PDB Short entry for 2FKC HEADER HYDROLASE/DNA 04-JAN-06 2FKC TITLE CRYSTAL FORM I OF PRE-REACTIVE COMPLEX OF RESTRICTION ENDONUCLEASE TITLE 2 HINP1I WITH COGNATE DNA AND CALCIUM ION COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*CP*CP*AP*GP*CP*GP*CP*TP*GP*G)-3'; COMPND 3 CHAIN: C, D, E, F; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: R.HINP1I RESTRICTION ENDONUCLEASE; COMPND 7 CHAIN: A, B; COMPND 8 EC: 3.1.21.4; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: SYNTHESIZED SELF-ANNEALING OLIGONUCLEOTIDE; SOURCE 4 MOL_ID: 2; SOURCE 5 ORGANISM_SCIENTIFIC: HAEMOPHILUS INFLUENZAE; SOURCE 6 ORGANISM_TAXID: 727; SOURCE 7 GENE: HINP1IR; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 10 EXPRESSION_SYSTEM_STRAIN: PR1; SOURCE 11 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 12 EXPRESSION_SYSTEM_PLASMID: PUC19 KEYWDS RESTRICTION ENDONUCLEASE, PROTEIN DIMERIZATON, DNA SUPERHELIX, KEYWDS 2 PROTEIN-DNA-METAL ION COMPLEX, HYDROLASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.R.HORTON REVDAT 5 30-AUG-23 2FKC 1 REMARK LINK REVDAT 4 31-JAN-18 2FKC 1 JRNL REVDAT 3 18-OCT-17 2FKC 1 REMARK REVDAT 2 24-FEB-09 2FKC 1 VERSN REVDAT 1 21-FEB-06 2FKC 0 JRNL AUTH J.R.HORTON,X.ZHANG,R.MAUNUS,Z.YANG,G.G.WILSON,R.J.ROBERTS, JRNL AUTH 2 X.CHENG JRNL TITL DNA NICKING BY HINP1I ENDONUCLEASE: BENDING, BASE FLIPPING JRNL TITL 2 AND MINOR GROOVE EXPANSION. JRNL REF NUCLEIC ACIDS RES. V. 34 939 2006 JRNL REFN ISSN 0305-1048 JRNL PMID 16473850 JRNL DOI 10.1093/NAR/GKJ484 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH Z.YANG,J.R.HORTON,R.MAUNUS,G.G.WILSON,R.J.ROBERTS,X.CHENG REMARK 1 TITL STRUCTURE OF HINP1I ENDONUCLEASE REVEALS A STRIKING REMARK 1 TITL 2 SIMILARITY TO THE MONOMERIC RESTRICTION ENZYME MSPI REMARK 1 REF NUCLEIC ACIDS RES. V. 33 1892 2005 REMARK 1 REFN ISSN 0305-1048 REMARK 2 REMARK 2 RESOLUTION. 2.39 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.39 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.89 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) (%) : 93.2 REMARK 3 NUMBER OF REFLECTIONS : 31145 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) : 0.222 REMARK 3 FREE R VALUE : 0.260 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 3124 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 : 3949 REMARK 3 NUCLEIC ACID ATOMS : 808 REMARK 3 HETEROGEN ATOMS : 3 REMARK 3 SOLVENT ATOMS : 44 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 47.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 59.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.31000 REMARK 3 B22 (A**2) : 1.41000 REMARK 3 B33 (A**2) : -3.73000 REMARK 3 B12 (A**2) : -0.63000 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) : 0.33 REMARK 3 ESD FROM SIGMAA (A) : 0.29 REMARK 3 LOW RESOLUTION CUTOFF (A) : 19.8 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.41 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.39 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 2.900 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ISOTROPIC REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL 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 2FKC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-JAN-06. REMARK 100 THE DEPOSITION ID IS D_1000035980. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-FEB-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97179 REMARK 200 MONOCHROMATOR : SI 220 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MAR REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31659 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.390 REMARK 200 RESOLUTION RANGE LOW (A) : 19.890 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.7 REMARK 200 DATA REDUNDANCY : 7.100 REMARK 200 R MERGE (I) : 0.10800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 19.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.39 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.48 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.2 REMARK 200 DATA REDUNDANCY IN SHELL : 7.10 REMARK 200 R MERGE FOR SHELL (I) : 0.36800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: GLRF REMARK 200 STARTING MODEL: PDB ENTRY 1YNM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.37 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.95 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 7.5%(V/V) ETHANOL, 1.5M NACL, 100MM REMARK 280 BIS-TRIS PROPANE PH 7.8, AND 20MM CACL2, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 289K 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 86.90667 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 43.45333 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 43.45333 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 86.90667 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D, A 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 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: E, F, 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 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 5 CG CD OE1 OE2 REMARK 470 LYS A 19 CG CD CE NZ REMARK 470 ASP A 23 CG OD1 OD2 REMARK 470 ASN A 27 CG OD1 ND2 REMARK 470 GLN A 35 CG CD OE1 NE2 REMARK 470 ASN A 44 CG OD1 ND2 REMARK 470 GLU A 47 CG CD OE1 OE2 REMARK 470 TYR A 71 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS A 72 CG CD CE NZ REMARK 470 ASP A 73 CB CG OD1 OD2 REMARK 470 LYS A 133 CG CD CE NZ REMARK 470 ASP A 170 CG OD1 OD2 REMARK 470 ASN A 184 CG OD1 ND2 REMARK 470 ASN A 185 CG OD1 ND2 REMARK 470 MET B 1 CG SD CE REMARK 470 GLU B 5 CG CD OE1 OE2 REMARK 470 LYS B 16 CG CD CE NZ REMARK 470 LYS B 29 CG CD CE NZ REMARK 470 GLU B 47 CG CD OE1 OE2 REMARK 470 ILE B 48 CG1 CG2 CD1 REMARK 470 LYS B 49 CG CD CE NZ REMARK 470 LEU B 68 CG CD1 CD2 REMARK 470 TYR B 71 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS B 72 CG CD CE NZ REMARK 470 ASP B 73 CG OD1 OD2 REMARK 470 GLU B 104 CG CD OE1 OE2 REMARK 470 LYS B 131 CG CD CE NZ REMARK 470 LYS B 133 CG CD CE NZ REMARK 470 ASN B 184 CG OD1 ND2 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 DA C 3 O4' - C1' - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 DG C 4 OP1 - P - OP2 ANGL. DEV. = -9.1 DEGREES REMARK 500 DG C 4 O4' - C1' - C2' ANGL. DEV. = 3.8 DEGREES REMARK 500 DG C 4 N9 - C1' - C2' ANGL. DEV. = -17.7 DEGREES REMARK 500 DG C 4 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 DG C 6 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 DG E 6 O4' - C1' - N9 ANGL. DEV. = 2.6 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 ASN A 2 136.37 77.07 REMARK 500 ASN A 27 46.27 -92.16 REMARK 500 LYS A 29 -31.84 101.86 REMARK 500 ASP A 73 8.71 92.02 REMARK 500 PRO A 125 150.41 -44.22 REMARK 500 SER A 183 168.94 168.99 REMARK 500 ASN A 184 -62.04 60.89 REMARK 500 SER A 212 -149.52 -96.99 REMARK 500 ASN B 27 43.91 -105.78 REMARK 500 TRP B 28 -152.32 -69.94 REMARK 500 LYS B 29 -36.61 68.41 REMARK 500 LYS B 49 -87.64 -78.56 REMARK 500 ASN B 129 39.91 79.03 REMARK 500 SER B 183 -98.41 65.17 REMARK 500 ASN B 227 27.48 48.00 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 DA C 3 0.15 SIDE CHAIN REMARK 500 DG C 4 0.10 SIDE CHAIN REMARK 500 DC C 5 0.07 SIDE CHAIN REMARK 500 DG C 6 0.09 SIDE CHAIN REMARK 500 DG D 14 0.09 SIDE CHAIN REMARK 500 DC D 15 0.09 SIDE CHAIN REMARK 500 DG D 16 0.11 SIDE CHAIN REMARK 500 DT D 18 0.08 SIDE CHAIN REMARK 500 DG E 4 0.05 SIDE CHAIN REMARK 500 DG E 6 0.07 SIDE CHAIN REMARK 500 DG F 14 0.09 SIDE CHAIN REMARK 500 DC F 15 0.08 SIDE CHAIN REMARK 500 DG F 16 0.11 SIDE CHAIN REMARK 500 DT F 18 0.07 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 CA C 52 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG C 4 O3' REMARK 620 2 DC C 5 OP1 53.2 REMARK 620 3 HOH C 54 O 79.7 106.6 REMARK 620 4 GLU A 18 OE1 131.5 92.8 148.5 REMARK 620 5 ASP A 62 OD1 117.0 72.4 88.9 73.3 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 248 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DC C 5 OP1 REMARK 620 2 HOH C 53 O 85.2 REMARK 620 3 ASP A 62 OD1 67.2 151.6 REMARK 620 4 ASP A 62 OD2 106.2 157.8 40.9 REMARK 620 5 GLN A 81 OE1 97.9 81.4 95.6 78.1 REMARK 620 6 VAL A 82 O 169.3 89.8 118.5 81.8 90.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 248 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DC E 5 OP1 REMARK 620 2 HOH E 12 O 78.0 REMARK 620 3 ASP B 62 OD2 106.8 160.2 REMARK 620 4 ASP B 62 OD1 68.7 146.2 40.4 REMARK 620 5 GLN B 81 OE1 95.7 78.1 82.2 99.1 REMARK 620 6 VAL B 82 O 163.2 92.0 87.2 121.7 95.4 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 CA A 248 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA C 52 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 248 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1YNM RELATED DB: PDB REMARK 900 THE SAME PROTEIN BUT NOT COMPLEXED WITH COGNATE DNA AND METAL ION. REMARK 900 RELATED ID: 2FKH RELATED DB: PDB REMARK 900 RELATED ID: 2FL3 RELATED DB: PDB REMARK 900 RELATED ID: 2FLC RELATED DB: PDB DBREF 2FKC A 1 247 GB 57116674 AAW33811 1 247 DBREF 2FKC B 1 247 GB 57116674 AAW33811 1 247 DBREF 2FKC C 1 10 PDB 2FKC 2FKC 1 10 DBREF 2FKC D 11 20 PDB 2FKC 2FKC 11 20 DBREF 2FKC E 1 10 PDB 2FKC 2FKC 1 10 DBREF 2FKC F 11 20 PDB 2FKC 2FKC 11 20 SEQRES 1 C 10 DC DC DA DG DC DG DC DT DG DG SEQRES 1 D 10 DC DC DA DG DC DG DC DT DG DG SEQRES 1 E 10 DC DC DA DG DC DG DC DT DG DG SEQRES 1 F 10 DC DC DA DG DC DG DC DT DG DG SEQRES 1 A 247 MET ASN LEU VAL GLU LEU GLY SER LYS THR ALA LYS ASP SEQRES 2 A 247 GLY PHE LYS ASN GLU LYS ASP ILE ALA ASP ARG PHE GLU SEQRES 3 A 247 ASN TRP LYS GLU ASN SER GLU ALA GLN ASP TRP LEU VAL SEQRES 4 A 247 THR MET GLY HIS ASN LEU ASP GLU ILE LYS SER VAL LYS SEQRES 5 A 247 ALA VAL VAL LEU SER GLY TYR LYS SER ASP ILE ASN VAL SEQRES 6 A 247 GLN VAL LEU VAL PHE TYR LYS ASP ALA LEU ASP ILE HIS SEQRES 7 A 247 ASN ILE GLN VAL LYS LEU VAL SER ASN LYS ARG GLY PHE SEQRES 8 A 247 ASN GLN ILE ASP LYS HIS TRP LEU ALA HIS TYR GLN GLU SEQRES 9 A 247 MET TRP LYS PHE ASP ASP ASN LEU LEU ARG ILE LEU ARG SEQRES 10 A 247 HIS PHE THR GLY GLU LEU PRO PRO TYR HIS SER ASN THR SEQRES 11 A 247 LYS ASP LYS ARG ARG MET PHE MET THR GLU PHE SER GLN SEQRES 12 A 247 GLU GLU GLN ASN ILE VAL LEU ASN TRP LEU GLU LYS ASN SEQRES 13 A 247 ARG VAL LEU VAL LEU THR ASP ILE LEU ARG GLY ARG GLY SEQRES 14 A 247 ASP PHE ALA ALA GLU TRP VAL LEU VAL ALA GLN LYS VAL SEQRES 15 A 247 SER ASN ASN ALA ARG TRP ILE LEU ARG ASN ILE ASN GLU SEQRES 16 A 247 VAL LEU GLN HIS TYR GLY SER GLY ASP ILE SER LEU SER SEQRES 17 A 247 PRO ARG GLY SER ILE ASN PHE GLY ARG VAL THR ILE GLN SEQRES 18 A 247 ARG LYS GLY GLY ASP ASN GLY ARG GLU THR ALA ASN MET SEQRES 19 A 247 LEU GLN PHE LYS ILE ASP PRO THR GLU LEU PHE ASP ILE SEQRES 1 B 247 MET ASN LEU VAL GLU LEU GLY SER LYS THR ALA LYS ASP SEQRES 2 B 247 GLY PHE LYS ASN GLU LYS ASP ILE ALA ASP ARG PHE GLU SEQRES 3 B 247 ASN TRP LYS GLU ASN SER GLU ALA GLN ASP TRP LEU VAL SEQRES 4 B 247 THR MET GLY HIS ASN LEU ASP GLU ILE LYS SER VAL LYS SEQRES 5 B 247 ALA VAL VAL LEU SER GLY TYR LYS SER ASP ILE ASN VAL SEQRES 6 B 247 GLN VAL LEU VAL PHE TYR LYS ASP ALA LEU ASP ILE HIS SEQRES 7 B 247 ASN ILE GLN VAL LYS LEU VAL SER ASN LYS ARG GLY PHE SEQRES 8 B 247 ASN GLN ILE ASP LYS HIS TRP LEU ALA HIS TYR GLN GLU SEQRES 9 B 247 MET TRP LYS PHE ASP ASP ASN LEU LEU ARG ILE LEU ARG SEQRES 10 B 247 HIS PHE THR GLY GLU LEU PRO PRO TYR HIS SER ASN THR SEQRES 11 B 247 LYS ASP LYS ARG ARG MET PHE MET THR GLU PHE SER GLN SEQRES 12 B 247 GLU GLU GLN ASN ILE VAL LEU ASN TRP LEU GLU LYS ASN SEQRES 13 B 247 ARG VAL LEU VAL LEU THR ASP ILE LEU ARG GLY ARG GLY SEQRES 14 B 247 ASP PHE ALA ALA GLU TRP VAL LEU VAL ALA GLN LYS VAL SEQRES 15 B 247 SER ASN ASN ALA ARG TRP ILE LEU ARG ASN ILE ASN GLU SEQRES 16 B 247 VAL LEU GLN HIS TYR GLY SER GLY ASP ILE SER LEU SER SEQRES 17 B 247 PRO ARG GLY SER ILE ASN PHE GLY ARG VAL THR ILE GLN SEQRES 18 B 247 ARG LYS GLY GLY ASP ASN GLY ARG GLU THR ALA ASN MET SEQRES 19 B 247 LEU GLN PHE LYS ILE ASP PRO THR GLU LEU PHE ASP ILE HET CA C 52 1 HET CA A 248 1 HET CA B 248 1 HETNAM CA CALCIUM ION FORMUL 7 CA 3(CA 2+) FORMUL 10 HOH *44(H2 O) HELIX 1 1 ASN A 2 ASN A 27 1 26 HELIX 2 2 ASN A 31 MET A 41 1 11 HELIX 3 3 ASN A 44 ASP A 46 5 3 HELIX 4 4 TRP A 98 LYS A 107 1 10 HELIX 5 5 ASP A 109 THR A 120 1 12 HELIX 6 6 PHE A 137 PHE A 141 5 5 HELIX 7 7 SER A 142 ASN A 156 1 15 HELIX 8 8 ASN A 156 ARG A 166 1 11 HELIX 9 9 ILE A 193 SER A 202 1 10 HELIX 10 10 GLY A 225 ASN A 233 5 9 HELIX 11 11 ASP A 240 ASP A 246 5 7 HELIX 12 12 MET B 1 ASN B 27 1 27 HELIX 13 13 ASN B 31 MET B 41 1 11 HELIX 14 14 ASN B 44 ASP B 46 5 3 HELIX 15 15 TRP B 98 LYS B 107 1 10 HELIX 16 16 ASP B 109 THR B 120 1 12 HELIX 17 17 PHE B 137 PHE B 141 5 5 HELIX 18 18 SER B 142 ASN B 156 1 15 HELIX 19 19 ASN B 156 ARG B 166 1 11 HELIX 20 20 ILE B 193 GLY B 201 1 9 HELIX 21 21 GLY B 225 ASN B 233 5 9 HELIX 22 22 THR B 242 ILE B 247 1 6 SHEET 1 A 5 ILE A 48 VAL A 55 0 SHEET 2 A 5 ILE A 63 VAL A 69 -1 O LEU A 68 N SER A 50 SHEET 3 A 5 ASP A 76 VAL A 85 -1 O ASP A 76 N VAL A 67 SHEET 4 A 5 TRP A 175 LYS A 181 1 O TRP A 175 N GLN A 81 SHEET 5 A 5 ALA A 186 ASN A 192 -1 O ARG A 191 N VAL A 176 SHEET 1 B 5 ASN A 92 HIS A 97 0 SHEET 2 B 5 LEU A 235 ILE A 239 -1 O ILE A 239 N ASN A 92 SHEET 3 B 5 VAL A 218 ARG A 222 -1 N THR A 219 O LYS A 238 SHEET 4 B 5 ILE A 213 PHE A 215 -1 N PHE A 215 O VAL A 218 SHEET 5 B 5 ILE A 205 LEU A 207 -1 N SER A 206 O ASN A 214 SHEET 1 C 5 ILE B 48 VAL B 55 0 SHEET 2 C 5 ILE B 63 VAL B 69 -1 O LEU B 68 N LYS B 49 SHEET 3 C 5 ASP B 76 VAL B 85 -1 O HIS B 78 N VAL B 65 SHEET 4 C 5 TRP B 175 VAL B 182 1 O TRP B 175 N GLN B 81 SHEET 5 C 5 ASN B 185 ASN B 192 -1 O ARG B 187 N GLN B 180 SHEET 1 D 5 ASN B 92 HIS B 97 0 SHEET 2 D 5 LEU B 235 ILE B 239 -1 O ILE B 239 N ASN B 92 SHEET 3 D 5 VAL B 218 ARG B 222 -1 N THR B 219 O LYS B 238 SHEET 4 D 5 ILE B 213 PHE B 215 -1 N PHE B 215 O VAL B 218 SHEET 5 D 5 ILE B 205 LEU B 207 -1 N SER B 206 O ASN B 214 LINK O3' DG C 4 CA CA C 52 1555 1555 2.65 LINK OP1 DC C 5 CA CA C 52 1555 1555 2.86 LINK OP1 DC C 5 CA CA A 248 1555 1555 2.08 LINK CA CA C 52 O HOH C 54 1555 1555 2.61 LINK CA CA C 52 OE1 GLU A 18 1555 1555 2.62 LINK CA CA C 52 OD1 ASP A 62 1555 1555 2.52 LINK O HOH C 53 CA CA A 248 1555 1555 2.35 LINK OP1 DC E 5 CA CA B 248 1555 1555 2.10 LINK O HOH E 12 CA CA B 248 1555 1555 2.40 LINK OD1 ASP A 62 CA CA A 248 1555 1555 3.35 LINK OD2 ASP A 62 CA CA A 248 1555 1555 2.47 LINK OE1 GLN A 81 CA CA A 248 1555 1555 2.53 LINK O VAL A 82 CA CA A 248 1555 1555 2.40 LINK OD2 ASP B 62 CA CA B 248 1555 1555 2.29 LINK OD1 ASP B 62 CA CA B 248 1555 1555 3.37 LINK OE1 GLN B 81 CA CA B 248 1555 1555 2.46 LINK O VAL B 82 CA CA B 248 1555 1555 2.25 SITE 1 AC1 5 ASP A 62 GLN A 81 VAL A 82 DC C 5 SITE 2 AC1 5 HOH C 53 SITE 1 AC2 5 GLU A 18 ASP A 62 DG C 4 DC C 5 SITE 2 AC2 5 HOH C 54 SITE 1 AC3 5 ASP B 62 GLN B 81 VAL B 82 DC E 5 SITE 2 AC3 5 HOH E 12 CRYST1 105.104 105.104 130.360 90.00 90.00 120.00 P 32 2 1 24 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 0.009514 0.005493 0.000000 0.00000 SCALE2 0.000000 0.010986 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007671 0.00000