PDB Short entry for 2QNC HEADER HYDROLASE/DNA 18-JUL-07 2QNC TITLE CRYSTAL STRUCTURE OF T4 ENDONUCLEASE VII N62D MUTANT IN COMPLEX WITH A TITLE 2 DNA HOLLIDAY JUNCTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'- COMPND 3 D(*DCP*DG*DAP*DAP*DGP*DAP*DAP*DTP*DTP*DCP*DCP*DGP*DGP*DAP*DTP*DTP*DAP COMPND 4 *DGP*DGP*DGP*DAP*DTP*DCP*DC)-3'); COMPND 5 CHAIN: C; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA (5'- COMPND 9 D(*DGP*DGP*DAP*DTP*DCP*DCP*DCP*DTP*DAP*DAP*DGP*DCP*DTP*DCP*DCP*DAP*DT COMPND 10 P*DCP*DGP*DAP*DTP*DGP*DTP*DG)-3'); COMPND 11 CHAIN: D; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: DNA (5'- COMPND 15 D(*DCP*DAP*DCP*DAP*DTP*DCP*DGP*DAP*DTP*DGP*DGP*DAP*DGP*DCP*DCP*DGP*DC COMPND 16 P*DTP*DAP*DGP*DGP*DCP*DCP*DT)-3'); COMPND 17 CHAIN: E; COMPND 18 ENGINEERED: YES; COMPND 19 MOL_ID: 4; COMPND 20 MOLECULE: DNA (5'- COMPND 21 D(*DAP*DGP*DGP*DCP*DCP*DTP*DAP*DGP*DCP*DGP*DTP*DCP*DCP*DGP*DGP*DAP*DA COMPND 22 P*DTP*DTP*DCP*DTP*DTP*DCP*DG)-3'); COMPND 23 CHAIN: F; COMPND 24 ENGINEERED: YES; COMPND 25 MOL_ID: 5; COMPND 26 MOLECULE: RECOMBINATION ENDONUCLEASE VII; COMPND 27 CHAIN: A, B; COMPND 28 SYNONYM: ENDO VII, PROTEIN GP49; COMPND 29 EC: 3.1.22.4; COMPND 30 ENGINEERED: YES; COMPND 31 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES; SOURCE 5 MOL_ID: 3; SOURCE 6 SYNTHETIC: YES; SOURCE 7 MOL_ID: 4; SOURCE 8 SYNTHETIC: YES; SOURCE 9 MOL_ID: 5; SOURCE 10 ORGANISM_SCIENTIFIC: ENTEROBACTERIA PHAGE T4; SOURCE 11 ORGANISM_TAXID: 10665; SOURCE 12 GENE: 49; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 15 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)PLYSS; SOURCE 16 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 17 EXPRESSION_SYSTEM_PLASMID: PET24D KEYWDS T4 ENDONUCLEASE VII, ENDO VII, HOLLIDAY JUNCTION, FOUR-WAY JUNCTION, KEYWDS 2 RESOLVASE, RESOLVING-ENZYME, ALTERNATIVE INITIATION, CALCIUM, KEYWDS 3 HYDROLASE, METAL-BINDING, ZINC, HYDROLASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR C.BIERTUMPFEL,W.YANG,D.SUCK REVDAT 6 03-APR-24 2QNC 1 REMARK REVDAT 5 21-FEB-24 2QNC 1 REMARK REVDAT 4 20-OCT-21 2QNC 1 REMARK SEQADV LINK REVDAT 3 25-OCT-17 2QNC 1 REMARK REVDAT 2 24-FEB-09 2QNC 1 VERSN REVDAT 1 29-JAN-08 2QNC 0 JRNL AUTH C.BIERTUMPFEL,W.YANG,D.SUCK JRNL TITL CRYSTAL STRUCTURE OF T4 ENDONUCLEASE VII RESOLVING A JRNL TITL 2 HOLLIDAY JUNCTION. JRNL REF NATURE V. 449 616 2007 JRNL REFN ISSN 0028-0836 JRNL PMID 17873859 JRNL DOI 10.1038/NATURE06152 REMARK 2 REMARK 2 RESOLUTION. 3.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.2 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) : 3.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.27 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 2691902.510 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 17475 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) : 0.258 REMARK 3 FREE R VALUE : 0.278 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.000 REMARK 3 FREE R VALUE TEST SET COUNT : 703 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.010 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) : 3.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.29 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.10 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2689 REMARK 3 BIN R VALUE (WORKING SET) : 0.4390 REMARK 3 BIN FREE R VALUE : 0.4320 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.10 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 114 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.040 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2544 REMARK 3 NUCLEIC ACID ATOMS : 1893 REMARK 3 HETEROGEN ATOMS : 12 REMARK 3 SOLVENT ATOMS : 11 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 77.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 102.7 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 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) : 0.53 REMARK 3 ESD FROM SIGMAA (A) : 0.66 REMARK 3 LOW RESOLUTION CUTOFF (A) : 45.0 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.59 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.70 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 19.60 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.110 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) : 1.000 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.750 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.400 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.360 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.30 REMARK 3 BSOL : 47.61 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 : DNA-RNA_REP.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : EDO_XPLOR.PARAM REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : DNA-RNA.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : EDO_XPLOR.TOP REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED REMARK 4 REMARK 4 2QNC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-SEP-07. REMARK 100 THE DEPOSITION ID IS D_1000043814. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-JUN-03 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 5.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.934 REMARK 200 MONOCHROMATOR : DIAMOND (111), GE(220) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS, XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17475 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.100 REMARK 200 RESOLUTION RANGE LOW (A) : 42.270 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 7.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06600 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 26.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.22 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.7 REMARK 200 DATA REDUNDANCY IN SHELL : 7.30 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.66000 REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.730 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: T4 ENDONUCLEASE VII-HETERODUPLEX COMPLEX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 64.77 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.49 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25 %(W/V) PEG 3350, 0.1 M BIS-TRIS, PH REMARK 280 5.5, VAPOR DIFFUSION, TEMPERATURE 293K, PH 5.50 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 93.44200 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 49.59850 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 49.59850 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 140.16300 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 49.59850 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 49.59850 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 46.72100 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 49.59850 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 49.59850 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 140.16300 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 49.59850 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 49.59850 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 46.72100 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 93.44200 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: 18200 ANGSTROM**2 REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D, E, F, 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 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 DC C 1 REMARK 465 DG C 2 REMARK 465 DG F 24 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 DA C 3 P OP1 OP2 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ILE A 145 CB CG1 CG2 CD1 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 LEU A 3 89.12 -67.73 REMARK 500 TYR A 16 -37.13 -38.36 REMARK 500 LEU A 24 -5.69 -56.04 REMARK 500 LEU A 30 159.29 -49.62 REMARK 500 SER A 97 158.75 -48.96 REMARK 500 LYS B 6 0.71 -67.27 REMARK 500 ILE B 25 -63.66 -101.77 REMARK 500 TYR B 99 42.94 -92.59 REMARK 500 GLN B 101 38.44 -97.20 REMARK 500 ASN B 102 -168.35 -108.61 REMARK 500 PHE B 108 -39.72 -36.61 REMARK 500 TYR B 135 -155.78 -165.14 REMARK 500 SER B 155 0.30 -69.30 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 MG A 159 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DC D 12 O3' REMARK 620 2 ASP A 40 OD1 94.3 REMARK 620 3 ASP A 62 OD1 80.9 100.3 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG F 24 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DC F 12 O3' REMARK 620 2 DC F 13 OP1 69.9 REMARK 620 3 ASP B 40 OD1 134.5 72.7 REMARK 620 4 HOH B 161 O 102.2 133.7 85.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 158 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 23 SG REMARK 620 2 CYS A 26 SG 125.4 REMARK 620 3 CYS A 58 SG 98.5 108.6 REMARK 620 4 CYS A 61 SG 124.8 99.9 94.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 158 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 23 SG REMARK 620 2 CYS B 26 SG 96.0 REMARK 620 3 CYS B 58 SG 128.7 131.4 REMARK 620 4 CYS B 61 SG 98.2 80.3 106.9 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 ZN A 158 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 159 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 158 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG F 24 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B 159 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1E7D RELATED DB: PDB REMARK 900 ENDONUCLEASE VII (ENDOVII) FROM PHAGE T4 REMARK 900 RELATED ID: 1E7L RELATED DB: PDB REMARK 900 ENDONUCLEASE VII (ENDOVII) N62D MUTANT FROM PHAGE T4 REMARK 900 RELATED ID: 1EN7 RELATED DB: PDB REMARK 900 ENDONUCLEASE VII (ENDOVII) FROM PHAGE T4 REMARK 900 RELATED ID: 2QNF RELATED DB: PDB REMARK 900 T4 ENDONUCLEASE VII H43N MUTANT IN COMPLEX WITH HETERODUPLEX DNA REMARK 900 CONTAINING BASE MISMATCHES DBREF 2QNC A 1 157 UNP P13340 END7_BPT4 1 157 DBREF 2QNC B 1 157 UNP P13340 END7_BPT4 1 157 DBREF 2QNC C 1 24 PDB 2QNC 2QNC 1 24 DBREF 2QNC D 1 24 PDB 2QNC 2QNC 1 24 DBREF 2QNC E 1 24 PDB 2QNC 2QNC 1 24 DBREF 2QNC F 1 24 PDB 2QNC 2QNC 1 24 SEQADV 2QNC ASP A 62 UNP P13340 ASN 62 ENGINEERED MUTATION SEQADV 2QNC ASP B 62 UNP P13340 ASN 62 ENGINEERED MUTATION SEQRES 1 C 24 DC DG DA DA DG DA DA DT DT DC DC DG DG SEQRES 2 C 24 DA DT DT DA DG DG DG DA DT DC DC SEQRES 1 D 24 DG DG DA DT DC DC DC DT DA DA DG DC DT SEQRES 2 D 24 DC DC DA DT DC DG DA DT DG DT DG SEQRES 1 E 24 DC DA DC DA DT DC DG DA DT DG DG DA DG SEQRES 2 E 24 DC DC DG DC DT DA DG DG DC DC DT SEQRES 1 F 24 DA DG DG DC DC DT DA DG DC DG DT DC DC SEQRES 2 F 24 DG DG DA DA DT DT DC DT DT DC DG SEQRES 1 A 157 MET LEU LEU THR GLY LYS LEU TYR LYS GLU GLU LYS GLN SEQRES 2 A 157 LYS PHE TYR ASP ALA GLN ASN GLY LYS CYS LEU ILE CYS SEQRES 3 A 157 GLN ARG GLU LEU ASN PRO ASP VAL GLN ALA ASN HIS LEU SEQRES 4 A 157 ASP HIS ASP HIS GLU LEU ASN GLY PRO LYS ALA GLY LYS SEQRES 5 A 157 VAL ARG GLY LEU LEU CYS ASN LEU CYS ASP ALA ALA GLU SEQRES 6 A 157 GLY GLN MET LYS HIS LYS PHE ASN ARG SER GLY LEU LYS SEQRES 7 A 157 GLY GLN GLY VAL ASP TYR LEU GLU TRP LEU GLU ASN LEU SEQRES 8 A 157 LEU THR TYR LEU LYS SER ASP TYR THR GLN ASN ASN ILE SEQRES 9 A 157 HIS PRO ASN PHE VAL GLY ASP LYS SER LYS GLU PHE SER SEQRES 10 A 157 ARG LEU GLY LYS GLU GLU MET MET ALA GLU MET LEU GLN SEQRES 11 A 157 ARG GLY PHE GLU TYR ASN GLU SER ASP THR LYS THR GLN SEQRES 12 A 157 LEU ILE ALA SER PHE LYS LYS GLN LEU ARG LYS SER LEU SEQRES 13 A 157 LYS SEQRES 1 B 157 MET LEU LEU THR GLY LYS LEU TYR LYS GLU GLU LYS GLN SEQRES 2 B 157 LYS PHE TYR ASP ALA GLN ASN GLY LYS CYS LEU ILE CYS SEQRES 3 B 157 GLN ARG GLU LEU ASN PRO ASP VAL GLN ALA ASN HIS LEU SEQRES 4 B 157 ASP HIS ASP HIS GLU LEU ASN GLY PRO LYS ALA GLY LYS SEQRES 5 B 157 VAL ARG GLY LEU LEU CYS ASN LEU CYS ASP ALA ALA GLU SEQRES 6 B 157 GLY GLN MET LYS HIS LYS PHE ASN ARG SER GLY LEU LYS SEQRES 7 B 157 GLY GLN GLY VAL ASP TYR LEU GLU TRP LEU GLU ASN LEU SEQRES 8 B 157 LEU THR TYR LEU LYS SER ASP TYR THR GLN ASN ASN ILE SEQRES 9 B 157 HIS PRO ASN PHE VAL GLY ASP LYS SER LYS GLU PHE SER SEQRES 10 B 157 ARG LEU GLY LYS GLU GLU MET MET ALA GLU MET LEU GLN SEQRES 11 B 157 ARG GLY PHE GLU TYR ASN GLU SER ASP THR LYS THR GLN SEQRES 12 B 157 LEU ILE ALA SER PHE LYS LYS GLN LEU ARG LYS SER LEU SEQRES 13 B 157 LYS HET MG F 24 1 HET ZN A 158 1 HET MG A 159 1 HET ZN B 158 1 HET EDO B 159 4 HET EDO B 160 4 HETNAM MG MAGNESIUM ION HETNAM ZN ZINC ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 7 MG 2(MG 2+) FORMUL 8 ZN 2(ZN 2+) FORMUL 11 EDO 2(C2 H6 O2) FORMUL 13 HOH *11(H2 O) HELIX 1 1 GLY A 5 ASN A 20 1 16 HELIX 2 2 ASP A 33 ASN A 37 5 5 HELIX 3 3 CYS A 58 GLY A 76 1 19 HELIX 4 4 ASP A 83 SER A 97 1 15 HELIX 5 5 PRO A 106 ARG A 118 1 13 HELIX 6 6 GLY A 120 ARG A 131 1 12 HELIX 7 7 THR A 140 LYS A 157 1 18 HELIX 8 8 LYS B 6 GLN B 19 1 14 HELIX 9 9 ASP B 33 ASN B 37 5 5 HELIX 10 10 CYS B 58 ARG B 74 1 17 HELIX 11 11 SER B 75 GLY B 76 5 2 HELIX 12 12 LEU B 77 GLY B 81 5 5 HELIX 13 13 ASP B 83 SER B 97 1 15 HELIX 14 14 PRO B 106 ARG B 118 1 13 HELIX 15 15 GLY B 120 ARG B 131 1 12 HELIX 16 16 THR B 140 SER B 155 1 16 SHEET 1 A 2 HIS A 38 HIS A 41 0 SHEET 2 A 2 VAL A 53 LEU A 57 -1 O LEU A 57 N HIS A 38 SHEET 1 B 2 HIS B 38 HIS B 41 0 SHEET 2 B 2 VAL B 53 LEU B 57 -1 O LEU B 57 N HIS B 38 LINK O3' DC D 12 MG MG A 159 1555 1555 2.10 LINK O3' DC F 12 MG MG F 24 1555 1555 2.19 LINK OP1 DC F 13 MG MG F 24 1555 1555 2.19 LINK MG MG F 24 OD1 ASP B 40 1555 1555 2.22 LINK MG MG F 24 O HOH B 161 1555 1555 2.27 LINK SG CYS A 23 ZN ZN A 158 1555 1555 1.90 LINK SG CYS A 26 ZN ZN A 158 1555 1555 1.92 LINK OD1 ASP A 40 MG MG A 159 1555 1555 2.09 LINK SG CYS A 58 ZN ZN A 158 1555 1555 2.23 LINK SG CYS A 61 ZN ZN A 158 1555 1555 2.26 LINK OD1 ASP A 62 MG MG A 159 1555 1555 1.91 LINK SG CYS B 23 ZN ZN B 158 1555 1555 2.38 LINK SG CYS B 26 ZN ZN B 158 1555 1555 2.22 LINK SG CYS B 58 ZN ZN B 158 1555 1555 2.18 LINK SG CYS B 61 ZN ZN B 158 1555 1555 2.37 SITE 1 AC1 4 CYS A 23 CYS A 26 CYS A 58 CYS A 61 SITE 1 AC2 6 ASP A 40 ASP A 62 GLU A 65 HOH A 160 SITE 2 AC2 6 DC D 12 DT D 13 SITE 1 AC3 4 CYS B 23 CYS B 26 CYS B 58 CYS B 61 SITE 1 AC4 7 ASP B 40 HIS B 41 ARG B 54 ASP B 62 SITE 2 AC4 7 HOH B 161 DC F 12 DC F 13 SITE 1 AC5 1 GLY B 79 CRYST1 99.197 99.197 186.884 90.00 90.00 90.00 P 43 21 2 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 0.010081 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010081 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005351 0.00000