HEADER TRANSCRIPTION 04-JAN-11 2Y3Y TITLE HOLO-NI(II) HPNIKR IS A SYMMETRIC TETRAMER CONTAINING FOUR CANONIC TITLE 2 SQUARE-PLANAR NI(II) IONS AT PHYSIOLOGICAL PH COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE NICKEL-RESPONSIVE REGULATOR; COMPND 3 CHAIN: A, B, C, D; COMPND 4 FRAGMENT: C-TERMINAL METAL-BINDING DOMAIN, RESIDUES 58-145; COMPND 5 SYNONYM: HOLO-NICKEL HPNIKR; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: UNDECAPEPTIDE-GSSSGSASGAG; COMPND 9 CHAIN: Q SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HELICOBACTER PYLORI G27; SOURCE 3 ORGANISM_TAXID: 563041; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR: PET22B; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: UNIDENTIFIED; SOURCE 10 ORGANISM_TAXID: 32644 KEYWDS TRANSCRIPTION, METAL BINDING EXPDTA X-RAY DIFFRACTION AUTHOR S.BENINI,M.CIANCI,S.CIURLI REVDAT 2 17-JUL-19 2Y3Y 1 REMARK REVDAT 1 17-AUG-11 2Y3Y 0 JRNL AUTH S.BENINI,M.CIANCI,S.CIURLI JRNL TITL HOLO-NI(2+)HELICOBACTER PYLORI NIKR CONTAINS FOUR JRNL TITL 2 SQUARE-PLANAR NICKEL-BINDING SITES AT PHYSIOLOGICAL PH. JRNL REF DALTON TRANS V. 40 7831 2011 JRNL REFN ISSN 1477-9226 JRNL PMID 21725560 JRNL DOI 10.1039/C1DT11107H REMARK 2 REMARK 2 RESOLUTION. 2.39 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 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) : 2.39 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 72.98 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 94.8 REMARK 3 NUMBER OF REFLECTIONS : 21766 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) : 0.229 REMARK 3 FREE R VALUE : 0.279 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1177 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) : 2.39 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.45 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1485 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 87.56 REMARK 3 BIN R VALUE (WORKING SET) : 0.2500 REMARK 3 BIN FREE R VALUE SET COUNT : 78 REMARK 3 BIN FREE R VALUE : 0.3070 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2686 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 55 REMARK 3 SOLVENT ATOMS : 66 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 52.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 43.38 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.26000 REMARK 3 B22 (A**2) : -0.26000 REMARK 3 B33 (A**2) : 0.51000 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): 0.294 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.248 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.170 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.966 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.921 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.885 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2773 ; 0.026 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3720 ; 2.216 ; 1.945 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 336 ; 7.667 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 136 ;40.883 ;24.706 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 516 ;19.572 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 16 ;19.779 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 429 ; 0.163 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2000 ; 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): 1673 ; 1.496 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2696 ; 2.803 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1100 ; 3.966 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1024 ; 6.428 ; 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 : 1.40 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. U VALUES REFINED INDIVIDUALLY. UNEXPECTED ELECTRON REMARK 3 DENSITY WAS MODELED AS ALPHA-CHAIN (Q) REMARK 4 REMARK 4 2Y3Y COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 04-JAN-11. REMARK 100 THE DEPOSITION ID IS D_1290046876. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-DEC-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.3 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : X12 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.459 REMARK 200 MONOCHROMATOR : NULL 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 : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24202 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.390 REMARK 200 RESOLUTION RANGE LOW (A) : 19.940 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.500 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 14.00 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 26.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.39 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.52 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 8.20 REMARK 200 R MERGE FOR SHELL (I) : 0.64000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: HKL2MAP REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 69.64 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.05 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 3350 AND 0.2 M K/NA-TARTRATE, REMARK 280 PH 7.3 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 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,X,Z+3/4 REMARK 290 4555 Y,-X,Z+1/4 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 58.36500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 87.54750 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 29.18250 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7220 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15220 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -95.5 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: Q 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 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 ASN A 58 REMARK 465 PRO A 59 REMARK 465 SER A 143 REMARK 465 PHE A 144 REMARK 465 GLU A 145 REMARK 465 HIS A 146 REMARK 465 ASN A 147 REMARK 465 GLU A 148 REMARK 465 ASN B 58 REMARK 465 PRO B 59 REMARK 465 SER B 143 REMARK 465 PHE B 144 REMARK 465 GLU B 145 REMARK 465 HIS B 146 REMARK 465 ASN B 147 REMARK 465 GLU B 148 REMARK 465 ASN C 58 REMARK 465 PRO C 59 REMARK 465 ASN C 60 REMARK 465 SER C 142 REMARK 465 SER C 143 REMARK 465 PHE C 144 REMARK 465 GLU C 145 REMARK 465 HIS C 146 REMARK 465 ASN C 147 REMARK 465 GLU C 148 REMARK 465 ASN D 58 REMARK 465 PRO D 59 REMARK 465 SER D 143 REMARK 465 PHE D 144 REMARK 465 GLU D 145 REMARK 465 HIS 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 SER A 142 OG REMARK 470 GLY Q 1 N REMARK 470 GLY Q 11 C O 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 ASP B 103 CB - CG - OD1 ANGL. DEV. = 6.5 DEGREES REMARK 500 LEU B 108 CA - CB - CG ANGL. DEV. = 13.9 DEGREES REMARK 500 LEU D 108 CA - CB - CG ANGL. DEV. = 16.6 DEGREES REMARK 500 LEU D 125 CB - CG - CD1 ANGL. DEV. = -10.6 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 ALA A 141 -79.12 -114.72 REMARK 500 ASP B 103 -173.39 -172.66 REMARK 500 ALA B 136 65.35 -158.24 REMARK 500 ASP D 61 62.53 0.29 REMARK 500 GLU D 62 -158.65 -164.71 REMARK 500 GLU D 78 -7.03 84.23 REMARK 500 ASP D 103 -173.30 -170.75 REMARK 500 PHE D 135 125.73 177.89 REMARK 500 ALA D 136 70.65 -157.10 REMARK 500 ALA D 141 -119.74 -115.83 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 60 ASP A 61 148.92 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 A1143 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 101 ND1 REMARK 620 2 HIS A 99 NE2 92.9 REMARK 620 3 CYS A 107 SG 176.7 89.0 REMARK 620 4 HIS B 88 NE2 92.8 167.4 84.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI B1143 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 88 NE2 REMARK 620 2 HIS B 99 NE2 173.1 REMARK 620 3 HIS B 101 ND1 89.7 96.7 REMARK 620 4 CYS B 107 SG 80.9 92.5 169.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI C1142 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS C 101 ND1 REMARK 620 2 CYS C 107 SG 172.8 REMARK 620 3 HIS C 99 NE2 86.1 93.5 REMARK 620 4 HIS D 88 NE2 90.1 90.1 175.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI D1143 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS D 107 SG REMARK 620 2 HIS D 99 NE2 96.1 REMARK 620 3 HIS D 101 ND1 168.4 94.7 REMARK 620 4 HIS C 88 NE2 84.0 175.5 84.9 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 1143 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI B 1143 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI C 1142 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG C 1144 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG C 1145 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG C 1146 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI D 1143 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: 2WVB RELATED DB: PDB REMARK 900 STRUCTURAL AND MECHANISTIC INSIGHTS INTO HELICOBACTER PYLORI NIKR REMARK 900 FUNCTION REMARK 900 RELATED ID: 2WVD RELATED DB: PDB REMARK 900 STRUCTURAL AND MECHANISTIC INSIGHTS INTO HELICOBACTER PYLORI NIKR REMARK 900 FUNCTION REMARK 900 RELATED ID: 2CA9 RELATED DB: PDB REMARK 900 APO-NIKR FROM HELICOBACTER PYLORI IN CLOSED TRANS-CONFORMATION 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 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 999 REMARK 999 SEQUENCE REMARK 999 ONLY C-TERMINAL METAL-BINDING DOMAIN PRESENT. DBREF 2Y3Y A 58 148 UNP B5Z8Y5 NIKR_HELPG 58 148 DBREF 2Y3Y B 58 148 UNP B5Z8Y5 NIKR_HELPG 58 148 DBREF 2Y3Y C 58 148 UNP B5Z8Y5 NIKR_HELPG 58 148 DBREF 2Y3Y D 58 148 UNP B5Z8Y5 NIKR_HELPG 58 148 DBREF 2Y3Y Q 1 11 PDB 2Y3Y 2Y3Y 1 11 SEQRES 1 A 91 ASN PRO ASN ASP GLU SER LYS ILE ALA VAL LEU VAL VAL SEQRES 2 A 91 ILE TYR ASP HIS HIS GLN ARG GLU LEU ASN GLN ARG MET SEQRES 3 A 91 ILE ASP ILE GLN HIS ALA SER GLY THR HIS VAL LEU CYS SEQRES 4 A 91 THR THR HIS ILE HIS MET ASP GLU HIS ASN CYS LEU GLU SEQRES 5 A 91 THR ILE ILE LEU GLN GLY ASN SER PHE GLU ILE GLN ARG SEQRES 6 A 91 LEU GLN LEU GLU ILE GLY GLY LEU ARG GLY VAL LYS PHE SEQRES 7 A 91 ALA LYS LEU THR LYS ALA SER SER PHE GLU HIS ASN GLU SEQRES 1 B 91 ASN PRO ASN ASP GLU SER LYS ILE ALA VAL LEU VAL VAL SEQRES 2 B 91 ILE TYR ASP HIS HIS GLN ARG GLU LEU ASN GLN ARG MET SEQRES 3 B 91 ILE ASP ILE GLN HIS ALA SER GLY THR HIS VAL LEU CYS SEQRES 4 B 91 THR THR HIS ILE HIS MET ASP GLU HIS ASN CYS LEU GLU SEQRES 5 B 91 THR ILE ILE LEU GLN GLY ASN SER PHE GLU ILE GLN ARG SEQRES 6 B 91 LEU GLN LEU GLU ILE GLY GLY LEU ARG GLY VAL LYS PHE SEQRES 7 B 91 ALA LYS LEU THR LYS ALA SER SER PHE GLU HIS ASN GLU SEQRES 1 C 91 ASN PRO ASN ASP GLU SER LYS ILE ALA VAL LEU VAL VAL SEQRES 2 C 91 ILE TYR ASP HIS HIS GLN ARG GLU LEU ASN GLN ARG MET SEQRES 3 C 91 ILE ASP ILE GLN HIS ALA SER GLY THR HIS VAL LEU CYS SEQRES 4 C 91 THR THR HIS ILE HIS MET ASP GLU HIS ASN CYS LEU GLU SEQRES 5 C 91 THR ILE ILE LEU GLN GLY ASN SER PHE GLU ILE GLN ARG SEQRES 6 C 91 LEU GLN LEU GLU ILE GLY GLY LEU ARG GLY VAL LYS PHE SEQRES 7 C 91 ALA LYS LEU THR LYS ALA SER SER PHE GLU HIS ASN GLU SEQRES 1 D 91 ASN PRO ASN ASP GLU SER LYS ILE ALA VAL LEU VAL VAL SEQRES 2 D 91 ILE TYR ASP HIS HIS GLN ARG GLU LEU ASN GLN ARG MET SEQRES 3 D 91 ILE ASP ILE GLN HIS ALA SER GLY THR HIS VAL LEU CYS SEQRES 4 D 91 THR THR HIS ILE HIS MET ASP GLU HIS ASN CYS LEU GLU SEQRES 5 D 91 THR ILE ILE LEU GLN GLY ASN SER PHE GLU ILE GLN ARG SEQRES 6 D 91 LEU GLN LEU GLU ILE GLY GLY LEU ARG GLY VAL LYS PHE SEQRES 7 D 91 ALA LYS LEU THR LYS ALA SER SER PHE GLU HIS ASN GLU SEQRES 1 Q 11 GLY SER SER SER GLY SER ALA SER GLY ALA GLY HET NI A1143 1 HET NI B1143 1 HET EPE B1144 15 HET NI C1142 1 HET EPE C1143 15 HET PEG C1144 7 HET PEG C1145 7 HET PEG C1146 7 HET NI D1143 1 HETNAM NI NICKEL (II) ION HETNAM EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID HETNAM PEG DI(HYDROXYETHYL)ETHER HETSYN EPE HEPES FORMUL 6 NI 4(NI 2+) FORMUL 8 EPE 2(C8 H18 N2 O4 S) FORMUL 11 PEG 3(C4 H10 O3) FORMUL 15 HOH *66(H2 O) HELIX 1 1 GLU A 78 SER A 90 1 13 HELIX 2 2 SER A 117 LEU A 130 1 14 HELIX 3 3 GLU B 78 SER B 90 1 13 HELIX 4 4 ASN B 116 GLY B 129 1 14 HELIX 5 5 GLU C 78 SER C 90 1 13 HELIX 6 6 ASN C 116 GLY C 129 1 14 HELIX 7 7 GLU D 78 SER D 90 1 13 HELIX 8 8 ASN D 116 GLY D 129 1 14 HELIX 9 9 SER Q 2 ALA Q 10 1 9 SHEET 1 AA 8 VAL A 133 LYS A 140 0 SHEET 2 AA 8 SER A 63 TYR A 72 -1 O VAL A 67 N THR A 139 SHEET 3 AA 8 ASN A 106 ASN A 116 -1 O CYS A 107 N TYR A 72 SHEET 4 AA 8 VAL A 94 ASP A 103 -1 N LEU A 95 O ILE A 112 SHEET 5 AA 8 HIS B 93 ASP B 103 -1 O THR B 97 N HIS A 99 SHEET 6 AA 8 ASN B 106 GLY B 115 -1 O ASN B 106 N MET B 102 SHEET 7 AA 8 LYS B 64 TYR B 72 -1 O LYS B 64 N GLY B 115 SHEET 8 AA 8 VAL B 133 LYS B 140 -1 N LYS B 134 O ILE B 71 SHEET 1 CA 8 VAL C 133 ALA C 141 0 SHEET 2 CA 8 LYS C 64 TYR C 72 -1 O ILE C 65 N ALA C 141 SHEET 3 CA 8 ASN C 106 GLY C 115 -1 O CYS C 107 N TYR C 72 SHEET 4 CA 8 VAL C 94 ASP C 103 -1 N LEU C 95 O ILE C 112 SHEET 5 CA 8 HIS D 93 ASP D 103 -1 O THR D 97 N HIS C 99 SHEET 6 CA 8 ASN D 106 GLY D 115 -1 O ASN D 106 N ASP D 103 SHEET 7 CA 8 LYS D 64 TYR D 72 -1 O LYS D 64 N GLY D 115 SHEET 8 CA 8 VAL D 133 LYS D 140 -1 N LYS D 134 O ILE D 71 LINK NI NI A1143 ND1 HIS A 101 1555 1555 1.98 LINK NI NI A1143 NE2 HIS A 99 1555 1555 2.09 LINK NI NI A1143 SG CYS A 107 1555 1555 2.18 LINK NI NI A1143 NE2 HIS B 88 1555 1555 1.98 LINK NI NI B1143 NE2 HIS A 88 1555 1555 1.94 LINK NI NI B1143 NE2 HIS B 99 1555 1555 1.99 LINK NI NI B1143 ND1 HIS B 101 1555 1555 2.02 LINK NI NI B1143 SG CYS B 107 1555 1555 2.20 LINK NI NI C1142 ND1 HIS C 101 1555 1555 1.90 LINK NI NI C1142 SG CYS C 107 1555 1555 2.14 LINK NI NI C1142 NE2 HIS C 99 1555 1555 2.07 LINK NI NI C1142 NE2 HIS D 88 1555 1555 2.05 LINK NI NI D1143 SG CYS D 107 1555 1555 2.22 LINK NI NI D1143 NE2 HIS D 99 1555 1555 1.94 LINK NI NI D1143 ND1 HIS D 101 1555 1555 2.04 LINK NI NI D1143 NE2 HIS C 88 1555 1555 1.90 SITE 1 AC1 4 HIS A 99 HIS A 101 CYS A 107 HIS B 88 SITE 1 AC2 4 HIS A 88 HIS B 99 HIS B 101 CYS B 107 SITE 1 AC3 5 HIS C 99 HIS C 101 CYS C 107 ILE D 84 SITE 2 AC3 5 HIS D 88 SITE 1 AC4 1 PEG C1145 SITE 1 AC5 2 PEG C1144 PEG C1146 SITE 1 AC6 1 PEG C1145 SITE 1 AC7 4 HIS C 88 HIS D 99 HIS D 101 CYS D 107 CRYST1 72.970 72.970 116.730 90.00 90.00 90.00 P 43 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 0.013704 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013704 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008567 0.00000