HEADER TRANSCRIPTION 16-OCT-09 2WVD 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, C, D; 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 DNA-BINDING, KEYWDS 2 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 2WVD 1 REMARK REVDAT 3 26-MAY-10 2WVD 1 JRNL REMARK REVDAT 2 02-FEB-10 2WVD 1 JRNL REVDAT 1 19-JAN-10 2WVD 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. 2.65 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) : 2.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.96 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.180 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 40515 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.206 REMARK 3 R VALUE (WORKING SET) : 0.205 REMARK 3 FREE R VALUE : 0.231 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2081 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 38.9623 - 5.7041 0.98 3777 216 0.2131 0.2280 REMARK 3 2 5.7041 - 4.5297 0.99 3776 212 0.1766 0.1875 REMARK 3 3 4.5297 - 3.9578 0.99 3875 196 0.1577 0.1893 REMARK 3 4 3.9578 - 3.5962 1.00 3883 169 0.1796 0.2155 REMARK 3 5 3.5962 - 3.3386 1.00 3821 230 0.1880 0.2178 REMARK 3 6 3.3386 - 3.1418 1.00 3905 195 0.2278 0.2521 REMARK 3 7 3.1418 - 2.9845 1.00 3828 238 0.2392 0.2733 REMARK 3 8 2.9845 - 2.8547 1.00 3861 224 0.2549 0.2892 REMARK 3 9 2.8547 - 2.7448 1.00 3860 183 0.2606 0.2708 REMARK 3 10 2.7448 - 2.6501 1.00 3848 218 0.2894 0.3140 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 : 0.34 REMARK 3 B_SOL : 37.30 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.840 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.870 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 48.78 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 52.49 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -7.51690 REMARK 3 B22 (A**2) : 1.50280 REMARK 3 B33 (A**2) : 6.01420 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 : 0.003 4368 REMARK 3 ANGLE : 0.782 5881 REMARK 3 CHIRALITY : 0.060 683 REMARK 3 PLANARITY : 0.002 751 REMARK 3 DIHEDRAL : 18.659 1606 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN A OR CHAIN B) AND RESSEQ 6:63 REMARK 3 ORIGIN FOR THE GROUP (A): -29.0376 15.0133 -48.6571 REMARK 3 T TENSOR REMARK 3 T11: 0.1927 T22: 0.1975 REMARK 3 T33: 0.1311 T12: -0.0107 REMARK 3 T13: -0.0101 T23: 0.0102 REMARK 3 L TENSOR REMARK 3 L11: 2.2274 L22: 3.1170 REMARK 3 L33: 1.7088 L12: 0.4864 REMARK 3 L13: 0.1315 L23: -0.6223 REMARK 3 S TENSOR REMARK 3 S11: 0.0540 S12: -0.2808 S13: 0.1447 REMARK 3 S21: 0.2021 S22: 0.1143 S23: 0.1664 REMARK 3 S31: -0.0433 S32: -0.1080 S33: -0.0000 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A OR CHAIN B) AND RESSEQ 64:143 REMARK 3 ORIGIN FOR THE GROUP (A): -14.9259 6.9152 -32.4653 REMARK 3 T TENSOR REMARK 3 T11: 0.1248 T22: 0.1693 REMARK 3 T33: 0.2025 T12: 0.0381 REMARK 3 T13: -0.0360 T23: 0.0456 REMARK 3 L TENSOR REMARK 3 L11: 0.7935 L22: 2.2701 REMARK 3 L33: 1.7980 L12: 0.8386 REMARK 3 L13: -0.4673 L23: -0.9247 REMARK 3 S TENSOR REMARK 3 S11: -0.0556 S12: -0.0268 S13: 0.0110 REMARK 3 S21: 0.0446 S22: -0.0254 S23: -0.0970 REMARK 3 S31: -0.0389 S32: 0.0443 S33: 0.0000 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN C OR CHAIN D) AND RESSEQ 8:63 REMARK 3 ORIGIN FOR THE GROUP (A): 16.1528 -15.8488 -15.5146 REMARK 3 T TENSOR REMARK 3 T11: 0.1922 T22: 0.1411 REMARK 3 T33: 0.1604 T12: 0.0072 REMARK 3 T13: -0.0007 T23: 0.0296 REMARK 3 L TENSOR REMARK 3 L11: 1.6680 L22: 0.6235 REMARK 3 L33: 2.2904 L12: 0.1812 REMARK 3 L13: 0.0966 L23: 0.2230 REMARK 3 S TENSOR REMARK 3 S11: 0.0429 S12: -0.0817 S13: 0.0894 REMARK 3 S21: -0.0466 S22: -0.0969 S23: 0.0087 REMARK 3 S31: -0.1095 S32: 0.0245 S33: -0.0000 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN C OR CHAIN D) AND RESSEQ 64:145 REMARK 3 ORIGIN FOR THE GROUP (A): 2.0870 -1.7498 -26.1187 REMARK 3 T TENSOR REMARK 3 T11: 0.2039 T22: 0.2614 REMARK 3 T33: 0.2303 T12: 0.0349 REMARK 3 T13: -0.0268 T23: 0.0481 REMARK 3 L TENSOR REMARK 3 L11: 1.1446 L22: 1.3414 REMARK 3 L33: 1.1869 L12: 0.1902 REMARK 3 L13: -0.4538 L23: -0.3676 REMARK 3 S TENSOR REMARK 3 S11: 0.0107 S12: 0.0338 S13: -0.0484 REMARK 3 S21: 0.0183 S22: 0.0614 S23: 0.0005 REMARK 3 S31: -0.0486 S32: -0.0953 S33: 0.0000 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURE WAS REFINED USING FOBS+ REMARK 3 AND FOBS- AND NOT FOBS TO VERIFY THE PRESENCE OF METAL IONS REMARK 4 REMARK 4 2WVD 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_1290041247. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-FEB-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 : ID23-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8726 REMARK 200 MONOCHROMATOR : SI (111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21767 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.650 REMARK 200 RESOLUTION RANGE LOW (A) : 46.320 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.79 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.90 REMARK 200 R MERGE FOR SHELL (I) : 0.49000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 2CA9 REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.72 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.4-0.7 M AMMONIUM SULFATE, 100 MM REMARK 280 CITRATE PH 5-5.4 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 24.98500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 61.97500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 58.49000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 61.97500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.98500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 58.49000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: 6800 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13300 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -75.1 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D 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 350 REMARK 350 BIOMOLECULE: 2 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: 6890 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13410 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -76.7 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 400 REMARK 400 COMPOUND REMARK 400 ENGINEERED RESIDUE IN CHAIN A, CYS 96 TO SER REMARK 400 ENGINEERED RESIDUE IN CHAIN B, CYS 96 TO SER REMARK 400 ENGINEERED RESIDUE IN CHAIN C, CYS 96 TO SER REMARK 400 ENGINEERED RESIDUE IN CHAIN D, CYS 96 TO SER 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 GLU A 56 REMARK 465 ASP A 57 REMARK 465 ASN A 58 REMARK 465 SER A 142 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 PHE B 144 REMARK 465 GLU B 145 REMARK 465 TYR B 146 REMARK 465 ASN B 147 REMARK 465 GLU B 148 REMARK 465 MET C 1 REMARK 465 ASP C 2 REMARK 465 THR C 3 REMARK 465 PRO C 4 REMARK 465 ASN C 5 REMARK 465 LYS C 6 REMARK 465 ASP C 7 REMARK 465 ALA C 55 REMARK 465 GLU C 56 REMARK 465 ASP C 57 REMARK 465 ASN C 58 REMARK 465 PRO C 59 REMARK 465 TYR C 146 REMARK 465 ASN C 147 REMARK 465 GLU C 148 REMARK 465 MET D 1 REMARK 465 ASP D 2 REMARK 465 THR D 3 REMARK 465 PRO D 4 REMARK 465 ASN D 5 REMARK 465 LYS D 6 REMARK 465 ASP D 7 REMARK 465 TYR D 146 REMARK 465 ASN D 147 REMARK 465 GLU D 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 LYS A 6 CG CD CE NZ REMARK 470 ASP A 7 CG OD1 OD2 REMARK 470 ASP A 8 CG OD1 OD2 REMARK 470 GLN A 18 CG CD OE1 NE2 REMARK 470 ASN A 53 CG OD1 ND2 REMARK 470 TRP A 54 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP A 54 CZ3 CH2 REMARK 470 ASN A 60 CG OD1 ND2 REMARK 470 ARG A 77 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 104 CG CD OE1 OE2 REMARK 470 LYS B 31 CE NZ REMARK 470 ARG B 77 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 104 CG CD OE1 OE2 REMARK 470 ARG B 131 CG CD NE CZ NH1 NH2 REMARK 470 ASP C 8 CG OD1 OD2 REMARK 470 GLN C 18 CG CD OE1 NE2 REMARK 470 ASN C 53 CG OD1 ND2 REMARK 470 ASN C 60 CG OD1 ND2 REMARK 470 GLU C 62 CG CD OE1 OE2 REMARK 470 ARG C 77 CG CD NE CZ NH1 NH2 REMARK 470 ARG C 131 NE CZ NH1 NH2 REMARK 470 GLU C 145 CG CD OE1 OE2 REMARK 470 ASP D 8 CG OD1 OD2 REMARK 470 ILE D 10 CD1 REMARK 470 LYS D 31 CG CD CE NZ REMARK 470 ARG D 77 CG CD NE CZ NH1 NH2 REMARK 470 GLU D 145 CG CD OE1 OE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT 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 OG SER D 36 O3 SO4 D 1146 2.17 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 ASP A 7 -65.10 -93.61 REMARK 500 ARG A 77 79.44 -63.14 REMARK 500 GLU B 78 45.70 39.35 REMARK 500 PHE B 135 130.21 -177.29 REMARK 500 SER B 142 -70.63 -126.09 REMARK 500 SER C 9 -165.29 125.77 REMARK 500 ALA C 136 86.59 -154.79 REMARK 500 ALA C 141 -66.43 -102.99 REMARK 500 GLU D 78 -9.74 78.86 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1142 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 1144 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 1145 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 C 1146 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 D 1146 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 D 1147 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1143 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL D 1148 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 1146 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL C 1147 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL D 1149 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL D 1150 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: 2WVE RELATED DB: PDB REMARK 900 STRUCTURAL AND MECHANISTIC INSIGHTS INTO HELICOBACTER PYLORI NIKR REMARK 900 FUNCTION REMARK 900 RELATED ID: 2WVF 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 2WVD A 1 148 UNP O25896 NIKR_HELPY 1 148 DBREF 2WVD B 1 148 UNP O25896 NIKR_HELPY 1 148 DBREF 2WVD C 1 148 UNP O25896 NIKR_HELPY 1 148 DBREF 2WVD D 1 148 UNP O25896 NIKR_HELPY 1 148 SEQADV 2WVD SER A 96 UNP O25896 CYS 96 ENGINEERED MUTATION SEQADV 2WVD SER B 96 UNP O25896 CYS 96 ENGINEERED MUTATION SEQADV 2WVD SER C 96 UNP O25896 CYS 96 ENGINEERED MUTATION SEQADV 2WVD SER D 96 UNP O25896 CYS 96 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 HIS HIS 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 SER 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 HIS HIS 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 SER 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 SEQRES 1 C 148 MET ASP THR PRO ASN LYS ASP ASP SER ILE ILE ARG PHE SEQRES 2 C 148 SER VAL SER LEU GLN GLN ASN LEU LEU ASP GLU LEU ASP SEQRES 3 C 148 ASN ARG ILE ILE LYS ASN GLY TYR SER SER ARG SER GLU SEQRES 4 C 148 LEU VAL ARG ASP MET ILE ARG GLU LYS LEU VAL GLU ASP SEQRES 5 C 148 ASN TRP ALA GLU ASP ASN PRO ASN ASP GLU SER LYS ILE SEQRES 6 C 148 ALA VAL LEU VAL VAL ILE TYR ASP HIS HIS GLN ARG GLU SEQRES 7 C 148 LEU ASN GLN ARG MET ILE ASP ILE GLN HIS ALA SER GLY SEQRES 8 C 148 THR HIS VAL LEU SER THR THR HIS ILE HIS MET ASP GLU SEQRES 9 C 148 HIS ASN CYS LEU GLU THR ILE ILE LEU GLN GLY ASN SER SEQRES 10 C 148 PHE GLU ILE GLN ARG LEU GLN LEU GLU ILE GLY GLY LEU SEQRES 11 C 148 ARG GLY VAL LYS PHE ALA LYS LEU THR LYS ALA SER SER SEQRES 12 C 148 PHE GLU TYR ASN GLU SEQRES 1 D 148 MET ASP THR PRO ASN LYS ASP ASP SER ILE ILE ARG PHE SEQRES 2 D 148 SER VAL SER LEU GLN GLN ASN LEU LEU ASP GLU LEU ASP SEQRES 3 D 148 ASN ARG ILE ILE LYS ASN GLY TYR SER SER ARG SER GLU SEQRES 4 D 148 LEU VAL ARG ASP MET ILE ARG GLU LYS LEU VAL GLU ASP SEQRES 5 D 148 ASN TRP ALA GLU ASP ASN PRO ASN ASP GLU SER LYS ILE SEQRES 6 D 148 ALA VAL LEU VAL VAL ILE TYR ASP HIS HIS GLN ARG GLU SEQRES 7 D 148 LEU ASN GLN ARG MET ILE ASP ILE GLN HIS ALA SER GLY SEQRES 8 D 148 THR HIS VAL LEU SER THR THR HIS ILE HIS MET ASP GLU SEQRES 9 D 148 HIS ASN CYS LEU GLU THR ILE ILE LEU GLN GLY ASN SER SEQRES 10 D 148 PHE GLU ILE GLN ARG LEU GLN LEU GLU ILE GLY GLY LEU SEQRES 11 D 148 ARG GLY VAL LYS PHE ALA LYS LEU THR LYS ALA SER SER SEQRES 12 D 148 PHE GLU TYR ASN GLU HET SO4 A1142 5 HET GOL A1143 6 HET SO4 B1144 5 HET SO4 B1145 5 HET GOL B1146 6 HET SO4 C1146 5 HET GOL C1147 6 HET SO4 D1146 5 HET SO4 D1147 5 HET GOL D1148 6 HET GOL D1149 6 HET GOL D1150 6 HETNAM SO4 SULFATE ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 5 SO4 6(O4 S 2-) FORMUL 6 GOL 6(C3 H8 O3) FORMUL 17 HOH *59(H2 O) HELIX 1 1 GLN A 19 GLY A 33 1 15 HELIX 2 2 SER A 36 ASP A 52 1 17 HELIX 3 3 GLU A 78 GLY A 91 1 14 HELIX 4 4 ASN A 116 GLY A 129 1 14 HELIX 5 5 GLN B 19 GLY B 33 1 15 HELIX 6 6 SER B 36 ASP B 57 1 22 HELIX 7 7 GLU B 78 ALA B 89 1 12 HELIX 8 8 ASN B 116 GLY B 129 1 14 HELIX 9 9 GLN C 18 ASN C 32 1 15 HELIX 10 10 SER C 36 ASP C 52 1 17 HELIX 11 11 GLU C 78 ALA C 89 1 12 HELIX 12 12 ASN C 116 GLY C 129 1 14 HELIX 13 13 GLN D 18 GLY D 33 1 16 HELIX 14 14 SER D 36 ASP D 57 1 22 HELIX 15 15 GLU D 78 GLY D 91 1 14 HELIX 16 16 ASN D 116 GLY D 129 1 14 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 8 VAL A 133 LYS A 140 0 SHEET 2 AB 8 LYS A 64 TYR A 72 -1 O VAL A 67 N THR A 139 SHEET 3 AB 8 CYS A 107 GLY A 115 -1 O CYS A 107 N TYR A 72 SHEET 4 AB 8 HIS A 93 HIS A 101 -1 O HIS A 93 N GLN A 114 SHEET 5 AB 8 HIS D 93 HIS D 101 -1 O LEU D 95 N HIS A 101 SHEET 6 AB 8 CYS D 107 GLN D 114 -1 O LEU D 108 N ILE D 100 SHEET 7 AB 8 ILE D 65 TYR D 72 -1 O ALA D 66 N LEU D 113 SHEET 8 AB 8 VAL D 133 ALA D 141 -1 N LYS D 134 O ILE D 71 SHEET 1 BA 8 VAL B 133 ALA B 141 0 SHEET 2 BA 8 ILE B 65 TYR B 72 -1 O ILE B 65 N ALA B 141 SHEET 3 BA 8 CYS B 107 GLN B 114 -1 O CYS B 107 N TYR B 72 SHEET 4 BA 8 HIS B 93 HIS B 101 -1 O HIS B 93 N GLN B 114 SHEET 5 BA 8 HIS C 93 HIS C 101 -1 O LEU C 95 N HIS B 99 SHEET 6 BA 8 CYS C 107 GLY C 115 -1 O LEU C 108 N ILE C 100 SHEET 7 BA 8 LYS C 64 TYR C 72 -1 O LYS C 64 N GLY C 115 SHEET 8 BA 8 VAL C 133 SER C 143 -1 N LYS C 134 O ILE C 71 SHEET 1 CA 2 ILE C 11 LEU C 17 0 SHEET 2 CA 2 ILE D 11 LEU D 17 -1 O ILE D 11 N LEU C 17 SITE 1 AC1 2 SER A 36 ARG A 42 SITE 1 AC2 3 SER B 36 SER B 38 ARG B 42 SITE 1 AC3 6 ARG B 37 HOH B2014 HOH B2015 HOH B2016 SITE 2 AC3 6 HOH B2017 ARG C 12 SITE 1 AC4 4 SER C 36 SER C 38 ARG C 42 GLU C 78 SITE 1 AC5 3 SER D 36 ARG D 42 HOH D2019 SITE 1 AC6 5 ARG A 12 SER D 36 ARG D 37 HOH D2004 SITE 2 AC6 5 HOH D2005 SITE 1 AC7 6 TYR A 72 HIS A 74 ASN A 80 HIS A 99 SITE 2 AC7 6 HIS A 101 HOH A2009 SITE 1 AC8 4 THR A 97 HIS A 99 TYR D 72 HIS D 99 SITE 1 AC9 2 ARG B 42 ARG B 46 SITE 1 BC1 4 GLN C 18 ASN C 20 LEU C 21 ARG D 46 SITE 1 BC2 6 HIS A 74 HIS A 75 HIS A 101 GLN D 87 SITE 2 BC2 6 HIS D 93 VAL D 94 SITE 1 BC3 6 GLN A 87 HIS A 88 VAL A 94 HIS D 75 SITE 2 BC3 6 HIS D 101 GLU D 104 CRYST1 49.970 116.980 123.950 90.00 90.00 90.00 P 21 21 21 16 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 0.020012 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008548 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008068 0.00000