10 20 30 40 50 60 70 80 2BJ7 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER TRANSCRIPTION 31-JAN-05 2BJ7
TITLE NIKR IN CLOSED CONFORMATION AND NICKEL BOUND TO HIGH- TITLE 2 AFFINITY SITES
COMPND MOL_ID: 1; COMPND 2 MOLECULE: NICKEL RESPONSIVE REGULATOR; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS HORIKOSHII; SOURCE 3 ORGANISM_TAXID: 70601; SOURCE 4 STRAIN: OT3; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET11A
KEYWDS TRANSCRIPTION, REPRESSOR, PYROCOCCUS HORIKOSHII, NIKR, DNA- KEYWDS 2 BINDING, METAL-BINDING, NICKEL, TRANSCRIPTION REGULATION, KEYWDS 3 RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE, RSGI, KEYWDS 4 STRUCTURAL GENOMICS
EXPDTA X-RAY DIFFRACTION
AUTHOR T.H.TAHIROV
REVDAT 2 24-FEB-09 2BJ7 1 VERSN REVDAT 1 08-APR-05 2BJ7 0
JRNL AUTH P.T.CHIVERS,T.H.TAHIROV JRNL TITL STRUCTURE OF PYROCOCCUS HORIKOSHII NIKR: NICKEL JRNL TITL 2 SENSING AND IMPLICATIONS FOR THE REGULATION OF DNA JRNL TITL 3 RECOGNITION JRNL REF J.MOL.BIOL. V. 348 597 2005 JRNL REFN ISSN 0022-2836 JRNL PMID 15826657 JRNL DOI 10.1016/J.JMB.2005.03.017
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH T.KITAO,C.KUROISHI,T.H.TAHIROV REMARK 1 TITL CRYSTALLIZATION AND PRELIMINARY CRYSTALLOGRAPHIC REMARK 1 TITL 2 ANALYSIS OF THE NICKEL-RESPONSIVE REGULATOR NIKR REMARK 1 TITL 3 FROM PYROCOCCUS HORIKOSHII REMARK 1 REF ACTA CRYSTALLOGR.,SECT.F V. 61 43 2005 REMARK 1 REFN ISSN 1744-3091 REMARK 1 PMID 16508086 REMARK 1 DOI 10.1107/S1744309104025473
REMARK 2 REMARK 2 RESOLUTION. 2.1 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.45 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.0 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1316363.53 REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 61372 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 SET) : 0.196 REMARK 3 FREE R VALUE : 0.215 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.0 REMARK 3 FREE R VALUE TEST SET COUNT : 3068 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.004 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.23 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.1 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 9568 REMARK 3 BIN R VALUE (WORKING SET) : 0.303 REMARK 3 BIN FREE R VALUE : 0.330 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.6 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 464 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.015 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2212 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 39 REMARK 3 SOLVENT ATOMS : 115 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.7 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 49.6 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.94 REMARK 3 B22 (A**2) : 2.94 REMARK 3 B33 (A**2) : -5.88 REMARK 3 B12 (A**2) : 3.60 REMARK 3 B13 (A**2) : 0.00 REMARK 3 B23 (A**2) : 0.00 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.25 REMARK 3 ESD FROM SIGMAA (A) : 0.29 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.27 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.33 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.1 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 21.2 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.64 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 3.93 ; 1.50 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 4.96 ; 2.00 REMARK 3 SIDE-CHAIN BOND (A**2) : 6.62 ; 2.00 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 9.13 ; 2.50 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.341008 REMARK 3 BSOL : 53.9836 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : ION.PARAM REMARK 3 PARAMETER FILE 3 : WATER.PARAM REMARK 3 PARAMETER FILE 4 : EGL.PAR REMARK 3 PARAMETER FILE 5 : PG4.PAR REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : ION.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : EGL.TOP REMARK 3 TOPOLOGY FILE 5 : PG4.TOP REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 2BJ7 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 31-JAN-05. REMARK 100 THE PDBE ID CODE IS EBI-22754.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-APR-04 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL26B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE (RAXIS-V) REMARK 200 DETECTOR MANUFACTURER : RIGAKU REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32158 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 8.300 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 24.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.2 REMARK 200 DATA REDUNDANCY IN SHELL : 5.90 REMARK 200 R MERGE FOR SHELL (I) : 0.28000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 5.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS, DM REMARK 200 STARTING MODEL: PDB ENTRY 2BJ1 REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): NULL REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA):NULL REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 52.66867 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 26.33433 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 26.33433 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 52.66867 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 GENERATING THE BIOMOLECULE 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 -0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -26.33407
REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 HOH A2011 LIES ON A SPECIAL POSITION. REMARK 375 HOH B2015 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 VAL A 138
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 LEU A 137 CA C O CB CG CD1 CD2
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 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 ASN A 51 15.36 -159.45 REMARK 500 GLU A 52 -172.54 -64.69 REMARK 500 TYR A 80 52.53 -116.77 REMARK 500 THR B 131 -156.74 -134.64 REMARK 500 REMARK 500 REMARK: NULL
REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE):
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 A1137 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 89 NE2 REMARK 620 2 HIS A 91 ND1 88.7 REMARK 620 3 CYS A 97 SG 95.1 173.9 REMARK 620 4 HIS B 78 NE2 177.0 90.7 85.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI B1140 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 78 NE2 REMARK 620 2 HIS B 89 NE2 176.2 REMARK 620 3 HIS B 91 ND1 85.3 91.0 REMARK 620 4 CYS B 97 SG 89.1 94.6 173.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI B1141 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 75 OD2 REMARK 620 2 HIS B 64 NE2 99.3 REMARK 620 3 ASP B 65 OD1 100.4 100.9 REMARK 620 4 ASP B 65 OD2 155.2 85.7 54.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI B1142 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 64 NE2 REMARK 620 2 ASP A 65 OD2 77.2 REMARK 620 3 HOH A2025 O 74.2 69.6 REMARK 620 4 ASP A 65 OD1 92.5 54.6 124.2 REMARK 620 5 ASP B 75 OD2 100.8 173.8 104.2 131.6 REMARK 620 6 HOH A2024 O 97.2 119.9 166.1 66.2 66.0 REMARK 620 N 1 2 3 4 5
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A1137 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B1139 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI B1140 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI B1141 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI B1142 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A1138 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PG4 A1139 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PG4 A1140 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B1143
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2BJ1 RELATED DB: PDB REMARK 900 NIKR IN OPEN CONFORMATION AND NICKEL BOUND REMARK 900 TO HIGH-AFFINITY SITES REMARK 900 RELATED ID: 2BJ3 RELATED DB: PDB REMARK 900 NIKR-APO REMARK 900 RELATED ID: 2BJ8 RELATED DB: PDB REMARK 900 NIKR IN CLOSED CONFORMATION AND NICKEL BOUND REMARK 900 TO HIGH AND LOW-AFFINITY SITES REMARK 900 RELATED ID: 2BJ9 RELATED DB: PDB REMARK 900 NIKR WITH BOUND NICKEL AND PHOSPHATE
DBREF 2BJ7 A 1 138 UNP O58316 NIKR_PYRHO 1 138 DBREF 2BJ7 B 1 138 UNP O58316 NIKR_PYRHO 1 138
SEQRES 1 A 138 MET GLU LEU ILE ARG PHE SER ILE SER ILE PRO SER LYS SEQRES 2 A 138 LEU LEU GLU LYS PHE ASP GLN ILE ILE GLU GLU ILE GLY SEQRES 3 A 138 TYR GLU ASN ARG SER GLU ALA ILE ARG ASP LEU ILE ARG SEQRES 4 A 138 ASP PHE ILE ILE ARG HIS GLU TRP GLU VAL GLY ASN GLU SEQRES 5 A 138 GLU VAL ALA GLY THR ILE THR ILE VAL TYR ASN HIS ASP SEQRES 6 A 138 GLU GLY ASP VAL VAL LYS ALA LEU LEU ASP LEU GLN HIS SEQRES 7 A 138 GLU TYR LEU ASP GLU ILE ILE SER SER LEU HIS VAL HIS SEQRES 8 A 138 MET ASP GLU HIS ASN CYS LEU GLU VAL ILE VAL VAL LYS SEQRES 9 A 138 GLY GLU ALA LYS LYS ILE LYS MET ILE ALA ASP LYS LEU SEQRES 10 A 138 LEU SER LEU LYS GLY VAL LYS HIS GLY LYS LEU VAL MET SEQRES 11 A 138 THR SER THR GLY LYS GLU LEU VAL SEQRES 1 B 138 MET GLU LEU ILE ARG PHE SER ILE SER ILE PRO SER LYS SEQRES 2 B 138 LEU LEU GLU LYS PHE ASP GLN ILE ILE GLU GLU ILE GLY SEQRES 3 B 138 TYR GLU ASN ARG SER GLU ALA ILE ARG ASP LEU ILE ARG SEQRES 4 B 138 ASP PHE ILE ILE ARG HIS GLU TRP GLU VAL GLY ASN GLU SEQRES 5 B 138 GLU VAL ALA GLY THR ILE THR ILE VAL TYR ASN HIS ASP SEQRES 6 B 138 GLU GLY ASP VAL VAL LYS ALA LEU LEU ASP LEU GLN HIS SEQRES 7 B 138 GLU TYR LEU ASP GLU ILE ILE SER SER LEU HIS VAL HIS SEQRES 8 B 138 MET ASP GLU HIS ASN CYS LEU GLU VAL ILE VAL VAL LYS SEQRES 9 B 138 GLY GLU ALA LYS LYS ILE LYS MET ILE ALA ASP LYS LEU SEQRES 10 B 138 LEU SER LEU LYS GLY VAL LYS HIS GLY LYS LEU VAL MET SEQRES 11 B 138 THR SER THR GLY LYS GLU LEU VAL
HET NI A1137 1 HET CL B1139 1 HET NI B1140 1 HET NI B1141 1 HET NI B1142 1 HET EDO A1138 4 HET PG4 A1139 13 HET PG4 A1140 13 HET EDO B1143 4
HETNAM NI NICKEL (II) ION HETNAM CL CHLORIDE ION HETNAM EDO 1,2-ETHANEDIOL HETNAM PG4 TETRAETHYLENE GLYCOL
HETSYN PG4 POLYETHYLENE GLYCOL PEG400
FORMUL 3 NI 4(NI 2+) FORMUL 4 CL CL 1- FORMUL 8 EDO 2(C2 H6 O2) FORMUL 9 PG4 2(C8 H18 O5) FORMUL 12 HOH *115(H2 O1)
HELIX 1 1 SER A 12 GLY A 26 1 15 HELIX 2 2 ASN A 29 HIS A 45 1 17 HELIX 3 3 ASP A 68 TYR A 80 1 13 HELIX 4 4 ALA A 107 SER A 119 1 13 HELIX 5 5 SER B 12 GLY B 26 1 15 HELIX 6 6 ASN B 29 VAL B 49 1 21 HELIX 7 7 ASP B 68 TYR B 80 1 13 HELIX 8 8 ALA B 107 SER B 119 1 13
SHEET 1 AA 2 LEU A 3 PRO A 11 0 SHEET 2 AA 2 LEU B 3 PRO B 11 -1 O ILE B 4 N ILE A 10 SHEET 1 AB 4 ILE A 84 HIS A 91 0 SHEET 2 AB 4 ASN A 96 GLU A 106 -1 O LEU A 98 N VAL A 90 SHEET 3 AB 4 GLU A 53 ASN A 63 -1 O VAL A 54 N GLY A 105 SHEET 4 AB 4 VAL A 123 THR A 131 -1 N LYS A 124 O VAL A 61 SHEET 1 BA 4 ILE B 84 HIS B 91 0 SHEET 2 BA 4 ASN B 96 GLU B 106 -1 O LEU B 98 N VAL B 90 SHEET 3 BA 4 GLU B 53 ASN B 63 -1 O VAL B 54 N GLY B 105 SHEET 4 BA 4 VAL B 123 THR B 131 -1 N LYS B 124 O VAL B 61
LINK NI NI A1137 NE2 HIS A 89 1555 1555 2.04 LINK NI NI A1137 ND1 HIS A 91 1555 1555 2.06 LINK NI NI A1137 SG CYS A 97 1555 1555 2.21 LINK NI NI A1137 NE2 HIS B 78 1555 6554 2.02 LINK NI NI B1140 NE2 HIS A 78 1555 6554 2.08 LINK NI NI B1140 NE2 HIS B 89 1555 1555 2.07 LINK NI NI B1140 ND1 HIS B 91 1555 1555 1.94 LINK NI NI B1140 SG CYS B 97 1555 1555 2.28 LINK NI NI B1141 OD1 ASP B 65 1555 1555 2.32 LINK NI NI B1141 NE2 HIS B 64 1555 1555 2.32 LINK NI NI B1141 OD2 ASP B 65 1555 1555 2.46 LINK NI NI B1141 OD2 ASP A 75 1555 6554 2.30 LINK NI NI B1142 OD2 ASP A 65 1555 6554 2.61 LINK NI NI B1142 O HOH A2025 1555 6554 2.08 LINK NI NI B1142 OD1 ASP A 65 1555 6554 2.09 LINK NI NI B1142 OD2 ASP B 75 1555 1555 2.18 LINK NI NI B1142 O HOH A2024 1555 6554 2.53 LINK NI NI B1142 NE2 HIS A 64 1555 6554 2.46
SITE 1 AC1 4 HIS A 89 HIS A 91 CYS A 97 HIS B 78 SITE 1 AC2 3 HOH A2004 ARG B 30 HOH B2023 SITE 1 AC3 5 LEU A 74 HIS A 78 HIS B 89 HIS B 91 SITE 2 AC3 5 CYS B 97 SITE 1 AC4 3 ASP A 75 HIS B 64 ASP B 65 SITE 1 AC5 5 HIS A 64 ASP A 65 HOH A2024 HOH A2025 SITE 2 AC5 5 ASP B 75 SITE 1 AC6 6 PHE A 6 SER A 7 HOH A2053 LYS B 127 SITE 2 AC6 6 LEU B 128 MET B 130 SITE 1 AC7 10 HIS A 45 LYS A 111 ASP A 115 LEU A 118 SITE 2 AC7 10 HIS A 125 GLY A 126 HOH A2043 ILE B 25 SITE 3 AC7 10 TYR B 27 HOH B2020 SITE 1 AC8 6 ASP A 19 ILE A 22 GLU A 23 TYR A 27 SITE 2 AC8 6 GLU A 28 ARG A 30 SITE 1 AC9 3 MET A 1 HIS B 125 GLY B 126
CRYST1 109.952 109.952 79.003 90.00 90.00 120.00 P 32 2 1 12
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 0.009095 0.005251 0.000000 0.00000
SCALE2 0.000000 0.010502 0.000000 0.00000
SCALE3 0.000000 0.000000 0.012658 0.00000