HEADER TRANSCRIPTION 31-JAN-05 2BJ7 TITLE NIKR IN CLOSED CONFORMATION AND NICKEL BOUND TO HIGH-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-BINDING, KEYWDS 2 METAL-BINDING, NICKEL, TRANSCRIPTION REGULATION, RIKEN STRUCTURAL KEYWDS 3 GENOMICS/PROTEOMICS INITIATIVE, RSGI, STRUCTURAL GENOMICS EXPDTA X-RAY DIFFRACTION AUTHOR T.H.TAHIROV REVDAT 3 13-DEC-23 2BJ7 1 LINK 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 SENSING AND JRNL TITL 2 IMPLICATIONS FOR THE REGULATION OF DNA 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 ANALYSIS OF REMARK 1 TITL 2 THE NICKEL-RESPONSIVE REGULATOR NIKR FROM PYROCOCCUS REMARK 1 TITL 3 HORIKOSHII REMARK 1 REF ACTA CRYSTALLOGR.,SECT.F V. 61 43 2005 REMARK 1 REFN ESSN 1744-3091 REMARK 1 PMID 16508086 REMARK 1 DOI 10.1107/S1744309104025473 REMARK 2 REMARK 2 RESOLUTION. 2.10 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)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1316363.530 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 (%) : 5.000 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) (%) : 96.10 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 9568 REMARK 3 BIN R VALUE (WORKING SET) : 0.3030 REMARK 3 BIN FREE R VALUE : 0.3300 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.60 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 : 2205 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) : 21.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 49.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.94000 REMARK 3 B22 (A**2) : 2.94000 REMARK 3 B33 (A**2) : -5.88000 REMARK 3 B12 (A**2) : 3.60000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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) : 1.100 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 21.20 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.640 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) : 3.930 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 4.960 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 6.620 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 9.130 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.34 REMARK 3 BSOL : 53.98 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. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 31-JAN-05. REMARK 100 THE DEPOSITION ID IS D_1290022754. 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 REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS-V 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 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 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 (%): 71.75 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.35 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 7.50 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 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 -26.33433 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 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 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 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 A 133 6.91 -53.89 REMARK 500 GLU A 136 155.68 -41.43 REMARK 500 THR B 131 -156.74 -134.64 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 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 ASP A 65 OD1 92.5 54.6 REMARK 620 4 HOH A2024 O 97.2 119.9 66.2 REMARK 620 5 HOH A2025 O 74.2 69.6 124.2 166.1 REMARK 620 6 ASP B 75 OD2 100.8 173.8 131.6 66.1 104.2 REMARK 620 N 1 2 3 4 5 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 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 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 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 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 TO HIGH AND LOW- REMARK 900 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 EDO A1138 4 HET PG4 A1139 13 HET PG4 A1140 13 HET CL B1139 1 HET NI B1140 1 HET NI B1141 1 HET NI B1142 1 HET EDO B1143 4 HETNAM NI NICKEL (II) ION HETNAM EDO 1,2-ETHANEDIOL HETNAM PG4 TETRAETHYLENE GLYCOL HETNAM CL CHLORIDE ION HETSYN EDO ETHYLENE GLYCOL FORMUL 3 NI 4(NI 2+) FORMUL 4 EDO 2(C2 H6 O2) FORMUL 5 PG4 2(C8 H18 O5) FORMUL 7 CL CL 1- FORMUL 12 HOH *115(H2 O) 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 NE2 HIS A 64 NI NI B1142 6554 1555 2.46 LINK OD2 ASP A 65 NI NI B1142 6554 1555 2.61 LINK OD1 ASP A 65 NI NI B1142 6554 1555 2.09 LINK OD2 ASP A 75 NI NI B1141 6554 1555 2.30 LINK NE2 HIS A 78 NI NI B1140 6554 1555 2.08 LINK NE2 HIS A 89 NI NI A1137 1555 1555 2.04 LINK ND1 HIS A 91 NI NI A1137 1555 1555 2.06 LINK SG CYS A 97 NI NI A1137 1555 1555 2.21 LINK NI NI A1137 NE2 HIS B 78 1555 6554 2.02 LINK O HOH A2024 NI NI B1142 6554 1555 2.53 LINK O HOH A2025 NI NI B1142 6554 1555 2.08 LINK NE2 HIS B 64 NI NI B1141 1555 1555 2.32 LINK OD1 ASP B 65 NI NI B1141 1555 1555 2.32 LINK OD2 ASP B 65 NI NI B1141 1555 1555 2.46 LINK OD2 ASP B 75 NI NI B1142 1555 1555 2.18 LINK NE2 HIS B 89 NI NI B1140 1555 1555 2.07 LINK ND1 HIS B 91 NI NI B1140 1555 1555 1.94 LINK SG CYS B 97 NI NI B1140 1555 1555 2.28 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