HEADER DNA BINDING PROTEIN/DNA 13-OCT-18 6MRJ TITLE CRYSTAL STRUCTURE OF H.PYLORI NIKR IN COMPLEX WITH DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: NICKEL-RESPONSIVE REGULATOR; COMPND 3 CHAIN: A, B, C, D; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (36-MER); COMPND 7 CHAIN: L; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: DNA (36-MER); COMPND 11 CHAIN: M; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HELICOBACTER PYLORI (STRAIN ATCC 700392 / SOURCE 3 26695); SOURCE 4 ORGANISM_TAXID: 85962; SOURCE 5 STRAIN: ATCC 700392 / 26695; SOURCE 6 GENE: HP_1338; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 12 ORGANISM_TAXID: 32630; SOURCE 13 MOL_ID: 3; SOURCE 14 SYNTHETIC: YES; SOURCE 15 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 16 ORGANISM_TAXID: 32630 KEYWDS NICKEL, PROTEIN-DNA COMPLEX, TRANSCRIPTION FACTOR, DNA BINDING KEYWDS 2 PROTEIN, DNA BINDING PROTEIN-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR E.POZHARSKI,V.DE SERRANO REVDAT 2 11-OCT-23 6MRJ 1 LINK REVDAT 1 20-NOV-19 6MRJ 0 JRNL AUTH E.POZHARSKI,V.DE SERRANO JRNL TITL CRYSTAL STRUCTURE OF H.PYLORI NIKR IN COMPLEX WITH DNA JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.10.2 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.47 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 35178 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) : 0.209 REMARK 3 R VALUE (WORKING SET) : 0.207 REMARK 3 FREE R VALUE : 0.241 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.890 REMARK 3 FREE R VALUE TEST SET COUNT : 1721 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 : 18 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 2.80 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.88 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 2858 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2608 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2717 REMARK 3 BIN R VALUE (WORKING SET) : 0.2589 REMARK 3 BIN FREE R VALUE : 0.2983 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.93 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 141 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 : 4452 REMARK 3 NUCLEIC ACID ATOMS : 1470 REMARK 3 HETEROGEN ATOMS : 6 REMARK 3 SOLVENT ATOMS : 35 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 79.37 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 100.2 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 15.91290 REMARK 3 B22 (A**2) : -34.31210 REMARK 3 B33 (A**2) : 18.39910 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.501 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.433 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.276 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.424 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.277 REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.926 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.904 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 6226 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 8722 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 2059 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 160 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 725 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 6226 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : 0 ; 5.000 ; SEMIHARMONIC REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 828 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 6662 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.05 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 2.47 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 21.81 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6MRJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-OCT-18. REMARK 100 THE DEPOSITION ID IS D_1000237436. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-MAR-13 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 : SSRL REMARK 200 BEAMLINE : BL7-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 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 : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35339 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 39.490 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 123.2 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.93 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 120.7 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 3LGH REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 72.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.02 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 3350, 0.2M NAF, 20MM HEPES PH REMARK 280 8.0, 0.1M NACL, 10MM MG2CL, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 285K 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 36.18500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 102.03000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 47.09000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 102.03000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 36.18500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 47.09000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 24920 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 32120 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -213.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, L, M 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 MET A 1 REMARK 465 ASP A 2 REMARK 465 THR A 3 REMARK 465 PRO A 4 REMARK 465 ASN A 5 REMARK 465 LYS A 6 REMARK 465 ASP A 7 REMARK 465 SER A 142 REMARK 465 SER A 143 REMARK 465 PHE A 144 REMARK 465 GLU A 145 REMARK 465 TYR A 146 REMARK 465 ASN A 147 REMARK 465 GLU A 148 REMARK 465 MET B 1 REMARK 465 ASP B 2 REMARK 465 THR B 3 REMARK 465 PRO B 4 REMARK 465 ASN B 5 REMARK 465 LYS B 6 REMARK 465 MET C 1 REMARK 465 ASP C 2 REMARK 465 THR C 3 REMARK 465 PRO C 4 REMARK 465 ASN C 5 REMARK 465 LYS C 6 REMARK 465 MET D 1 REMARK 465 ASP D 2 REMARK 465 THR D 3 REMARK 465 PRO D 4 REMARK 465 ASN D 5 REMARK 465 PHE D 144 REMARK 465 GLU D 145 REMARK 465 TYR 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 ILE A 11 CG1 CG2 CD1 REMARK 470 LYS A 64 CG CD CE NZ REMARK 470 ARG A 77 CG CD NE CZ NH1 NH2 REMARK 470 PHE A 118 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ARG A 122 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 131 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 31 CG CD CE NZ REMARK 470 GLU B 56 CG CD OE1 OE2 REMARK 470 ASP B 57 CG OD1 OD2 REMARK 470 ARG B 77 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 78 CG CD OE1 OE2 REMARK 470 LYS B 137 CD CE NZ REMARK 470 PHE C 118 CG CD1 CD2 CE1 CE2 CZ 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 DT L 22 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DT L 28 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 DT L 30 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 DA M 4 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 DT M 7 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 DC M 12 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DT M 16 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 DT M 20 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 DT M 30 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 DT M 34 O4' - C1' - N1 ANGL. DEV. = 2.5 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 ILE A 29 -77.94 -63.65 REMARK 500 ASP A 61 37.77 -78.22 REMARK 500 ARG A 77 113.24 -38.92 REMARK 500 THR A 92 -14.69 66.66 REMARK 500 GLN B 76 109.56 -59.09 REMARK 500 GLU B 78 15.12 57.98 REMARK 500 PHE C 13 138.94 -178.72 REMARK 500 ILE C 29 -60.49 -124.50 REMARK 500 ASP D 52 38.86 -96.32 REMARK 500 GLU D 56 -12.57 61.82 REMARK 500 ASN D 60 -8.36 70.00 REMARK 500 ALA D 141 -117.10 -128.94 REMARK 500 SER D 142 149.87 -173.77 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 203 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 88 NE2 REMARK 620 2 HIS D 99 NE2 168.0 REMARK 620 3 HIS D 101 ND1 84.8 90.9 REMARK 620 4 CYS D 107 SG 87.3 95.1 168.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI A 201 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 99 NE2 REMARK 620 2 HIS A 101 ND1 89.4 REMARK 620 3 CYS A 107 SG 95.6 172.1 REMARK 620 4 HIS D 88 NE2 170.3 85.5 88.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 202 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LEU A 130 O REMARK 620 2 VAL A 133 O 114.2 REMARK 620 3 GLU B 39 OE1 106.2 120.0 REMARK 620 4 ASP B 43 OD2 154.1 85.6 74.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI B 202 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 88 NE2 REMARK 620 2 HIS C 99 NE2 175.8 REMARK 620 3 HIS C 101 ND1 90.0 88.3 REMARK 620 4 CYS C 107 SG 91.7 89.7 173.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI B 201 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 99 NE2 REMARK 620 2 HIS B 101 ND1 93.5 REMARK 620 3 CYS B 107 SG 96.4 168.5 REMARK 620 4 HIS C 88 NE2 170.2 83.8 85.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG C 201 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU C 39 OE1 REMARK 620 2 ASP C 43 OD2 82.0 REMARK 620 3 GLY D 128 O 130.9 68.3 REMARK 620 4 LEU D 130 O 105.4 158.4 92.4 REMARK 620 5 VAL D 133 O 120.8 91.4 98.9 101.4 REMARK 620 N 1 2 3 4 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 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NI A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NI B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NI B 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG C 201 DBREF 6MRJ A 1 148 UNP O25896 NIKR_HELPY 1 148 DBREF 6MRJ B 1 148 UNP O25896 NIKR_HELPY 1 148 DBREF 6MRJ C 1 148 UNP O25896 NIKR_HELPY 1 148 DBREF 6MRJ D 1 148 UNP O25896 NIKR_HELPY 1 148 DBREF 6MRJ L 0 35 PDB 6MRJ 6MRJ 0 35 DBREF 6MRJ M 0 35 PDB 6MRJ 6MRJ 0 35 SEQRES 1 A 148 MET ASP THR PRO ASN LYS ASP ASP SER ILE ILE ARG PHE SEQRES 2 A 148 SER VAL SER LEU GLN GLN ASN LEU LEU ASP GLU LEU ASP SEQRES 3 A 148 ASN ARG ILE ILE LYS ASN GLY TYR SER SER ARG SER GLU SEQRES 4 A 148 LEU VAL ARG ASP MET ILE ARG GLU LYS LEU VAL GLU ASP SEQRES 5 A 148 ASN TRP ALA GLU ASP ASN PRO ASN ASP GLU SER LYS ILE SEQRES 6 A 148 ALA VAL LEU VAL VAL ILE TYR ASP HIS HIS GLN ARG GLU SEQRES 7 A 148 LEU ASN GLN ARG MET ILE ASP ILE GLN HIS ALA SER GLY SEQRES 8 A 148 THR HIS VAL LEU CYS THR THR HIS ILE HIS MET ASP GLU SEQRES 9 A 148 HIS ASN CYS LEU GLU THR ILE ILE LEU GLN GLY ASN SER SEQRES 10 A 148 PHE GLU ILE GLN ARG LEU GLN LEU GLU ILE GLY GLY LEU SEQRES 11 A 148 ARG GLY VAL LYS PHE ALA LYS LEU THR LYS ALA SER SER SEQRES 12 A 148 PHE GLU TYR ASN GLU SEQRES 1 B 148 MET ASP THR PRO ASN LYS ASP ASP SER ILE ILE ARG PHE SEQRES 2 B 148 SER VAL SER LEU GLN GLN ASN LEU LEU ASP GLU LEU ASP SEQRES 3 B 148 ASN ARG ILE ILE LYS ASN GLY TYR SER SER ARG SER GLU SEQRES 4 B 148 LEU VAL ARG ASP MET ILE ARG GLU LYS LEU VAL GLU ASP SEQRES 5 B 148 ASN TRP ALA GLU ASP ASN PRO ASN ASP GLU SER LYS ILE SEQRES 6 B 148 ALA VAL LEU VAL VAL ILE TYR ASP HIS HIS GLN ARG GLU SEQRES 7 B 148 LEU ASN GLN ARG MET ILE ASP ILE GLN HIS ALA SER GLY SEQRES 8 B 148 THR HIS VAL LEU CYS THR THR HIS ILE HIS MET ASP GLU SEQRES 9 B 148 HIS ASN CYS LEU GLU THR ILE ILE LEU GLN GLY ASN SER SEQRES 10 B 148 PHE GLU ILE GLN ARG LEU GLN LEU GLU ILE GLY GLY LEU SEQRES 11 B 148 ARG GLY VAL LYS PHE ALA LYS LEU THR LYS ALA SER SER SEQRES 12 B 148 PHE GLU TYR ASN GLU SEQRES 1 C 148 MET ASP THR PRO ASN LYS ASP ASP SER ILE ILE ARG PHE SEQRES 2 C 148 SER VAL SER LEU GLN GLN ASN LEU LEU ASP GLU LEU ASP SEQRES 3 C 148 ASN ARG ILE ILE LYS ASN GLY TYR SER SER ARG SER GLU SEQRES 4 C 148 LEU VAL ARG ASP MET ILE ARG GLU LYS LEU VAL GLU ASP SEQRES 5 C 148 ASN TRP ALA GLU ASP ASN PRO ASN ASP GLU SER LYS ILE SEQRES 6 C 148 ALA VAL LEU VAL VAL ILE TYR ASP HIS HIS GLN ARG GLU SEQRES 7 C 148 LEU ASN GLN ARG MET ILE ASP ILE GLN HIS ALA SER GLY SEQRES 8 C 148 THR HIS VAL LEU CYS THR THR HIS ILE HIS MET ASP GLU SEQRES 9 C 148 HIS ASN CYS LEU GLU THR ILE ILE LEU GLN GLY ASN SER SEQRES 10 C 148 PHE GLU ILE GLN ARG LEU GLN LEU GLU ILE GLY GLY LEU SEQRES 11 C 148 ARG GLY VAL LYS PHE ALA LYS LEU THR LYS ALA SER SER SEQRES 12 C 148 PHE GLU TYR ASN GLU SEQRES 1 D 148 MET ASP THR PRO ASN LYS ASP ASP SER ILE ILE ARG PHE SEQRES 2 D 148 SER VAL SER LEU GLN GLN ASN LEU LEU ASP GLU LEU ASP SEQRES 3 D 148 ASN ARG ILE ILE LYS ASN GLY TYR SER SER ARG SER GLU SEQRES 4 D 148 LEU VAL ARG ASP MET ILE ARG GLU LYS LEU VAL GLU ASP SEQRES 5 D 148 ASN TRP ALA GLU ASP ASN PRO ASN ASP GLU SER LYS ILE SEQRES 6 D 148 ALA VAL LEU VAL VAL ILE TYR ASP HIS HIS GLN ARG GLU SEQRES 7 D 148 LEU ASN GLN ARG MET ILE ASP ILE GLN HIS ALA SER GLY SEQRES 8 D 148 THR HIS VAL LEU CYS THR THR HIS ILE HIS MET ASP GLU SEQRES 9 D 148 HIS ASN CYS LEU GLU THR ILE ILE LEU GLN GLY ASN SER SEQRES 10 D 148 PHE GLU ILE GLN ARG LEU GLN LEU GLU ILE GLY GLY LEU SEQRES 11 D 148 ARG GLY VAL LYS PHE ALA LYS LEU THR LYS ALA SER SER SEQRES 12 D 148 PHE GLU TYR ASN GLU SEQRES 1 L 36 DG DT DA DA DT DT DA DT DT DA DT DT DT SEQRES 2 L 36 DA DA DA DA DT DG DA DA DT DT DA DG DT SEQRES 3 L 36 DG DT DT DA DT DA DT DC DT DG SEQRES 1 M 36 DC DC DA DG DA DT DA DT DA DA DC DA DC SEQRES 2 M 36 DT DA DA DT DT DC DA DT DT DT DT DA DA SEQRES 3 M 36 DA DT DA DA DT DA DA DT DT DA HET NI A 201 1 HET MG A 202 1 HET NI A 203 1 HET NI B 201 1 HET NI B 202 1 HET MG C 201 1 HETNAM NI NICKEL (II) ION HETNAM MG MAGNESIUM ION FORMUL 7 NI 4(NI 2+) FORMUL 8 MG 2(MG 2+) FORMUL 13 HOH *35(H2 O) HELIX 1 AA1 GLN A 19 ASN A 27 1 9 HELIX 2 AA2 ASN A 27 ASN A 32 1 6 HELIX 3 AA3 SER A 36 ASP A 57 1 22 HELIX 4 AA4 GLU A 78 SER A 90 1 13 HELIX 5 AA5 ASN A 116 GLY A 129 1 14 HELIX 6 AA6 GLN B 19 ASN B 32 1 14 HELIX 7 AA7 SER B 36 GLU B 56 1 21 HELIX 8 AA8 GLU B 78 SER B 90 1 13 HELIX 9 AA9 ASN B 116 LEU B 130 1 15 HELIX 10 AB1 GLN C 19 ILE C 29 1 11 HELIX 11 AB2 SER C 36 GLU C 56 1 21 HELIX 12 AB3 GLU C 78 SER C 90 1 13 HELIX 13 AB4 ASN C 116 LEU C 130 1 15 HELIX 14 AB5 GLN D 19 ILE D 30 1 12 HELIX 15 AB6 SER D 36 ASP D 52 1 17 HELIX 16 AB7 ASN D 58 GLU D 62 5 5 HELIX 17 AB8 GLU D 78 SER D 90 1 13 HELIX 18 AB9 ASN D 116 GLY D 129 1 14 SHEET 1 AA1 2 ILE A 10 GLN A 18 0 SHEET 2 AA1 2 ILE B 10 GLN B 18 -1 O ILE B 11 N LEU A 17 SHEET 1 AA2 8 VAL A 133 ALA A 141 0 SHEET 2 AA2 8 LYS A 64 TYR A 72 -1 N VAL A 69 O LYS A 137 SHEET 3 AA2 8 ASN A 106 GLY A 115 -1 O LEU A 113 N ALA A 66 SHEET 4 AA2 8 VAL A 94 ASP A 103 -1 N ILE A 100 O LEU A 108 SHEET 5 AA2 8 VAL D 94 ASP D 103 -1 O HIS D 99 N THR A 97 SHEET 6 AA2 8 ASN D 106 GLY D 115 -1 O LEU D 108 N ILE D 100 SHEET 7 AA2 8 LYS D 64 TYR D 72 -1 N LYS D 64 O GLY D 115 SHEET 8 AA2 8 VAL D 133 LYS D 140 -1 O THR D 139 N VAL D 67 SHEET 1 AA3 8 VAL B 133 ALA B 141 0 SHEET 2 AA3 8 LYS B 64 TYR B 72 -1 N VAL B 67 O THR B 139 SHEET 3 AA3 8 ASN B 106 GLY B 115 -1 O LEU B 113 N ALA B 66 SHEET 4 AA3 8 HIS B 93 ASP B 103 -1 N HIS B 93 O GLN B 114 SHEET 5 AA3 8 HIS C 93 ASP C 103 -1 O THR C 97 N HIS B 99 SHEET 6 AA3 8 ASN C 106 GLN C 114 -1 O LEU C 108 N ILE C 100 SHEET 7 AA3 8 ILE C 65 TYR C 72 -1 N ALA C 66 O LEU C 113 SHEET 8 AA3 8 VAL C 133 LYS C 140 -1 O THR C 139 N VAL C 67 SHEET 1 AA4 2 ILE C 10 ILE C 11 0 SHEET 2 AA4 2 LEU D 17 GLN D 18 -1 O LEU D 17 N ILE C 11 SHEET 1 AA5 2 SER C 14 GLN C 18 0 SHEET 2 AA5 2 ILE D 10 SER D 14 -1 O ILE D 11 N LEU C 17 LINK NE2 HIS A 88 NI NI A 203 1555 1555 2.15 LINK NE2 HIS A 99 NI NI A 201 1555 1555 2.02 LINK ND1 HIS A 101 NI NI A 201 1555 1555 2.08 LINK SG CYS A 107 NI NI A 201 1555 1555 2.31 LINK O LEU A 130 MG MG A 202 1555 1555 2.63 LINK O VAL A 133 MG MG A 202 1555 1555 2.15 LINK NI NI A 201 NE2 HIS D 88 1555 1555 2.05 LINK MG MG A 202 OE1 GLU B 39 1555 1555 1.95 LINK MG MG A 202 OD2 ASP B 43 1555 1555 2.82 LINK NI NI A 203 NE2 HIS D 99 1555 1555 2.03 LINK NI NI A 203 ND1 HIS D 101 1555 1555 2.03 LINK NI NI A 203 SG CYS D 107 1555 1555 2.22 LINK NE2 HIS B 88 NI NI B 202 1555 1555 2.07 LINK NE2 HIS B 99 NI NI B 201 1555 1555 2.01 LINK ND1 HIS B 101 NI NI B 201 1555 1555 1.99 LINK SG CYS B 107 NI NI B 201 1555 1555 2.25 LINK NI NI B 201 NE2 HIS C 88 1555 1555 2.32 LINK NI NI B 202 NE2 HIS C 99 1555 1555 2.19 LINK NI NI B 202 ND1 HIS C 101 1555 1555 1.98 LINK NI NI B 202 SG CYS C 107 1555 1555 2.24 LINK OE1 GLU C 39 MG MG C 201 1555 1555 1.99 LINK OD2 ASP C 43 MG MG C 201 1555 1555 2.49 LINK MG MG C 201 O GLY D 128 1555 1555 2.67 LINK MG MG C 201 O LEU D 130 1555 1555 2.54 LINK MG MG C 201 O VAL D 133 1555 1555 2.54 SITE 1 AC1 4 HIS A 99 HIS A 101 CYS A 107 HIS D 88 SITE 1 AC2 5 GLY A 128 LEU A 130 VAL A 133 GLU B 39 SITE 2 AC2 5 ASP B 43 SITE 1 AC3 5 ILE A 84 HIS A 88 HIS D 99 HIS D 101 SITE 2 AC3 5 CYS D 107 SITE 1 AC4 5 HIS B 99 HIS B 101 CYS B 107 ILE C 84 SITE 2 AC4 5 HIS C 88 SITE 1 AC5 5 ILE B 84 HIS B 88 HIS C 99 HIS C 101 SITE 2 AC5 5 CYS C 107 SITE 1 AC6 5 GLU C 39 ASP C 43 GLY D 128 LEU D 130 SITE 2 AC6 5 VAL D 133 CRYST1 72.370 94.180 204.060 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 0.013818 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010618 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004901 0.00000