HEADER TRANSCRIPTION 16-OCT-09 2WVF TITLE STRUCTURAL AND MECHANISTIC INSIGHTS INTO HELICOBACTER PYLORI NIKR TITLE 2 FUNCTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE NICKEL-RESPONSIVE REGULATOR; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: HPNIKR; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HELICOBACTER PYLORI; SOURCE 3 ORGANISM_TAXID: 85962; SOURCE 4 STRAIN: 26695; SOURCE 5 ATCC: 43504; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; 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: PET11A KEYWDS TRANSCRIPTION FACTOR, TRANSCRIPTION REGULATION, RHH, NIKR, DNA- KEYWDS 2 BINDING, TRANSCRIPTION, METAL-BINDING, METALLOREGULATOR EXPDTA X-RAY DIFFRACTION AUTHOR C.DIAN,C.BAHLAWANE,C.MULLER,A.ROUND,C.DELAY,C.FAUQUANT,K.SCHAUER,H.DE AUTHOR 2 REUSE,I.MICHAUD-SORET,L.TERRADOT REVDAT 4 20-DEC-23 2WVF 1 REMARK LINK REVDAT 3 26-MAY-10 2WVF 1 JRNL REMARK REVDAT 2 02-FEB-10 2WVF 1 JRNL REVDAT 1 19-JAN-10 2WVF 0 JRNL AUTH C.BAHLAWANE,C.DIAN,C.MULLER,A.ROUND,C.FAUQUANT,K.SCHAUER, JRNL AUTH 2 H.DE REUSE,L.TERRADOT,I.MICHAUD-SORET JRNL TITL STRUCTURAL AND MECHANISTIC INSIGHTS INTO HELICOBACTER PYLORI JRNL TITL 2 NIKR ACTIVATION. JRNL REF NUCLEIC ACIDS RES. V. 38 3106 2010 JRNL REFN ISSN 0305-1048 JRNL PMID 20089510 JRNL DOI 10.1093/NAR/GKP1216 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.08 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.850 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 82300 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.200 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 4162 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 32.0870 - 3.4458 0.96 7582 415 0.1789 0.1857 REMARK 3 2 3.4458 - 2.7355 0.99 7810 446 0.1695 0.1859 REMARK 3 3 2.7355 - 2.3899 1.00 7882 387 0.1794 0.1985 REMARK 3 4 2.3899 - 2.1714 1.00 7889 399 0.1712 0.2114 REMARK 3 5 2.1714 - 2.0158 1.00 7871 434 0.1682 0.1736 REMARK 3 6 2.0158 - 1.8970 1.00 7858 435 0.1797 0.2130 REMARK 3 7 1.8970 - 1.8020 1.00 7867 425 0.1937 0.2020 REMARK 3 8 1.8020 - 1.7235 1.00 7867 422 0.2098 0.2276 REMARK 3 9 1.7235 - 1.6572 1.00 7903 430 0.2307 0.2619 REMARK 3 10 1.6572 - 1.6000 0.97 7609 369 0.2765 0.2677 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 : 0.43 REMARK 3 B_SOL : 75.02 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.070 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.370 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.15 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.71 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.80570 REMARK 3 B22 (A**2) : 0.80570 REMARK 3 B33 (A**2) : -1.61140 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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 : 0.005 2256 REMARK 3 ANGLE : 0.998 3032 REMARK 3 CHIRALITY : 0.082 349 REMARK 3 PLANARITY : 0.004 389 REMARK 3 DIHEDRAL : 17.910 842 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN 'A' OR CHAIN 'B') AND (RESSEQ 9:63) REMARK 3 ORIGIN FOR THE GROUP (A): 32.2094 31.7162 -3.9015 REMARK 3 T TENSOR REMARK 3 T11: 0.1228 T22: 0.0654 REMARK 3 T33: 0.1379 T12: -0.0417 REMARK 3 T13: 0.0385 T23: -0.0105 REMARK 3 L TENSOR REMARK 3 L11: 1.1691 L22: 0.2163 REMARK 3 L33: 0.4112 L12: 1.0865 REMARK 3 L13: -0.2455 L23: -0.1088 REMARK 3 S TENSOR REMARK 3 S11: 0.1530 S12: 0.0883 S13: 0.2244 REMARK 3 S21: 0.0984 S22: -0.1054 S23: 0.2536 REMARK 3 S31: -0.0675 S32: -0.1305 S33: -0.0393 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN 'A' OR CHAIN 'B') AND (RESSEQ 64:147) REMARK 3 ORIGIN FOR THE GROUP (A): 28.8660 9.0878 -3.7485 REMARK 3 T TENSOR REMARK 3 T11: 0.1277 T22: 0.0364 REMARK 3 T33: 0.0902 T12: -0.0080 REMARK 3 T13: -0.0024 T23: 0.0002 REMARK 3 L TENSOR REMARK 3 L11: 0.2239 L22: 0.5963 REMARK 3 L33: 1.3473 L12: 0.1863 REMARK 3 L13: 0.1096 L23: 0.2443 REMARK 3 S TENSOR REMARK 3 S11: -0.0487 S12: 0.0029 S13: -0.0219 REMARK 3 S21: -0.0706 S22: 0.0367 S23: -0.0084 REMARK 3 S31: -0.1358 S32: 0.0511 S33: 0.0260 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REFINED USING FOBS+ AND FOBS-, NOT FOBS REMARK 3 TO VERIFY THE PRESENCE OF METAL IONS. REMARK 4 REMARK 4 2WVF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-OCT-09. REMARK 100 THE DEPOSITION ID IS D_1290041249. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-APR-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9725 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 44866 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 61.080 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 7.600 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.40 REMARK 200 R MERGE FOR SHELL (I) : 0.51000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.500 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: PDB ENTRY 2CAD REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.44 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.4 TO 0.7 M AMMONIUM SULFATE AND 100 REMARK 280 MM CITRATE PH 5-5.4 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+5/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 75.39600 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 150.79200 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 113.09400 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 188.49000 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 37.69800 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 75.39600 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 150.79200 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 188.49000 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 113.09400 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 37.69800 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 8070 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13720 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -82.1 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A2022 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2044 LIES ON A SPECIAL POSITION. REMARK 400 REMARK 400 COMPOUND REMARK 400 ENGINEERED RESIDUE IN CHAIN A, HIS 74 TO GLY REMARK 400 ENGINEERED RESIDUE IN CHAIN A, HIS 75 TO GLY REMARK 400 ENGINEERED RESIDUE IN CHAIN B, HIS 74 TO GLY REMARK 400 ENGINEERED RESIDUE IN CHAIN B, HIS 75 TO GLY 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 MET A 1 REMARK 465 ASP A 2 REMARK 465 THR A 3 REMARK 465 PRO A 4 REMARK 465 ASN A 5 REMARK 465 LYS A 6 REMARK 465 ASP A 7 REMARK 465 ASP A 8 REMARK 465 SER A 143 REMARK 465 PHE A 144 REMARK 465 GLU A 145 REMARK 465 TYR A 146 REMARK 465 ASN A 147 REMARK 465 GLU A 148 REMARK 465 MET B 1 REMARK 465 ASP B 2 REMARK 465 THR B 3 REMARK 465 PRO B 4 REMARK 465 ASN B 5 REMARK 465 LYS B 6 REMARK 465 ASP B 7 REMARK 465 ASP B 8 REMARK 465 GLU B 148 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLN A 18 CD OE1 NE2 REMARK 470 LYS A 48 CG CD CE NZ REMARK 470 GLU A 56 CG CD OE1 OE2 REMARK 470 ASP A 57 CG OD1 OD2 REMARK 470 GLU A 62 CD OE1 OE2 REMARK 470 GLU A 104 CG CD OE1 OE2 REMARK 470 ARG B 12 CG CD NE CZ NH1 NH2 REMARK 470 ASN B 20 CG OD1 ND2 REMARK 470 GLU B 24 CG CD OE1 OE2 REMARK 470 GLU B 39 CG CD OE1 OE2 REMARK 470 ASN B 58 CG OD1 ND2 REMARK 470 GLU B 104 CD OE1 OE2 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 ASP A 57 -140.13 30.71 REMARK 500 ASP A 103 -156.80 -148.68 REMARK 500 ASP B 57 -123.47 36.72 REMARK 500 GLU B 78 -15.72 75.94 REMARK 500 ASP B 103 -167.78 -160.71 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 B1148 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 88 NE2 REMARK 620 2 HIS B 99 NE2 173.8 REMARK 620 3 HIS B 101 ND1 88.4 87.2 REMARK 620 4 CYS B 107 SG 89.9 94.9 175.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI A1143 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 101 NE2 REMARK 620 2 HOH A2058 O 89.1 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI B 1148 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 1143 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1144 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 1149 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 1150 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1145 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT A 1146 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT B 1151 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT A 1147 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT A 1148 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT A 1149 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT B 1152 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT A 1150 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1151 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1152 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2CAJ RELATED DB: PDB REMARK 900 NI2-HPNIKR HPNIKR IN CLOSED TRANS- CONFORMATION AND NICKEL BOUND TO REMARK 900 4 INTERMEDIARY SITES REMARK 900 RELATED ID: 2CA9 RELATED DB: PDB REMARK 900 APO-NIKR FROM HELICOBACTER PYLORI IN CLOSED TRANS-CONFORMATION REMARK 900 RELATED ID: 2CAD RELATED DB: PDB REMARK 900 NIKR FROM HELICOBACTER PYLORI IN CLOSED TRANS-CONFORMATION AND REMARK 900 NICKEL BOUND TO 2F, 2X AND 2I SITES REMARK 900 RELATED ID: 2WVB RELATED DB: PDB REMARK 900 STRUCTURAL AND MECHANISTIC INSIGHTS INTO HELICOBACTER PYLORI NIKR REMARK 900 FUNCTION REMARK 900 RELATED ID: 2WVD RELATED DB: PDB REMARK 900 STRUCTURAL AND MECHANISTIC INSIGHTS INTO HELICOBACTER PYLORI NIKR REMARK 900 FUNCTION REMARK 900 RELATED ID: 2WVE RELATED DB: PDB REMARK 900 STRUCTURAL AND MECHANISTIC INSIGHTS INTO HELICOBACTER PYLORI NIKR REMARK 900 FUNCTION REMARK 900 RELATED ID: 2WVC RELATED DB: PDB REMARK 900 STRUCTURAL AND MECHANISTIC INSIGHTS INTO HELICOBACTER PYLORI NIKR REMARK 900 FUNCTION DBREF 2WVF A 1 148 UNP O25896 NIKR_HELPY 1 148 DBREF 2WVF B 1 148 UNP O25896 NIKR_HELPY 1 148 SEQADV 2WVF GLY A 74 UNP O25896 HIS 74 ENGINEERED MUTATION SEQADV 2WVF GLY A 75 UNP O25896 HIS 75 ENGINEERED MUTATION SEQADV 2WVF GLY B 74 UNP O25896 HIS 74 ENGINEERED MUTATION SEQADV 2WVF GLY B 75 UNP O25896 HIS 75 ENGINEERED MUTATION SEQRES 1 A 148 MET ASP THR PRO ASN LYS ASP ASP SER ILE ILE ARG PHE SEQRES 2 A 148 SER VAL SER LEU GLN GLN ASN LEU LEU ASP GLU LEU ASP SEQRES 3 A 148 ASN ARG ILE ILE LYS ASN GLY TYR SER SER ARG SER GLU SEQRES 4 A 148 LEU VAL ARG ASP MET ILE ARG GLU LYS LEU VAL GLU ASP SEQRES 5 A 148 ASN TRP ALA GLU ASP ASN PRO ASN ASP GLU SER LYS ILE SEQRES 6 A 148 ALA VAL LEU VAL VAL ILE TYR ASP GLY GLY GLN ARG GLU SEQRES 7 A 148 LEU ASN GLN ARG MET ILE ASP ILE GLN HIS ALA SER GLY SEQRES 8 A 148 THR HIS VAL LEU CYS THR THR HIS ILE HIS MET ASP GLU SEQRES 9 A 148 HIS ASN CYS LEU GLU THR ILE ILE LEU GLN GLY ASN SER SEQRES 10 A 148 PHE GLU ILE GLN ARG LEU GLN LEU GLU ILE GLY GLY LEU SEQRES 11 A 148 ARG GLY VAL LYS PHE ALA LYS LEU THR LYS ALA SER SER SEQRES 12 A 148 PHE GLU TYR ASN GLU SEQRES 1 B 148 MET ASP THR PRO ASN LYS ASP ASP SER ILE ILE ARG PHE SEQRES 2 B 148 SER VAL SER LEU GLN GLN ASN LEU LEU ASP GLU LEU ASP SEQRES 3 B 148 ASN ARG ILE ILE LYS ASN GLY TYR SER SER ARG SER GLU SEQRES 4 B 148 LEU VAL ARG ASP MET ILE ARG GLU LYS LEU VAL GLU ASP SEQRES 5 B 148 ASN TRP ALA GLU ASP ASN PRO ASN ASP GLU SER LYS ILE SEQRES 6 B 148 ALA VAL LEU VAL VAL ILE TYR ASP GLY GLY GLN ARG GLU SEQRES 7 B 148 LEU ASN GLN ARG MET ILE ASP ILE GLN HIS ALA SER GLY SEQRES 8 B 148 THR HIS VAL LEU CYS THR THR HIS ILE HIS MET ASP GLU SEQRES 9 B 148 HIS ASN CYS LEU GLU THR ILE ILE LEU GLN GLY ASN SER SEQRES 10 B 148 PHE GLU ILE GLN ARG LEU GLN LEU GLU ILE GLY GLY LEU SEQRES 11 B 148 ARG GLY VAL LYS PHE ALA LYS LEU THR LYS ALA SER SER SEQRES 12 B 148 PHE GLU TYR ASN GLU HET NI A1143 1 HET GOL A1144 6 HET GOL A1145 6 HET FMT A1146 3 HET FMT A1147 3 HET FMT A1148 3 HET FMT A1149 3 HET FMT A1150 3 HET SO4 A1151 5 HET SO4 A1152 5 HET NI B1148 1 HET GOL B1149 6 HET GOL B1150 6 HET FMT B1151 3 HET FMT B1152 3 HETNAM NI NICKEL (II) ION HETNAM GOL GLYCEROL HETNAM FMT FORMIC ACID HETNAM SO4 SULFATE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 NI 2(NI 2+) FORMUL 4 GOL 4(C3 H8 O3) FORMUL 6 FMT 7(C H2 O2) FORMUL 11 SO4 2(O4 S 2-) FORMUL 18 HOH *174(H2 O) HELIX 1 1 GLN A 19 GLY A 33 1 15 HELIX 2 2 SER A 36 GLU A 51 1 16 HELIX 3 3 GLU A 78 SER A 90 1 13 HELIX 4 4 ASN A 116 GLY A 129 1 14 HELIX 5 5 GLN B 19 LYS B 31 1 13 HELIX 6 6 SER B 36 ALA B 55 1 20 HELIX 7 7 GLU B 78 GLY B 91 1 14 HELIX 8 8 ASN B 116 GLY B 129 1 14 HELIX 9 9 SER B 142 TYR B 146 5 5 SHEET 1 AA 2 ILE A 10 GLN A 18 0 SHEET 2 AA 2 ILE B 10 GLN B 18 -1 O ILE B 11 N LEU A 17 SHEET 1 AB 4 HIS A 93 HIS A 101 0 SHEET 2 AB 4 ASN A 106 GLY A 115 -1 O LEU A 108 N ILE A 100 SHEET 3 AB 4 LYS A 64 ASP A 73 -1 O LYS A 64 N GLY A 115 SHEET 4 AB 4 VAL A 133 ALA A 141 -1 N LYS A 134 O ILE A 71 SHEET 1 BA 4 HIS B 93 ASP B 103 0 SHEET 2 BA 4 ASN B 106 GLY B 115 -1 O ASN B 106 N MET B 102 SHEET 3 BA 4 LYS B 64 TYR B 72 -1 O LYS B 64 N GLY B 115 SHEET 4 BA 4 VAL B 133 ALA B 141 -1 N LYS B 134 O ILE B 71 LINK NE2 HIS A 88 NI NI B1148 8555 1555 2.06 LINK NE2 HIS A 101 NI NI A1143 1555 1555 2.32 LINK NI NI A1143 O HOH A2058 1555 1555 2.42 LINK NE2 HIS B 99 NI NI B1148 1555 1555 2.05 LINK ND1 HIS B 101 NI NI B1148 1555 1555 2.04 LINK SG CYS B 107 NI NI B1148 1555 1555 2.21 SITE 1 AC1 4 HIS A 88 HIS B 99 HIS B 101 CYS B 107 SITE 1 AC2 4 HIS A 101 HOH A2058 HIS B 88 HOH B2038 SITE 1 AC3 6 GLU A 78 ARG A 82 ILE A 86 FMT A1146 SITE 2 AC3 6 HOH A2044 ARG B 77 SITE 1 AC4 6 ASN B 80 MET B 83 GLN B 87 THR B 97 SITE 2 AC4 6 GLU B 109 ILE B 111 SITE 1 AC5 2 SER A 142 ILE B 71 SITE 1 AC6 10 ILE A 30 LYS A 31 GLY A 33 ARG A 122 SITE 2 AC6 10 HOH A2085 HOH A2086 GLU B 78 ARG B 82 SITE 3 AC6 10 HOH B2004 HOH B2062 SITE 1 AC7 4 GLU A 78 GOL A1144 HOH A2087 HOH A2088 SITE 1 AC8 5 TYR A 34 LYS B 48 ASP B 52 GLY B 129 SITE 2 AC8 5 HOH B2076 SITE 1 AC9 7 GLN A 87 THR A 97 HIS A 99 HOH A2089 SITE 2 AC9 7 HOH A2090 HIS B 99 HIS B 101 SITE 1 BC1 5 ARG A 77 ARG A 82 GLY A 129 ARG A 131 SITE 2 BC1 5 HOH A2092 SITE 1 BC2 2 THR A 139 LYS A 140 SITE 1 BC3 4 HIS A 88 ASP B 103 GLU B 104 HOH B2077 SITE 1 BC4 3 ARG A 37 HOH A2093 ILE B 11 SITE 1 BC5 4 GLU A 39 ARG A 42 ASP A 43 ARG A 46 SITE 1 BC6 9 SER A 35 GLY A 91 GLU A 119 ARG A 122 SITE 2 BC6 9 HOH A2049 HOH A2094 HOH A2096 HOH A2097 SITE 3 BC6 9 ARG B 131 CRYST1 70.534 70.534 226.188 90.00 90.00 120.00 P 61 2 2 24 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 0.014178 0.008185 0.000000 0.00000 SCALE2 0.000000 0.016371 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004421 0.00000