HOH A 817 HOH A 818 SITE 1 AD1 10 ASP A 256 ARG A 261 THR A 277 PRO A 290 SITE 2 AD1 10 LYS A 291 THR A 293 SER A 431 HOH A 783 SITE 3 AD1 10 HOH A 805 HOH A 815 SITE 1 AD2 9 GLN A 58 ASN A 60 ASP A 61 THR A 63 SITE 2 AD2 9 THR A 119 ALA A 122 TYR A 123 HOH A 777 SITE 3 AD2 9 HOH A1039 SITE 1 AD3 9 SER A 144 ASP A 145 THR A 149 ILE A 348 SITE 2 AD3 9 LYS A 349 SER A 350 GOL A 519 HOH A 606 SITE 3 AD3 9 HOH A 668 SITE 1 AD4 7 TYR A 463 HOH A 750 HOH A 806 HOH A 819 SITE 2 AD4 7 HOH A 865 HOH A 891 HOH A 952 SITE 1 AD5 4 LYS A 226 LYS A 453 ASN A 454 TYR A 455 SITE 1 AD6 7 LYS A 143 LYS A 349 VAL A 351 ASP A 352 SITE 2 AD6 7 ASP A 353 HOH A 627 HOH A 885 SITE 1 AD7 11 LYS A 114 HIS A 242 LYS A 245 MET A 247 SITE 2 AD7 11 THR A 248 ARG A 252 GOL A 518 HOH A 605 SITE 3 AD7 11 HOH A 615 HOH A 683 HOH A 684 SITE 1 AD8 4 LYS A 54 LYS A 69 ASP A 70 ASN A 402 SITE 1 AD9 9 SER A 55 GLU A 67 ARG A 252 ASN A 399 SITE 2 AD9 9 ASN A 400 GOL A 516 HOH A 603 HOH A 605 SITE 3 AD9 9 HOH A 674 SITE 1 AE1 8 THR A 149 GLN A 157 ILE A 158 LYS A 159 SITE 2 AE1 8 LYS A 349 GOL A 512 HOH A 601 HOH A 665 SITE 1 AE2 5 ALA A 110 ASN A 296 ILE A 297 GLU A 298 SITE 2 AE2 5 GOL A 507 SITE 1 AE3 4 GLU A 90 ILE A 108 HOH A 829 HOH A 944 CRYST1 62.490 67.200 115.530 90.00 90.00 90.00 P 21 21 21 4 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 0.016003 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014881 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008656 0.00000