HEADER TRANSCRIPTION 20-DEC-05 2CA9 TITLE APO-NIKR FROM HELICOBACTER PYLORI IN CLOSED TRANS-CONFORMATION COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE NICKEL-RESPONSIVE REGULATOR; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HELICOBACTER PYLORI; SOURCE 3 ORGANISM_TAXID: 85962; SOURCE 4 STRAIN: 26695; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET11A KEYWDS NICKEL UPTAKE, TRANSCRIPTION REGULATOR, RIBBON-HELIX-HELIX, ACIDIC- KEYWDS 2 ADAPTIVE RESPONSE, TRANSCRIPTIONAL REGULATION, DNA-BINDING, METAL- KEYWDS 3 BINDING, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR C.DIAN,K.SCHAUER,U.KAPP,S.M.MCSWEENEY,A.LABIGNE,L.TERRADOT REVDAT 6 23-OCT-24 2CA9 1 REMARK REVDAT 5 01-MAY-24 2CA9 1 REMARK REVDAT 4 06-MAR-13 2CA9 1 HEADER KEYWDS REMARK VERSN REVDAT 4 2 1 HETNAM HETSYN FORMUL REVDAT 3 24-FEB-09 2CA9 1 VERSN REVDAT 2 16-AUG-06 2CA9 1 JRNL REVDAT 1 17-JUL-06 2CA9 0 JRNL AUTH C.DIAN,K.SCHAUER,U.KAPP,S.M.MCSWEENEY,A.LABIGNE,L.TERRADOT JRNL TITL STRUCTURAL BASIS OF THE NICKEL RESPONSE IN HELICOBACTER JRNL TITL 2 PYLORI: CRYSTAL STRUCTURES OF HPNIKR IN APO AND NICKEL-BOUND JRNL TITL 3 STATES. JRNL REF J.MOL.BIOL. V. 361 715 2006 JRNL REFN ISSN 0022-2836 JRNL PMID 16872629 JRNL DOI 10.1016/J.JMB.2006.06.058 REMARK 2 REMARK 2 RESOLUTION. 2.05 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 61.55 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 21171 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.201 REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.250 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1140 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.05 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.10 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1517 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2220 REMARK 3 BIN FREE R VALUE SET COUNT : 85 REMARK 3 BIN FREE R VALUE : 0.2860 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2171 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 39 REMARK 3 SOLVENT ATOMS : 127 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.66 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.02000 REMARK 3 B22 (A**2) : -0.02000 REMARK 3 B33 (A**2) : 0.03000 REMARK 3 B12 (A**2) : -0.01000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.192 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.178 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.118 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.171 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.943 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.909 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2344 ; 0.018 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3161 ; 1.673 ; 1.938 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 292 ; 6.913 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 126 ;38.215 ;24.444 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 429 ;17.517 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;22.545 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 354 ; 0.134 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1774 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1023 ; 0.232 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1587 ; 0.304 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 160 ; 0.176 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 69 ; 0.245 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 22 ; 0.343 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1469 ; 1.518 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2277 ; 2.338 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 965 ; 3.340 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 880 ; 5.163 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. REMARK 4 REMARK 4 2CA9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 20-DEC-05. REMARK 100 THE DEPOSITION ID IS D_1290026892. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 4.80 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9340 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 : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24159 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.050 REMARK 200 RESOLUTION RANGE LOW (A) : 61.550 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 5.400 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.16 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : 5.50 REMARK 200 R MERGE FOR SHELL (I) : 0.44000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NIKR FROM HELICOBACTER PYLORI SOLVED BY SAD METHOD REMARK 200 USING MERCURY DERIVATIVE. REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.9-1 M NA-FORMATE, O.1 M NA-CITRATE REMARK 280 PH 4, PH 4.80 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 76.34100 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 152.68200 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 114.51150 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 190.85250 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 38.17050 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 76.34100 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 152.68200 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 190.85250 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 114.51150 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 38.17050 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 18050 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23590 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -92.7 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 350 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 C FMT A1148 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2030 LIES ON A SPECIAL POSITION. REMARK 400 REMARK 400 COMPOUND REMARK 400 TRANSCRIPTIONAL REGULATOR. 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 GLU A 51 REMARK 465 ASP A 52 REMARK 465 ASN A 53 REMARK 465 TRP A 54 REMARK 465 ALA A 55 REMARK 465 GLU A 56 REMARK 465 ASP A 57 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 ASP A 8 CG OD1 OD2 REMARK 470 ILE A 11 CD1 REMARK 470 LYS A 48 CG CD CE NZ REMARK 470 SER A 143 OG REMARK 470 PHE A 144 CG CD1 CD2 CE1 CE2 CZ REMARK 470 SER B 9 OG REMARK 470 ARG B 12 CG CD NE CZ NH1 NH2 REMARK 470 ASP B 57 CB CG OD1 OD2 REMARK 470 LYS B 137 CE NZ 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 SER A 9 163.20 172.04 REMARK 500 GLU A 78 -0.90 66.25 REMARK 500 CYS A 96 145.45 -177.28 REMARK 500 ASP A 103 -159.65 -153.07 REMARK 500 GLU A 145 46.55 -85.21 REMARK 500 ASP B 57 113.70 -38.38 REMARK 500 ASN B 58 130.64 -38.42 REMARK 500 GLU B 78 -19.96 80.23 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ASP A 8 SER A 9 -144.66 REMARK 500 REMARK 500 REMARK: NULL REMARK 650 REMARK 650 HELIX REMARK 650 DETERMINATION METHOD: AUTHOR PROVIDED. REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: AUTHOR PROVIDED. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT A 1147 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT A 1148 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT A 1149 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT A 1150 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1151 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1152 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT B 1148 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT B 1149 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT B 1150 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 1151 REMARK 900 REMARK 900 RELATED ENTRIES 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: 2CAJ RELATED DB: PDB REMARK 900 NI2-HPNIKR HPNIKR IN CLOSED TRANS- CONFORMATION AND NICKEL BOUND TO REMARK 900 4 INTERMEDIARY SITES DBREF 2CA9 A 1 148 UNP O25896 NIKR_HELPY 1 148 DBREF 2CA9 B 1 148 UNP O25896 NIKR_HELPY 1 148 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 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 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 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 FMT A1147 3 HET FMT A1148 3 HET FMT A1149 3 HET FMT A1150 3 HET GOL A1151 6 HET GOL A1152 6 HET FMT B1148 3 HET FMT B1149 3 HET FMT B1150 3 HET GOL B1151 6 HETNAM FMT FORMIC ACID HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 FMT 7(C H2 O2) FORMUL 7 GOL 3(C3 H8 O3) FORMUL 13 HOH *127(H2 O) HELIX 1 1 GLN A 19 ASN A 32 1 14 HELIX 2 2 ARG A 37 LEU A 49 1 13 HELIX 3 3 LEU A 79 SER A 90 1 12 HELIX 4 4 SER A 117 GLY A 128 1 12 HELIX 5 5 GLN B 19 ASP B 26 1 8 HELIX 6 6 ILE B 30 ASN B 32 5 3 HELIX 7 7 ARG B 37 GLU B 56 1 20 HELIX 8 8 LEU B 79 SER B 90 1 12 HELIX 9 9 SER B 117 GLY B 128 1 12 HELIX 10 10 SER B 143 GLU B 145 5 3 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 HIS B 101 0 SHEET 2 BA 4 CYS B 107 GLY B 115 -1 O LEU B 108 N ILE B 100 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 SSBOND 1 CYS A 96 CYS A 96 1555 8555 2.81 SITE 1 AC1 5 TYR A 72 HIS A 74 ASN A 80 HOH A2037 SITE 2 AC1 5 HIS B 88 SITE 1 AC2 3 ARG A 82 ARG A 131 GOL A1152 SITE 1 AC3 4 LYS A 137 LEU A 138 LEU B 138 THR B 139 SITE 1 AC4 5 HIS A 74 HIS A 75 HOH A2064 HOH A2065 SITE 2 AC4 5 HIS B 88 SITE 1 AC5 7 GLU A 78 GLN A 81 ARG A 82 LEU A 130 SITE 2 AC5 7 HOH A2030 HOH A2066 ARG B 77 SITE 1 AC6 7 ARG A 82 GLY A 129 LEU A 130 ARG A 131 SITE 2 AC6 7 FMT A1148 HOH A2067 HOH A2068 SITE 1 AC7 4 LYS A 31 ARG B 82 ILE B 86 HOH B2033 SITE 1 AC8 4 TYR B 72 HIS B 99 HIS B 101 HOH B2019 SITE 1 AC9 7 TYR A 34 LEU A 40 LYS B 48 ASP B 52 SITE 2 AC9 7 GLY B 129 HOH B2011 HOH B2059 SITE 1 BC1 4 ASN B 80 MET B 83 GLN B 87 GLU B 109 CRYST1 71.055 71.055 229.023 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 0.014074 0.008125 0.000000 0.00000 SCALE2 0.000000 0.016251 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004366 0.00000