HEADER TRANSCRIPTIONAL REGULATION 21-DEC-05 2CAJ TITLE NIKR FROM HELICOBACTER PYLORI IN CLOSED TRANS-CONFORMATION AND NICKEL TITLE 2 BOUND TO 4 INTERMEDIARY SITES 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, KEYWDS 3 HYPOTHETICAL PROTEIN, METAL-BINDING, NICKEL EXPDTA X-RAY DIFFRACTION AUTHOR C.DIAN,K.SCHAUER,U.KAPP,S.M.MCSWEENEY,A.LABIGNE,L.TERRADOT REVDAT 5 06-NOV-24 2CAJ 1 REMARK REVDAT 4 01-MAY-24 2CAJ 1 LINK REVDAT 3 24-FEB-09 2CAJ 1 VERSN REVDAT 2 16-AUG-06 2CAJ 1 JRNL REVDAT 1 17-JUL-06 2CAJ 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. 2.35 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) : 2.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 62.02 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 14496 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) : 0.232 REMARK 3 R VALUE (WORKING SET) : 0.230 REMARK 3 FREE R VALUE : 0.282 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 788 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) : 2.35 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.41 REMARK 3 REFLECTION IN BIN (WORKING SET) : 995 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.56 REMARK 3 BIN R VALUE (WORKING SET) : 0.2370 REMARK 3 BIN FREE R VALUE SET COUNT : 60 REMARK 3 BIN FREE R VALUE : 0.2770 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2085 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 39 REMARK 3 SOLVENT ATOMS : 64 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.68 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.23000 REMARK 3 B22 (A**2) : -0.23000 REMARK 3 B33 (A**2) : 0.35000 REMARK 3 B12 (A**2) : -0.12000 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): 0.342 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.263 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.187 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.558 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.928 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.901 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2160 ; 0.017 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 1968 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2910 ; 1.643 ; 1.954 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4551 ; 0.866 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 270 ; 7.334 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 106 ;37.570 ;24.623 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 383 ;17.228 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 15 ;20.427 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 337 ; 0.087 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2392 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 414 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 448 ; 0.214 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2099 ; 0.195 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1027 ; 0.173 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 1403 ; 0.092 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 86 ; 0.186 ; 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): 28 ; 0.323 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 91 ; 0.322 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 11 ; 0.187 ; 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): 1366 ; 1.190 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 552 ; 0.185 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2139 ; 1.996 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 859 ; 2.477 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 769 ; 4.135 ; 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 2CAJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 21-DEC-05. REMARK 100 THE DEPOSITION ID IS D_1290026895. 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 : 5.00 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9756 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 : 15378 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.350 REMARK 200 RESOLUTION RANGE LOW (A) : 62.020 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 7.400 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.48 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 6.70 REMARK 200 R MERGE FOR SHELL (I) : 0.49000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: 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 (%): 49.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.9-1.0 M NA-FORMATE, 0.1M NA-CITRATE REMARK 280 PH 4.0. CRYSTAL WAS SOAKED IN MOTHER LIQUOR WITH 30% GLYCEROL REMARK 280 AND 0.02 M NICKEL CHLORIDE DURING ONE HOUR., PH 5.00 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 76.27800 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 152.55600 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 114.41700 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 190.69500 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 38.13900 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 76.27800 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 152.55600 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 190.69500 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 114.41700 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 38.13900 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: PQS 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 HOH A2016 LIES ON A SPECIAL POSITION. 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 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 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 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 SER A 9 OG REMARK 470 ILE A 10 CG1 CG2 CD1 REMARK 470 ILE A 11 CG1 CG2 CD1 REMARK 470 ARG A 12 CG CD NE CZ NH1 NH2 REMARK 470 SER A 16 OG REMARK 470 GLN A 18 CG CD OE1 NE2 REMARK 470 ARG A 46 CG CD NE CZ NH1 NH2 REMARK 470 ASN A 58 CG OD1 ND2 REMARK 470 GLU A 62 CG CD OE1 OE2 REMARK 470 GLU A 104 CG CD OE1 OE2 REMARK 470 LYS A 140 CG CD CE NZ REMARK 470 ILE B 10 CG1 CG2 CD1 REMARK 470 ARG B 12 CG CD NE CZ NH1 NH2 REMARK 470 LEU B 17 CG CD1 CD2 REMARK 470 GLN B 19 CG CD OE1 NE2 REMARK 470 ASN B 20 CG OD1 ND2 REMARK 470 GLU B 24 CG CD OE1 OE2 REMARK 470 ILE B 30 CG1 CG2 CD1 REMARK 470 LYS B 31 CG CD CE NZ REMARK 470 ASN B 60 CG OD1 ND2 REMARK 470 GLU B 104 CG CD OE1 OE2 REMARK 470 ASN B 147 CG OD1 ND2 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 NZ LYS A 64 OG SER A 117 2.07 REMARK 500 O3 GOL A 1143 O HOH A 2030 2.10 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 C3 GOL A 1145 O3 GOL A 1145 8555 1.57 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG B 77 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES 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 ILE A 10 -7.53 69.07 REMARK 500 LYS A 31 -84.34 -42.92 REMARK 500 ASN A 32 -6.20 -53.61 REMARK 500 GLU A 51 -61.67 -138.62 REMARK 500 ASP A 103 -168.46 -172.74 REMARK 500 ILE B 10 104.73 -14.20 REMARK 500 ILE B 30 -77.22 -61.04 REMARK 500 ASN B 32 -13.51 177.39 REMARK 500 GLU B 62 33.12 -96.81 REMARK 500 GLN B 76 98.93 -64.36 REMARK 500 GLU B 78 -0.63 69.74 REMARK 500 ASP B 103 -175.75 -176.52 REMARK 500 PHE B 135 132.18 -177.57 REMARK 500 SER B 143 -36.12 -37.96 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 ASN A 58 PRO A 59 140.54 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 B1152 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 88 NE2 REMARK 620 2 HIS B 74 NE2 82.5 REMARK 620 N 1 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 CL B1150 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI B1151 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI B1152 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A1142 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A1143 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A1144 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A1145 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B1148 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B1149 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2CA9 RELATED DB: PDB REMARK 900 APO-HPNIKR 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 DBREF 2CAJ A 1 148 UNP O25896 NIKR_HELPY 1 148 DBREF 2CAJ 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 GOL A1142 6 HET GOL A1143 6 HET GOL A1144 6 HET GOL A1145 6 HET GOL B1148 6 HET GOL B1149 6 HET CL B1150 1 HET NI B1151 1 HET NI B1152 1 HETNAM GOL GLYCEROL HETNAM CL CHLORIDE ION HETNAM NI NICKEL (II) ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 GOL 6(C3 H8 O3) FORMUL 9 CL CL 1- FORMUL 10 NI 2(NI 2+) FORMUL 12 HOH *64(H2 O) HELIX 1 1 GLN A 19 LYS A 31 1 13 HELIX 2 2 ARG A 37 LYS A 48 1 12 HELIX 3 3 LEU A 79 GLY A 91 1 13 HELIX 4 4 SER A 117 GLY A 128 1 12 HELIX 5 5 LEU B 21 ILE B 30 1 10 HELIX 6 6 ARG B 37 ALA B 55 1 19 HELIX 7 7 GLU B 78 SER B 90 1 13 HELIX 8 8 SER B 117 GLY B 128 1 12 SHEET 1 AA 2 PHE A 13 LEU A 17 0 SHEET 2 AA 2 ILE B 11 VAL B 15 -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 LYS A 140 -1 N LYS A 134 O ILE A 71 SHEET 1 BA 4 HIS B 93 HIS B 101 0 SHEET 2 BA 4 ASN B 106 GLY B 115 -1 O LEU B 108 N ILE B 100 SHEET 3 BA 4 LYS B 64 ASP B 73 -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 2.53 LINK NE2 HIS A 74 NI NI B1151 8555 1555 2.10 LINK NE2 HIS A 88 NI NI B1152 8555 1555 2.48 LINK NE2 HIS B 74 NI NI B1152 1555 1555 2.58 SITE 1 AC1 4 HIS A 101 GLN B 87 HIS B 93 NI B1151 SITE 1 AC2 3 HIS A 74 HIS B 88 CL B1150 SITE 1 AC3 4 HIS A 88 HIS B 74 HIS B 75 HIS B 101 SITE 1 AC4 7 GLU A 78 GLN A 81 ARG A 82 HOH A2016 SITE 2 AC4 7 HOH A2028 ARG B 77 GLU B 78 SITE 1 AC5 6 LEU A 130 ARG A 131 GLY A 132 VAL A 133 SITE 2 AC5 6 HOH A2029 HOH A2030 SITE 1 AC6 7 ASN A 80 MET A 83 GLN A 87 THR A 97 SITE 2 AC6 7 GLU A 109 ILE A 111 HOH A2031 SITE 1 AC7 4 VAL A 94 LEU A 95 ILE B 100 HIS B 101 SITE 1 AC8 4 ASN B 80 MET B 83 GLU B 109 HOH B2033 SITE 1 AC9 6 GLN A 81 ASP A 85 HIS A 88 HIS B 74 SITE 2 AC9 6 HIS B 75 ARG B 77 CRYST1 71.598 71.598 228.834 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 0.013967 0.008064 0.000000 0.00000 SCALE2 0.000000 0.016128 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004370 0.00000