HEADER METAL BINDING PROTEIN 07-DEC-07 3BKT TITLE COPPER-BOUND C-TERMINAL DOMAIN OF NIKR COMPND MOL_ID: 1; COMPND 2 MOLECULE: NICKEL-RESPONSIVE REGULATOR; COMPND 3 CHAIN: A, B, C, D; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: NIKR; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); 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: PET28 KEYWDS NIKR, NICKEL REGULATORY PROTEIN, TRANSCRIPTION FACTOR, BETA SANDWICH, KEYWDS 2 DNA-BINDING, METAL-BINDING, REPRESSOR, TRANSCRIPTION REGULATION, KEYWDS 3 METAL BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR C.M.PHILLIPS,E.R.SCHREITER,C.L.DRENNAN REVDAT 4 30-AUG-23 3BKT 1 REMARK LINK REVDAT 3 25-OCT-17 3BKT 1 REMARK REVDAT 2 24-FEB-09 3BKT 1 VERSN REVDAT 1 19-FEB-08 3BKT 0 JRNL AUTH C.M.PHILLIPS,E.R.SCHREITER,Y.GUO,S.C.WANG,D.B.ZAMBLE, JRNL AUTH 2 C.L.DRENNAN JRNL TITL STRUCTURAL BASIS OF THE METAL SPECIFICITY FOR NICKEL JRNL TITL 2 REGULATORY PROTEIN NIKR. JRNL REF BIOCHEMISTRY V. 47 1938 2008 JRNL REFN ISSN 0006-2960 JRNL PMID 18193897 JRNL DOI 10.1021/BI702006H REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.17 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 3 NUMBER OF REFLECTIONS : 46629 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) : 0.198 REMARK 3 R VALUE (WORKING SET) : 0.196 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2360 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) : 1.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.54 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2713 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 82.54 REMARK 3 BIN R VALUE (WORKING SET) : 0.2200 REMARK 3 BIN FREE R VALUE SET COUNT : 138 REMARK 3 BIN FREE R VALUE : 0.2990 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2536 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 4 REMARK 3 SOLVENT ATOMS : 171 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.05 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.04000 REMARK 3 B22 (A**2) : -0.02000 REMARK 3 B33 (A**2) : -0.01000 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): 0.115 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.088 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.054 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.108 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.959 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.949 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2689 ; 0.011 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 1650 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3669 ; 1.346 ; 1.894 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4060 ; 0.877 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 343 ; 5.878 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 140 ;34.752 ;24.286 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 419 ;14.148 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 9 ;17.066 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 419 ; 0.085 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3083 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 534 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 526 ; 0.209 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 1647 ; 0.187 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1240 ; 0.170 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 1402 ; 0.086 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 151 ; 0.179 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 5 ; 0.040 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 20 ; 0.159 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 41 ; 0.183 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 8 ; 0.219 ; 0.200 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): 1722 ; 1.403 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 682 ; 0.527 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2681 ; 2.105 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1059 ; 2.808 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 982 ; 3.800 ; 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): 4676 ; 2.663 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 175 ; 6.882 ; 3.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 4267 ; 3.062 ; 3.000 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 REMARK 4 REMARK 4 3BKT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-DEC-07. REMARK 100 THE DEPOSITION ID IS D_1000045643. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-FEB-04 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 8-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9791 REMARK 200 MONOCHROMATOR : SI 111 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, XFIT REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 46684 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 200 DATA REDUNDANCY : 8.100 REMARK 200 R MERGE (I) : 0.05900 REMARK 200 R SYM (I) : 0.05700 REMARK 200 FOR THE DATA SET : 16.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 85.2 REMARK 200 DATA REDUNDANCY IN SHELL : 6.10 REMARK 200 R MERGE FOR SHELL (I) : 0.26300 REMARK 200 R SYM FOR SHELL (I) : 0.25400 REMARK 200 FOR SHELL : 5.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: XFIT REMARK 200 STARTING MODEL: THE TETRAMER OF NICKEL-BOUND C-TERMINAL DOMAIN OF REMARK 200 NIKR, 1Q5Y REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.82 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.89 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M NA TARTRATE, 20% PEG 3350, PH REMARK 280 8.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z 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 22.97450 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 40.73000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 39.22100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 40.73000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.97450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 39.22100 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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: 7620 ANGSTROM**2 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: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1750 ANGSTROM**2 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 REMARK 350 BIOMOLECULE: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1640 ANGSTROM**2 REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 HIS A 48 REMARK 465 GLY A 49 REMARK 465 ASP A 133 REMARK 465 HIS B 48 REMARK 465 GLY B 49 REMARK 465 ASP B 133 REMARK 465 HIS C 48 REMARK 465 GLY C 49 REMARK 465 THR C 50 REMARK 465 ASP C 133 REMARK 465 HIS D 48 REMARK 465 GLY D 49 REMARK 465 LYS D 64 REMARK 465 ARG D 65 REMARK 465 ASP D 66 REMARK 465 GLU D 132 REMARK 465 ASP D 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 GLU A 63 CG CD OE1 OE2 REMARK 470 ARG A 119 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 65 CG CD NE CZ NH1 NH2 REMARK 470 ASP B 66 CG OD1 OD2 REMARK 470 ARG B 70 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 119 CG CD NE CZ NH1 NH2 REMARK 470 GLN C 51 CG CD OE1 NE2 REMARK 470 THR D 50 OG1 CG2 REMARK 470 ARG D 70 CG CD NE CZ NH1 NH2 REMARK 470 HIS D 110 CG ND1 CD2 CE1 NE2 REMARK 470 ASP D 113 CG OD1 OD2 REMARK 470 ASP D 114 CG OD1 OD2 REMARK 470 ARG D 119 CG CD NE CZ NH1 NH2 REMARK 470 LYS D 131 CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 177 O HOH B 180 2.02 REMARK 500 OD1 ASP C 113 O HOH C 180 2.14 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 HIS A 78 55.96 -101.19 REMARK 500 LYS B 64 77.42 -68.23 REMARK 500 ARG B 65 45.56 -147.74 REMARK 500 VAL B 83 -69.05 -95.23 REMARK 500 VAL C 83 -67.25 -98.07 REMARK 500 VAL D 83 -62.73 -94.46 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 ARG B 65 ASP B 66 139.22 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 CU A 2 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 87 NE2 REMARK 620 2 HIS A 89 ND1 85.8 REMARK 620 3 HIS C 76 NE2 171.5 87.9 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU C 1 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 76 NE2 REMARK 620 2 HIS C 87 NE2 166.1 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU B 4 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 87 NE2 REMARK 620 2 HIS B 89 ND1 87.4 REMARK 620 3 HIS D 76 NE2 171.0 85.1 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU D 3 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 76 NE2 REMARK 620 2 HIS D 87 NE2 162.6 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CU A 2 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CU B 4 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CU C 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CU D 3 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3BKF RELATED DB: PDB REMARK 900 ZN-BOUND C-TERMINAL DOMAIN OF NIKR REMARK 900 RELATED ID: 3BKU RELATED DB: PDB REMARK 900 APO C-TERMINAL DOMAIN OF NIKR DBREF 3BKT A 48 133 UNP P0A6Z6 NIKR_ECOLI 48 133 DBREF 3BKT B 48 133 UNP P0A6Z6 NIKR_ECOLI 48 133 DBREF 3BKT C 48 133 UNP P0A6Z6 NIKR_ECOLI 48 133 DBREF 3BKT D 48 133 UNP P0A6Z6 NIKR_ECOLI 48 133 SEQRES 1 A 86 HIS GLY THR GLN GLY PHE ALA VAL LEU SER TYR VAL TYR SEQRES 2 A 86 GLU HIS GLU LYS ARG ASP LEU ALA SER ARG ILE VAL SER SEQRES 3 A 86 THR GLN HIS HIS HIS HIS ASP LEU SER VAL ALA THR LEU SEQRES 4 A 86 HIS VAL HIS ILE ASN HIS ASP ASP CYS LEU GLU ILE ALA SEQRES 5 A 86 VAL LEU LYS GLY ASP MET GLY ASP VAL GLN HIS PHE ALA SEQRES 6 A 86 ASP ASP VAL ILE ALA GLN ARG GLY VAL ARG HIS GLY HIS SEQRES 7 A 86 LEU GLN CYS LEU PRO LYS GLU ASP SEQRES 1 B 86 HIS GLY THR GLN GLY PHE ALA VAL LEU SER TYR VAL TYR SEQRES 2 B 86 GLU HIS GLU LYS ARG ASP LEU ALA SER ARG ILE VAL SER SEQRES 3 B 86 THR GLN HIS HIS HIS HIS ASP LEU SER VAL ALA THR LEU SEQRES 4 B 86 HIS VAL HIS ILE ASN HIS ASP ASP CYS LEU GLU ILE ALA SEQRES 5 B 86 VAL LEU LYS GLY ASP MET GLY ASP VAL GLN HIS PHE ALA SEQRES 6 B 86 ASP ASP VAL ILE ALA GLN ARG GLY VAL ARG HIS GLY HIS SEQRES 7 B 86 LEU GLN CYS LEU PRO LYS GLU ASP SEQRES 1 C 86 HIS GLY THR GLN GLY PHE ALA VAL LEU SER TYR VAL TYR SEQRES 2 C 86 GLU HIS GLU LYS ARG ASP LEU ALA SER ARG ILE VAL SER SEQRES 3 C 86 THR GLN HIS HIS HIS HIS ASP LEU SER VAL ALA THR LEU SEQRES 4 C 86 HIS VAL HIS ILE ASN HIS ASP ASP CYS LEU GLU ILE ALA SEQRES 5 C 86 VAL LEU LYS GLY ASP MET GLY ASP VAL GLN HIS PHE ALA SEQRES 6 C 86 ASP ASP VAL ILE ALA GLN ARG GLY VAL ARG HIS GLY HIS SEQRES 7 C 86 LEU GLN CYS LEU PRO LYS GLU ASP SEQRES 1 D 86 HIS GLY THR GLN GLY PHE ALA VAL LEU SER TYR VAL TYR SEQRES 2 D 86 GLU HIS GLU LYS ARG ASP LEU ALA SER ARG ILE VAL SER SEQRES 3 D 86 THR GLN HIS HIS HIS HIS ASP LEU SER VAL ALA THR LEU SEQRES 4 D 86 HIS VAL HIS ILE ASN HIS ASP ASP CYS LEU GLU ILE ALA SEQRES 5 D 86 VAL LEU LYS GLY ASP MET GLY ASP VAL GLN HIS PHE ALA SEQRES 6 D 86 ASP ASP VAL ILE ALA GLN ARG GLY VAL ARG HIS GLY HIS SEQRES 7 D 86 LEU GLN CYS LEU PRO LYS GLU ASP HET CU A 2 1 HET CU B 4 1 HET CU C 1 1 HET CU D 3 1 HETNAM CU COPPER (II) ION FORMUL 5 CU 4(CU 2+) FORMUL 9 HOH *171(H2 O) HELIX 1 1 LYS A 64 HIS A 78 1 15 HELIX 2 2 MET A 105 ALA A 117 1 13 HELIX 3 3 ARG B 65 HIS B 78 1 14 HELIX 4 4 MET B 105 ALA B 117 1 13 HELIX 5 5 LYS C 64 HIS C 78 1 15 HELIX 6 6 ASP C 104 ALA C 117 1 14 HELIX 7 7 LEU D 67 HIS D 77 1 11 HELIX 8 8 MET D 105 ALA D 117 1 13 SHEET 1 A 8 ARG A 122 PRO A 130 0 SHEET 2 A 8 GLN A 51 GLU A 61 -1 N VAL A 59 O ARG A 122 SHEET 3 A 8 ASP A 94 ASP A 104 -1 O CYS A 95 N TYR A 60 SHEET 4 A 8 SER A 82 HIS A 89 -1 N VAL A 83 O VAL A 100 SHEET 5 A 8 SER C 82 HIS C 89 -1 O HIS C 87 N THR A 85 SHEET 6 A 8 ASP C 94 GLY C 103 -1 O VAL C 100 N VAL C 83 SHEET 7 A 8 GLY C 52 GLU C 61 -1 N LEU C 56 O ALA C 99 SHEET 8 A 8 ARG C 122 PRO C 130 -1 O LEU C 129 N PHE C 53 SHEET 1 B 8 ARG B 122 PRO B 130 0 SHEET 2 B 8 GLN B 51 GLU B 61 -1 N PHE B 53 O LEU B 129 SHEET 3 B 8 ASP B 94 ASP B 104 -1 O ALA B 99 N LEU B 56 SHEET 4 B 8 SER B 82 HIS B 89 -1 N VAL B 83 O VAL B 100 SHEET 5 B 8 SER D 82 HIS D 89 -1 O HIS D 87 N THR B 85 SHEET 6 B 8 ASP D 94 ASP D 104 -1 O VAL D 100 N VAL D 83 SHEET 7 B 8 GLN D 51 GLU D 61 -1 N TYR D 60 O CYS D 95 SHEET 8 B 8 VAL D 121 PRO D 130 -1 O ARG D 122 N VAL D 59 LINK CU CU A 2 NE2 HIS A 87 1555 1555 2.01 LINK CU CU A 2 ND1 HIS A 89 1555 1555 2.39 LINK CU CU A 2 NE2 HIS C 76 1555 1555 1.99 LINK NE2 HIS A 76 CU CU C 1 1555 1555 2.11 LINK CU CU B 4 NE2 HIS B 87 1555 1555 2.07 LINK CU CU B 4 ND1 HIS B 89 1555 1555 2.24 LINK CU CU B 4 NE2 HIS D 76 1555 1555 1.96 LINK NE2 HIS B 76 CU CU D 3 1555 1555 2.01 LINK CU CU C 1 NE2 HIS C 87 1555 1555 2.07 LINK CU CU D 3 NE2 HIS D 87 1555 1555 2.03 SITE 1 AC1 4 HIS A 87 HIS A 89 CYS A 95 HIS C 76 SITE 1 AC2 5 HIS B 87 HIS B 89 CYS B 95 VAL D 72 SITE 2 AC2 5 HIS D 76 SITE 1 AC3 5 VAL A 72 HIS A 76 HIS C 87 HIS C 89 SITE 2 AC3 5 CYS C 95 SITE 1 AC4 5 VAL B 72 HIS B 76 HIS D 87 HIS D 89 SITE 2 AC4 5 CYS D 95 CRYST1 45.949 78.442 81.460 90.00 90.00 90.00 P 21 21 21 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 0.021763 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012748 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012276 0.00000