HEADER TRANSCRIPTION 10-AUG-10 3OD2 TITLE E. COLI NIKR SOAKED WITH EXCESS NICKEL IONS COMPND MOL_ID: 1; COMPND 2 MOLECULE: NICKEL-RESPONSIVE REGULATORY PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: ECS4348; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS RIBBON-HELIX-HELIX, FERREDOXIN-LIKE FOLD, TRANSCRIPTION FACTOR, KEYWDS 2 TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR C.M.PHILLIPS,E.R.SCHREITER,C.L.DRENNAN REVDAT 3 06-SEP-23 3OD2 1 REMARK LINK REVDAT 2 22-SEP-10 3OD2 1 JRNL REVDAT 1 08-SEP-10 3OD2 0 JRNL AUTH C.M.PHILLIPS,E.R.SCHREITER,C.M.STULTZ,C.L.DRENNAN JRNL TITL STRUCTURAL BASIS OF LOW-AFFINITY NICKEL BINDING TO THE JRNL TITL 2 NICKEL-RESPONSIVE TRANSCRIPTION FACTOR NIKR FROM ESCHERICHIA JRNL TITL 3 COLI. JRNL REF BIOCHEMISTRY V. 49 7830 2010 JRNL REFN ISSN 0006-2960 JRNL PMID 20704276 JRNL DOI 10.1021/BI100923J REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 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) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 91.5 REMARK 3 NUMBER OF REFLECTIONS : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.236 REMARK 3 FREE R VALUE : 0.287 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.300 REMARK 3 FREE R VALUE TEST SET COUNT : 867 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2012 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 43 REMARK 3 SOLVENT ATOMS : 62 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 76.32 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -16.18400 REMARK 3 B22 (A**2) : -16.18400 REMARK 3 B33 (A**2) : 32.36700 REMARK 3 B12 (A**2) : -14.29800 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) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : NULL REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 2.164 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 3.690 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.811 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.345 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 37.00 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3OD2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-AUG-10. REMARK 100 THE DEPOSITION ID IS D_1000060962. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-FEB-04 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.4845 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8681 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : 9.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08900 REMARK 200 FOR THE DATA SET : 16.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.69 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.28800 REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: 2HZA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.33 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.25 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 200 MM MGCL2, 100 MM HEPES, 30% REMARK 280 VOL/VOL PEG 400, 0.5 ML OF 345 MM CYCLOHEXYL-PROPYL-B-D- REMARK 280 MALTOSIDE (CYMAL-3), PH 8.5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 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+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 61.03800 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 122.07600 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 122.07600 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 61.03800 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: 12870 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24430 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -99.0 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 -0.500000 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 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 ASP A 133 REMARK 465 GLN B 46 REMARK 465 GLN B 47 REMARK 465 HIS B 48 REMARK 465 ASP B 133 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 ARG A 22 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 61 CG CD OE1 OE2 REMARK 470 ARG A 65 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 118 CG CD OE1 NE2 REMARK 470 ARG A 119 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 131 CG CD CE NZ REMARK 470 ARG B 3 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 22 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 23 CG CD NE CZ NH1 NH2 REMARK 470 GLN B 51 CG CD OE1 NE2 REMARK 470 LYS B 64 CG CD CE NZ REMARK 470 LYS B 131 CG CD CE NZ REMARK 470 GLU B 132 CG CD OE1 OE2 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 THR A 45 -7.37 -46.28 REMARK 500 GLN A 47 151.33 -37.62 REMARK 500 TYR A 58 156.85 176.56 REMARK 500 LYS A 64 -108.57 11.14 REMARK 500 HIS A 92 -16.63 -47.89 REMARK 500 ALA A 117 43.96 -98.63 REMARK 500 ARG A 119 106.71 -50.51 REMARK 500 TYR B 58 160.35 178.08 REMARK 500 GLU B 63 -78.75 -77.19 REMARK 500 LYS B 64 -133.14 9.69 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 122 0.24 SIDE CHAIN 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 A 135 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 MET A 1 O REMARK 620 2 HOH A 149 O 66.1 REMARK 620 3 HOH A 150 O 78.9 110.3 REMARK 620 4 HOH B 145 O 158.4 92.5 106.8 REMARK 620 5 HOH B 156 O 105.4 165.3 78.3 96.2 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI A 137 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 78 NE2 REMARK 620 2 HIS A 110 NE2 101.2 REMARK 620 3 ASP A 114 OD2 109.6 88.4 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI A 138 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 79 NE2 REMARK 620 2 HOH A 156 O 86.0 REMARK 620 3 HOH A 161 O 106.2 88.7 REMARK 620 4 HOH A 171 O 120.9 152.4 89.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI A 134 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 87 NE2 REMARK 620 2 HIS A 89 ND1 95.8 REMARK 620 3 CYS A 95 SG 89.4 174.4 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI A 139 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 123 NE2 REMARK 620 2 HOH A 153 O 80.9 REMARK 620 3 HOH A 164 O 63.2 65.9 REMARK 620 4 HOH B 165 O 129.4 63.4 69.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI A 136 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 125 NE2 REMARK 620 2 HOH A 147 O 103.2 REMARK 620 3 HOH A 148 O 61.7 164.2 REMARK 620 4 HIS B 125 NE2 73.2 117.3 65.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI B 139 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 157 O REMARK 620 2 HOH A 158 O 75.8 REMARK 620 3 MET B 1 O 164.7 96.5 REMARK 620 4 MET B 1 N 96.8 65.1 67.8 REMARK 620 5 HOH B 142 O 79.9 137.3 98.0 83.9 REMARK 620 6 HOH B 170 O 104.9 127.8 90.4 156.9 92.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI B 137 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 160 O REMARK 620 2 HOH A 165 O 96.3 REMARK 620 3 HIS B 123 NE2 149.2 84.8 REMARK 620 4 HOH B 149 O 99.8 162.3 85.2 REMARK 620 5 HOH B 169 O 81.7 112.9 126.3 62.5 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI B 136 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 78 NE2 REMARK 620 2 HIS B 110 NE2 78.5 REMARK 620 3 ASP B 114 OD2 79.2 70.6 REMARK 620 4 HOH B 146 O 168.4 104.6 91.3 REMARK 620 5 HOH B 148 O 86.5 164.2 111.4 91.1 REMARK 620 6 HOH B 158 O 80.6 82.4 148.9 110.8 90.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI B 138 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 79 NE2 REMARK 620 2 HOH B 160 O 110.3 REMARK 620 3 HOH B 161 O 145.7 102.4 REMARK 620 4 HOH B 162 O 81.7 149.1 64.6 REMARK 620 5 HOH B 164 O 89.6 61.6 115.6 149.0 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI B 135 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 87 NE2 REMARK 620 2 HIS B 89 ND1 96.5 REMARK 620 3 CYS B 95 SG 100.1 155.9 REMARK 620 N 1 2 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 134 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 135 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 136 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 137 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 138 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 139 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 3CM B 134 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI B 135 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI B 136 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI B 137 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI B 138 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI B 139 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2HZA RELATED DB: PDB REMARK 900 NICKEL-BOUND FULL-LENGTH ESCHERICHIA COLI NIKR REMARK 900 RELATED ID: 2HZV RELATED DB: PDB REMARK 900 NIKR-OPERATOR DNA COMPLEX REMARK 900 RELATED ID: 1Q5V RELATED DB: PDB REMARK 900 APO E. COLI NIKR DBREF 3OD2 A 1 133 UNP C3SP37 C3SP37_ECOLX 1 133 DBREF 3OD2 B 1 133 UNP C3SP37 C3SP37_ECOLX 1 133 SEQRES 1 A 133 MET GLN ARG VAL THR ILE THR LEU ASP ASP ASP LEU LEU SEQRES 2 A 133 GLU THR LEU ASP SER LEU SER GLN ARG ARG GLY TYR ASN SEQRES 3 A 133 ASN ARG SER GLU ALA ILE ARG ASP ILE LEU ARG SER ALA SEQRES 4 A 133 LEU ALA GLN GLU ALA THR GLN GLN HIS GLY THR GLN GLY SEQRES 5 A 133 PHE ALA VAL LEU SER TYR VAL TYR GLU HIS GLU LYS ARG SEQRES 6 A 133 ASP LEU ALA SER ARG ILE VAL SER THR GLN HIS HIS HIS SEQRES 7 A 133 HIS ASP LEU SER VAL ALA THR LEU HIS VAL HIS ILE ASN SEQRES 8 A 133 HIS ASP ASP CYS LEU GLU ILE ALA VAL LEU LYS GLY ASP SEQRES 9 A 133 MET GLY ASP VAL GLN HIS PHE ALA ASP ASP VAL ILE ALA SEQRES 10 A 133 GLN ARG GLY VAL ARG HIS GLY HIS LEU GLN CYS LEU PRO SEQRES 11 A 133 LYS GLU ASP SEQRES 1 B 133 MET GLN ARG VAL THR ILE THR LEU ASP ASP ASP LEU LEU SEQRES 2 B 133 GLU THR LEU ASP SER LEU SER GLN ARG ARG GLY TYR ASN SEQRES 3 B 133 ASN ARG SER GLU ALA ILE ARG ASP ILE LEU ARG SER ALA SEQRES 4 B 133 LEU ALA GLN GLU ALA THR GLN GLN HIS GLY THR GLN GLY SEQRES 5 B 133 PHE ALA VAL LEU SER TYR VAL TYR GLU HIS GLU LYS ARG SEQRES 6 B 133 ASP LEU ALA SER ARG ILE VAL SER THR GLN HIS HIS HIS SEQRES 7 B 133 HIS ASP LEU SER VAL ALA THR LEU HIS VAL HIS ILE ASN SEQRES 8 B 133 HIS ASP ASP CYS LEU GLU ILE ALA VAL LEU LYS GLY ASP SEQRES 9 B 133 MET GLY ASP VAL GLN HIS PHE ALA ASP ASP VAL ILE ALA SEQRES 10 B 133 GLN ARG GLY VAL ARG HIS GLY HIS LEU GLN CYS LEU PRO SEQRES 11 B 133 LYS GLU ASP HET NI A 134 1 HET NI A 135 1 HET NI A 136 1 HET NI A 137 1 HET NI A 138 1 HET NI A 139 1 HET 3CM B 134 32 HET NI B 135 1 HET NI B 136 1 HET NI B 137 1 HET NI B 138 1 HET NI B 139 1 HETNAM NI NICKEL (II) ION HETNAM 3CM 3-CYCLOHEXYLPROPYL 4-O-ALPHA-D-GLUCOPYRANOSYL-BETA-D- HETNAM 2 3CM GLUCOPYRANOSIDE HETSYN 3CM CYMAL-3 FORMUL 3 NI 11(NI 2+) FORMUL 9 3CM C21 H38 O11 FORMUL 15 HOH *62(H2 O) HELIX 1 1 ASP A 9 ARG A 23 1 15 HELIX 2 2 ASN A 27 THR A 45 1 19 HELIX 3 3 ASP A 66 HIS A 78 1 13 HELIX 4 4 ASP A 104 ALA A 117 1 14 HELIX 5 5 ASP B 9 ARG B 23 1 15 HELIX 6 6 ASN B 27 GLN B 42 1 16 HELIX 7 7 ASP B 66 HIS B 78 1 13 HELIX 8 8 MET B 105 ALA B 117 1 13 SHEET 1 A 2 GLN A 2 LEU A 8 0 SHEET 2 A 2 GLN B 2 LEU B 8 -1 O ILE B 6 N VAL A 4 SHEET 1 B 4 SER A 82 HIS A 89 0 SHEET 2 B 4 ASP A 94 LYS A 102 -1 O ILE A 98 N LEU A 86 SHEET 3 B 4 GLY A 52 GLU A 61 -1 N TYR A 60 O CYS A 95 SHEET 4 B 4 VAL A 121 PRO A 130 -1 O LEU A 129 N PHE A 53 SHEET 1 C 4 SER B 82 HIS B 89 0 SHEET 2 C 4 ASP B 94 ASP B 104 -1 O ILE B 98 N LEU B 86 SHEET 3 C 4 GLN B 51 GLU B 61 -1 N TYR B 58 O GLU B 97 SHEET 4 C 4 VAL B 121 PRO B 130 -1 O ARG B 122 N VAL B 59 LINK O MET A 1 NI NI A 135 1555 1555 2.18 LINK NE2 HIS A 78 NI NI A 137 1555 1555 2.22 LINK NE2 HIS A 79 NI NI A 138 1555 1555 2.46 LINK NE2 HIS A 87 NI NI A 134 1555 1555 1.89 LINK ND1 HIS A 89 NI NI A 134 1555 1555 2.10 LINK SG CYS A 95 NI NI A 134 1555 1555 2.22 LINK NE2 HIS A 110 NI NI A 137 1555 1555 2.18 LINK OD2 ASP A 114 NI NI A 137 1555 1555 2.41 LINK NE2 HIS A 123 NI NI A 139 1555 1555 2.05 LINK NE2 HIS A 125 NI NI A 136 1555 1555 2.40 LINK NI NI A 135 O HOH A 149 1555 1555 2.32 LINK NI NI A 135 O HOH A 150 1555 1555 2.66 LINK NI NI A 135 O HOH B 145 1555 1555 2.24 LINK NI NI A 135 O HOH B 156 1555 1555 2.05 LINK NI NI A 136 O HOH A 147 1555 1555 2.51 LINK NI NI A 136 O HOH A 148 1555 1555 2.17 LINK NI NI A 136 NE2 HIS B 125 1555 1555 2.39 LINK NI NI A 138 O HOH A 156 1555 1555 2.31 LINK NI NI A 138 O HOH A 161 1555 1555 2.20 LINK NI NI A 138 O HOH A 171 1555 1555 1.86 LINK NI NI A 139 O HOH A 153 1555 1555 2.54 LINK NI NI A 139 O HOH A 164 1555 1555 2.69 LINK NI NI A 139 O HOH B 165 1555 1555 2.34 LINK O HOH A 157 NI NI B 139 1555 1555 1.99 LINK O HOH A 158 NI NI B 139 1555 1555 1.99 LINK O HOH A 160 NI NI B 137 1555 1555 2.05 LINK O HOH A 165 NI NI B 137 1555 1555 2.21 LINK O MET B 1 NI NI B 139 1555 1555 2.66 LINK N MET B 1 NI NI B 139 1555 1555 2.71 LINK NE2 HIS B 78 NI NI B 136 1555 1555 2.45 LINK NE2 HIS B 79 NI NI B 138 1555 1555 2.47 LINK NE2 HIS B 87 NI NI B 135 1555 1555 2.13 LINK ND1 HIS B 89 NI NI B 135 1555 1555 1.86 LINK SG CYS B 95 NI NI B 135 1555 1555 2.30 LINK NE2 HIS B 110 NI NI B 136 1555 1555 2.49 LINK OD2 ASP B 114 NI NI B 136 1555 1555 2.37 LINK NE2 HIS B 123 NI NI B 137 1555 1555 2.47 LINK NI NI B 136 O HOH B 146 1555 1555 1.85 LINK NI NI B 136 O HOH B 148 1555 1555 2.32 LINK NI NI B 136 O HOH B 158 1555 1555 2.11 LINK NI NI B 137 O HOH B 149 1555 1555 2.22 LINK NI NI B 137 O HOH B 169 1555 1555 2.49 LINK NI NI B 138 O HOH B 160 1555 1555 2.33 LINK NI NI B 138 O HOH B 161 1555 1555 2.32 LINK NI NI B 138 O HOH B 162 1555 1555 2.35 LINK NI NI B 138 O HOH B 164 1555 1555 2.24 LINK NI NI B 139 O HOH B 142 1555 1555 2.17 LINK NI NI B 139 O HOH B 170 1555 1555 2.28 SITE 1 AC1 5 HIS A 87 HIS A 89 CYS A 95 VAL B 72 SITE 2 AC1 5 HIS B 76 SITE 1 AC2 5 MET A 1 HOH A 149 HOH A 150 HOH B 145 SITE 2 AC2 5 HOH B 156 SITE 1 AC3 4 HIS A 125 HOH A 147 HOH A 148 HIS B 125 SITE 1 AC4 4 HIS A 78 HIS A 110 ASP A 114 HOH A 144 SITE 1 AC5 6 HIS A 79 HOH A 156 HOH A 161 HOH A 162 SITE 2 AC5 6 HOH A 171 HIS B 92 SITE 1 AC6 5 HIS A 123 HOH A 153 HOH A 164 PRO B 130 SITE 2 AC6 5 HOH B 165 SITE 1 AC7 10 ARG A 3 LEU A 19 SER A 20 ARG A 23 SITE 2 AC7 10 TYR A 25 ILE A 35 GLU B 43 GLY B 124 SITE 3 AC7 10 HIS B 125 LEU B 126 SITE 1 AC8 4 HIS A 76 HIS B 87 HIS B 89 CYS B 95 SITE 1 AC9 6 HIS B 78 HIS B 110 ASP B 114 HOH B 146 SITE 2 AC9 6 HOH B 148 HOH B 158 SITE 1 BC1 6 HOH A 160 HOH A 165 HIS B 123 HOH B 149 SITE 2 BC1 6 HOH B 168 HOH B 169 SITE 1 BC2 7 HIS A 92 HIS B 79 ASP B 80 HOH B 160 SITE 2 BC2 7 HOH B 161 HOH B 162 HOH B 164 SITE 1 BC3 5 HOH A 157 HOH A 158 MET B 1 HOH B 142 SITE 2 BC3 5 HOH B 170 CRYST1 50.735 50.735 183.114 90.00 90.00 120.00 P 31 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 0.019710 0.011380 0.000000 0.00000 SCALE2 0.000000 0.022759 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005461 0.00000