HEADER TRANSCRIPTION 04-NOV-10 3PHT TITLE CRYSTAL STRUCTURE OF H74A MUTANT OF HELICOBACTER PYLORI NIKR 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_COMMON: CAMPYLOBACTER PYLORI; SOURCE 4 ORGANISM_TAXID: 210; SOURCE 5 GENE: HP_1338; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TRANSCRIPTION FACTOR, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR E.POZHARSKI,S.EVANS,S.MICHEL REVDAT 5 06-SEP-23 3PHT 1 REMARK SEQADV LINK REVDAT 4 25-APR-12 3PHT 1 JRNL REVDAT 3 11-APR-12 3PHT 1 JRNL REVDAT 2 04-APR-12 3PHT 1 JRNL REVDAT 1 23-NOV-11 3PHT 0 JRNL AUTH A.L.WEST,S.E.EVANS,J.M.GONZALEZ,L.G.CARTER,H.TSURUTA, JRNL AUTH 2 E.POZHARSKI,S.L.MICHEL JRNL TITL NI(II) COORDINATION TO MIXED SITES MODULATES DNA BINDING OF JRNL TITL 2 HPNIKR VIA A LONG-RANGE EFFECT. JRNL REF PROC.NATL.ACAD.SCI.USA V. 109 5633 2012 JRNL REFN ISSN 0027-8424 JRNL PMID 22451934 JRNL DOI 10.1073/PNAS.1120283109 REMARK 2 REMARK 2 RESOLUTION. 2.04 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0077 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) : 2.04 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 61.65 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 19253 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) : 0.193 REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1038 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) : 2.04 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.09 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1383 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.58 REMARK 3 BIN R VALUE (WORKING SET) : 0.5380 REMARK 3 BIN FREE R VALUE SET COUNT : 75 REMARK 3 BIN FREE R VALUE : 0.5040 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1535 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 95 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 39.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 54.87 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.29000 REMARK 3 B22 (A**2) : -0.29000 REMARK 3 B33 (A**2) : 0.59000 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 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.143 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.093 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.489 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.955 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.939 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1656 ; 0.024 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2263 ; 2.093 ; 1.933 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 226 ; 6.607 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 85 ;40.945 ;24.706 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 304 ;18.421 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 12 ;18.428 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 270 ; 0.176 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1255 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 29 A 89 REMARK 3 ORIGIN FOR THE GROUP (A): 2.4240 20.7270 5.1840 REMARK 3 T TENSOR REMARK 3 T11: 0.0628 T22: 0.4266 REMARK 3 T33: 0.2579 T12: 0.0251 REMARK 3 T13: -0.0169 T23: -0.0953 REMARK 3 L TENSOR REMARK 3 L11: 3.0374 L22: 2.5251 REMARK 3 L33: 2.0101 L12: 0.6385 REMARK 3 L13: -1.6111 L23: -0.4353 REMARK 3 S TENSOR REMARK 3 S11: 0.0332 S12: 0.0640 S13: 0.2408 REMARK 3 S21: -0.0648 S22: -0.0946 S23: 0.4306 REMARK 3 S31: -0.0436 S32: -0.7163 S33: 0.0614 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 90 A 144 REMARK 3 ORIGIN FOR THE GROUP (A): 4.4770 17.4980 8.6970 REMARK 3 T TENSOR REMARK 3 T11: 0.0723 T22: 0.2050 REMARK 3 T33: 0.1703 T12: -0.0150 REMARK 3 T13: 0.0136 T23: -0.0478 REMARK 3 L TENSOR REMARK 3 L11: 3.6871 L22: 1.3072 REMARK 3 L33: 2.1464 L12: 0.5131 REMARK 3 L13: 0.1030 L23: 0.6357 REMARK 3 S TENSOR REMARK 3 S11: -0.0580 S12: -0.2510 S13: 0.0641 REMARK 3 S21: 0.0627 S22: -0.1680 S23: 0.2718 REMARK 3 S31: 0.0818 S32: -0.4013 S33: 0.2261 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 60 B 120 REMARK 3 ORIGIN FOR THE GROUP (A): 10.6400 22.2520 -8.6370 REMARK 3 T TENSOR REMARK 3 T11: 0.1680 T22: 0.0843 REMARK 3 T33: 0.1258 T12: 0.0476 REMARK 3 T13: -0.0362 T23: -0.0062 REMARK 3 L TENSOR REMARK 3 L11: 1.9025 L22: 3.1900 REMARK 3 L33: 4.6189 L12: 0.0761 REMARK 3 L13: -0.9016 L23: 0.0385 REMARK 3 S TENSOR REMARK 3 S11: 0.0237 S12: 0.1025 S13: -0.0203 REMARK 3 S21: -0.3959 S22: -0.0571 S23: 0.1455 REMARK 3 S31: -0.3430 S32: -0.4334 S33: 0.0334 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 121 B 141 REMARK 3 ORIGIN FOR THE GROUP (A): 5.7200 28.4910 -9.0140 REMARK 3 T TENSOR REMARK 3 T11: 0.5308 T22: 0.3040 REMARK 3 T33: 0.4414 T12: 0.1631 REMARK 3 T13: -0.1000 T23: 0.0064 REMARK 3 L TENSOR REMARK 3 L11: 5.2776 L22: 1.4404 REMARK 3 L33: 8.4797 L12: 2.1828 REMARK 3 L13: 2.3595 L23: 1.3642 REMARK 3 S TENSOR REMARK 3 S11: -0.0448 S12: 0.0723 S13: 0.3083 REMARK 3 S21: -0.3913 S22: 0.0336 S23: 0.4929 REMARK 3 S31: -0.8380 S32: -1.0563 S33: 0.0112 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: NULL REMARK 4 REMARK 4 3PHT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-NOV-10. REMARK 100 THE DEPOSITION ID IS D_1000062389. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-AUG-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : OSMIC MIRRORS REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20487 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.040 REMARK 200 RESOLUTION RANGE LOW (A) : 61.650 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 24.30 REMARK 200 R MERGE (I) : 0.12200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 25.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.04 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 22.10 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.100 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: 3LGH, RESIDUES 60-140 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.07 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 12% PEG20K, 0.1M MES PH 6.5, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 57.22050 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 36.58700 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 36.58700 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 85.83075 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 36.58700 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 36.58700 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 28.61025 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 36.58700 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 36.58700 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 85.83075 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 36.58700 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 36.58700 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 28.61025 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 57.22050 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: 8790 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17480 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -98.0 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 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 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 9 REMARK 465 ILE A 10 REMARK 465 ILE A 11 REMARK 465 ARG A 12 REMARK 465 PHE A 13 REMARK 465 SER A 14 REMARK 465 VAL A 15 REMARK 465 SER A 16 REMARK 465 LEU A 17 REMARK 465 GLN A 18 REMARK 465 GLN A 19 REMARK 465 ASN A 20 REMARK 465 LEU A 21 REMARK 465 LEU A 22 REMARK 465 ASP A 23 REMARK 465 GLU A 24 REMARK 465 LEU A 25 REMARK 465 ASP A 26 REMARK 465 ASN A 27 REMARK 465 ARG A 28 REMARK 465 LYS A 31 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 SER B 9 REMARK 465 ILE B 10 REMARK 465 ILE B 11 REMARK 465 ARG B 12 REMARK 465 PHE B 13 REMARK 465 SER B 14 REMARK 465 VAL B 15 REMARK 465 SER B 16 REMARK 465 LEU B 17 REMARK 465 GLN B 18 REMARK 465 GLN B 19 REMARK 465 ASN B 20 REMARK 465 LEU B 21 REMARK 465 LEU B 22 REMARK 465 ASP B 23 REMARK 465 GLU B 24 REMARK 465 LEU B 25 REMARK 465 ASP B 26 REMARK 465 ASN B 27 REMARK 465 ARG B 28 REMARK 465 ILE B 29 REMARK 465 ILE B 30 REMARK 465 LYS B 31 REMARK 465 ASN B 32 REMARK 465 GLY B 33 REMARK 465 TYR B 34 REMARK 465 SER B 35 REMARK 465 SER B 36 REMARK 465 ARG B 37 REMARK 465 SER B 38 REMARK 465 GLU B 39 REMARK 465 LEU B 40 REMARK 465 VAL B 41 REMARK 465 ARG B 42 REMARK 465 ASP B 43 REMARK 465 MET B 44 REMARK 465 ILE B 45 REMARK 465 ARG B 46 REMARK 465 GLU B 47 REMARK 465 LYS B 48 REMARK 465 LEU B 49 REMARK 465 VAL B 50 REMARK 465 GLU B 51 REMARK 465 ASP B 52 REMARK 465 ASN B 53 REMARK 465 TRP B 54 REMARK 465 ALA B 55 REMARK 465 GLU B 56 REMARK 465 ASP B 57 REMARK 465 ASN B 58 REMARK 465 PRO B 59 REMARK 465 SER B 142 REMARK 465 SER B 143 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 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 ILE A 30 CG1 CG2 CD1 REMARK 470 ASN A 32 CG OD1 ND2 REMARK 470 TYR A 34 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 SER A 35 OG REMARK 470 ARG A 37 CG CD NE CZ NH1 NH2 REMARK 470 SER A 38 OG REMARK 470 LEU A 40 CG CD1 CD2 REMARK 470 LYS A 48 CG CD CE NZ REMARK 470 LEU A 49 CG CD1 CD2 REMARK 470 ASN A 60 CG OD1 ND2 REMARK 470 LYS B 64 CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 ARG B 122 CB ARG B 122 CG 0.167 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 LEU B 108 CA - CB - CG ANGL. DEV. = 14.4 DEGREES REMARK 500 LEU B 123 CA - CB - CG ANGL. DEV. = 14.4 DEGREES REMARK 500 LEU B 125 CA - CB - CG ANGL. DEV. = 20.6 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 ARG A 37 -75.23 -67.74 REMARK 500 SER A 38 21.36 -73.44 REMARK 500 GLU A 56 69.57 -109.30 REMARK 500 ASN A 58 99.64 -1.36 REMARK 500 PRO A 59 -38.61 -39.82 REMARK 500 ARG A 77 124.94 -32.85 REMARK 500 GLU A 78 -5.06 75.71 REMARK 500 ALA B 74 4.03 -59.51 REMARK 500 GLU B 78 -12.19 69.65 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 B 149 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 88 NE2 REMARK 620 2 HIS B 99 NE2 176.6 REMARK 620 3 HIS B 101 ND1 94.5 88.9 REMARK 620 4 CYS B 107 SG 83.6 93.0 176.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI A 149 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 99 NE2 REMARK 620 2 HIS A 101 ND1 91.1 REMARK 620 3 CYS A 107 SG 92.6 176.2 REMARK 620 4 HIS B 88 NE2 175.5 93.4 83.0 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 149 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI B 149 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3LGH RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF NIKR FROM HELICOBACTER PYLORI WITH VARIABLE NI REMARK 900 SITE COORDINATION DBREF 3PHT A 1 148 UNP O25896 NIKR_HELPY 1 148 DBREF 3PHT B 1 148 UNP O25896 NIKR_HELPY 1 148 SEQADV 3PHT ALA A 74 UNP O25896 HIS 74 ENGINEERED MUTATION SEQADV 3PHT ALA B 74 UNP O25896 HIS 74 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 ALA 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 ALA 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 NI A 149 1 HET NI B 149 1 HETNAM NI NICKEL (II) ION FORMUL 3 NI 2(NI 2+) FORMUL 5 HOH *95(H2 O) HELIX 1 1 SER A 36 GLU A 56 1 21 HELIX 2 2 GLU A 78 GLY A 91 1 14 HELIX 3 3 ASN A 116 GLY A 129 1 14 HELIX 4 4 GLU B 78 SER B 90 1 13 HELIX 5 5 ASN B 116 GLY B 129 1 14 SHEET 1 A 4 VAL A 94 ASP A 103 0 SHEET 2 A 4 ASN A 106 GLN A 114 -1 O LEU A 108 N ILE A 100 SHEET 3 A 4 ILE A 65 ASP A 73 -1 N ALA A 66 O LEU A 113 SHEET 4 A 4 VAL A 133 ALA A 141 -1 O THR A 139 N VAL A 67 SHEET 1 B 4 VAL B 94 ASP B 103 0 SHEET 2 B 4 ASN B 106 GLY B 115 -1 O ILE B 112 N LEU B 95 SHEET 3 B 4 LYS B 64 ASP B 73 -1 N LEU B 68 O ILE B 111 SHEET 4 B 4 VAL B 133 LYS B 140 -1 O THR B 139 N VAL B 67 LINK NE2 HIS A 88 NI NI B 149 7555 1555 2.11 LINK NE2 HIS A 99 NI NI A 149 1555 1555 2.05 LINK ND1 HIS A 101 NI NI A 149 1555 1555 2.06 LINK SG CYS A 107 NI NI A 149 1555 1555 2.25 LINK NI NI A 149 NE2 HIS B 88 1555 7555 2.08 LINK NE2 HIS B 99 NI NI B 149 1555 1555 2.11 LINK ND1 HIS B 101 NI NI B 149 1555 1555 2.02 LINK SG CYS B 107 NI NI B 149 1555 1555 2.22 SITE 1 AC1 4 HIS A 99 HIS A 101 CYS A 107 HIS B 88 SITE 1 AC2 5 ILE A 84 HIS A 88 HIS B 99 HIS B 101 SITE 2 AC2 5 CYS B 107 CRYST1 73.174 73.174 114.441 90.00 90.00 90.00 P 43 21 2 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 0.013666 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013666 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008738 0.00000