PDB Short entry for 6KI3 HEADER DNA BINDING PROTEIN/DNA 17-JUL-19 6KI3 TITLE THE CRYSTAL STRUCTURE OF ASFVAP:DF COMMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROBABLE AP ENDONUCLEASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: APE; COMPND 5 EC: 3.1.21.-; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA (5'-D(*GP*CP*AP*GP*CP*GP*TP*CP*C)-3'); COMPND 9 CHAIN: C, F; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: DNA (5'-D(P*(3DR)P*CP*GP*AP*CP*GP*AP*G)-3'); COMPND 13 CHAIN: D, G; COMPND 14 ENGINEERED: YES; COMPND 15 MOL_ID: 4; COMPND 16 MOLECULE: DNA (5'- COMPND 17 D(*CP*CP*TP*CP*GP*TP*CP*GP*GP*GP*GP*AP*CP*GP*CP*TP*G)-3'); COMPND 18 CHAIN: E, H; COMPND 19 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AFRICAN SWINE FEVER VIRUS (ISOLATE TICK/SOUTH SOURCE 3 AFRICA/PRETORIUSKOP PR4/1996); SOURCE 4 ORGANISM_COMMON: ASFV; SOURCE 5 ORGANISM_TAXID: 561443; SOURCE 6 STRAIN: ISOLATE TICK/SOUTH AFRICA/PRETORIUSKOP PR4/1996; SOURCE 7 GENE: PRET-146; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: AFRICAN SWINE FEVER VIRUS; SOURCE 13 ORGANISM_TAXID: 10497; SOURCE 14 MOL_ID: 3; SOURCE 15 SYNTHETIC: YES; SOURCE 16 ORGANISM_SCIENTIFIC: AFRICAN SWINE FEVER VIRUS; SOURCE 17 ORGANISM_TAXID: 10497; SOURCE 18 MOL_ID: 4; SOURCE 19 SYNTHETIC: YES; SOURCE 20 ORGANISM_SCIENTIFIC: AFRICAN SWINE FEVER VIRUS; SOURCE 21 ORGANISM_TAXID: 10497 KEYWDS ENDONUCLEASEIV, ASFV, DNA BINDING PROTEIN-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Y.CHEN,J.GAN REVDAT 1 27-MAY-20 6KI3 0 JRNL AUTH Y.CHEN,X.CHEN,Q.HUANG,Z.SHAO,Y.GAO,Y.LI,C.YANG,H.LIU,J.LI, JRNL AUTH 2 Q.WANG,J.MA,Y.Z.ZHANG,Y.GU,J.GAN JRNL TITL A UNIQUE DNA-BINDING MODE OF AFRICAN SWINE FEVER VIRUS AP JRNL TITL 2 ENDONUCLEASE. JRNL REF CELL DISCOV V. 6 13 2020 JRNL REFN ESSN 2056-5968 JRNL PMID 32194979 JRNL DOI 10.1038/S41421-020-0146-2 REMARK 2 REMARK 2 RESOLUTION. 2.35 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.10.1_2155 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.35 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.390 REMARK 3 COMPLETENESS FOR RANGE (%) : 89.3 REMARK 3 NUMBER OF REFLECTIONS : 30862 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.209 REMARK 3 R VALUE (WORKING SET) : 0.208 REMARK 3 FREE R VALUE : 0.244 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 1550 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 28.3480 - 5.2246 0.98 2989 177 0.1703 0.1879 REMARK 3 2 5.2246 - 4.1511 0.99 2969 152 0.1662 0.2044 REMARK 3 3 4.1511 - 3.6276 0.99 2958 158 0.1833 0.2192 REMARK 3 4 3.6276 - 3.2964 0.99 2975 134 0.2062 0.2406 REMARK 3 5 3.2964 - 3.0605 0.97 2893 150 0.2259 0.2782 REMARK 3 6 3.0605 - 2.8802 0.98 2937 161 0.2524 0.3116 REMARK 3 7 2.8802 - 2.7361 0.95 2813 148 0.2543 0.3045 REMARK 3 8 2.7361 - 2.6171 0.90 2681 150 0.2629 0.3047 REMARK 3 9 2.6171 - 2.5164 0.83 2461 108 0.2568 0.2796 REMARK 3 10 2.5164 - 2.4296 0.67 1972 119 0.2676 0.3167 REMARK 3 11 2.4296 - 2.3540 0.57 1664 93 0.2823 0.2926 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.290 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.050 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 30.95 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.67 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.003 6218 REMARK 3 ANGLE : 0.570 8734 REMARK 3 CHIRALITY : 0.041 1002 REMARK 3 PLANARITY : 0.003 866 REMARK 3 DIHEDRAL : 20.723 3387 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6KI3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 22-JUL-19. REMARK 100 THE DEPOSITION ID IS D_1300013028. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-MAR-18 REMARK 200 TEMPERATURE (KELVIN) : 90 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9793 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34031 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.350 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.13700 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.39 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.9 REMARK 200 DATA REDUNDANCY IN SHELL : 2.60 REMARK 200 R MERGE FOR SHELL (I) : 0.52600 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: SAD REMARK 200 SOFTWARE USED: HKL2MAP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.72 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS PH 5.5 13% W/V PEG REMARK 280 10,000 0.1 M AMMONIUM ACETATE, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 291.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 42.34900 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4930 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16170 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -145.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C, D, E 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4840 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16820 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -140.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, F, G, H 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 GLY A -4 REMARK 465 SER A -3 REMARK 465 GLY A -2 REMARK 465 GLY B -4 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 33 CD OE1 OE2 REMARK 470 PRO A 38 CG CD REMARK 470 LYS A 40 CG CD CE NZ REMARK 470 LYS A 51 CG CD CE NZ REMARK 470 GLU A 58 CG CD OE1 OE2 REMARK 470 LYS A 70 NZ REMARK 470 ARG A 88 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 89 CG CD NE CZ NH1 NH2 REMARK 470 PHE A 92 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LEU A 102 CG CD1 CD2 REMARK 470 GLU A 106 CD OE1 OE2 REMARK 470 GLU A 120 CG CD OE1 OE2 REMARK 470 GLU A 122 CG CD OE1 OE2 REMARK 470 LEU A 123 CG CD1 CD2 REMARK 470 LYS A 129 CG CD CE NZ REMARK 470 LYS A 132 CG CD CE NZ REMARK 470 GLU A 135 CG CD OE1 OE2 REMARK 470 GLU A 157 CG CD OE1 OE2 REMARK 470 LYS A 160 CG CD CE NZ REMARK 470 ARG A 170 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 172 CG CD CE NZ REMARK 470 GLN A 198 CG CD OE1 NE2 REMARK 470 ARG A 201 CG CD NE CZ NH1 NH2 REMARK 470 SER A 208 OG REMARK 470 GLU A 225 CG CD OE1 OE2 REMARK 470 LYS A 243 CG CD CE NZ REMARK 470 LYS A 248 CG CD CE NZ REMARK 470 ARG A 263 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 296 CG CD CE NZ REMARK 470 GLU B 58 CG CD OE1 OE2 REMARK 470 ARG B 88 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 120 CG CD OE1 OE2 REMARK 470 GLU B 122 CG CD OE1 OE2 REMARK 470 LEU B 123 CG CD1 CD2 REMARK 470 GLU B 126 CG CD OE1 OE2 REMARK 470 LYS B 129 CD CE NZ REMARK 470 LYS B 132 CG CD CE NZ REMARK 470 LYS B 160 CG CD CE NZ REMARK 470 LYS B 172 CG CD CE NZ REMARK 470 GLU B 238 OE1 OE2 REMARK 470 LYS B 243 CG CD CE NZ REMARK 470 LYS B 248 CG CD CE NZ REMARK 470 LYS B 296 CG CD CE NZ 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 G 16 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 DG H 11 O5' - P - OP1 ANGL. DEV. = -9.7 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 TRP A 11 -32.54 -132.11 REMARK 500 THR A 17 -103.92 51.37 REMARK 500 ARG A 88 -72.98 -60.46 REMARK 500 ALA A 223 44.38 -92.71 REMARK 500 LEU A 295 -69.13 -99.00 REMARK 500 TRP B 11 -30.77 -133.01 REMARK 500 THR B 17 -104.52 51.77 REMARK 500 THR B 150 -53.28 -142.75 REMARK 500 ALA B 223 57.63 -90.46 REMARK 500 SER B 244 8.20 -69.55 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 ZN A 303 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 78 NE2 REMARK 620 2 HIS A 115 NE2 89.2 REMARK 620 3 GLU A 142 OE2 110.9 85.8 REMARK 620 4 3DR D 10 OP1 106.1 89.0 142.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 302 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 142 OE1 REMARK 620 2 ASP A 179 OD2 82.4 REMARK 620 3 HIS A 218 ND1 90.9 91.8 REMARK 620 4 GLU A 271 OE2 159.7 81.7 77.1 REMARK 620 5 3DR D 10 OP2 93.5 84.1 173.5 97.3 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 182 NE2 REMARK 620 2 ASP A 231 OD2 106.8 REMARK 620 3 HIS A 233 NE2 116.5 105.1 REMARK 620 4 3DR D 10 OP2 80.2 151.3 95.8 REMARK 620 5 3DR D 10 OP3 111.4 85.7 124.5 66.1 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 303 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 78 NE2 REMARK 620 2 HIS B 115 NE2 93.3 REMARK 620 3 GLU B 142 OE2 127.7 80.9 REMARK 620 4 3DR G 10 OP1 109.6 86.8 121.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 302 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 142 OE1 REMARK 620 2 ASP B 179 OD2 91.4 REMARK 620 3 HIS B 218 ND1 80.3 96.0 REMARK 620 4 GLU B 271 OE2 157.7 86.5 77.9 REMARK 620 5 3DR G 10 OP2 109.3 88.8 169.2 92.8 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 182 NE2 REMARK 620 2 ASP B 231 OD2 100.6 REMARK 620 3 HIS B 233 NE2 124.5 118.3 REMARK 620 4 3DR G 10 OP2 76.3 144.7 90.1 REMARK 620 5 3DR G 10 OP3 114.5 87.9 105.5 63.1 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 ZN A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-nucleotide 3DR G 10 and DC G REMARK 800 11 DBREF 6KI3 A 1 296 UNP P0C9C6 APE_ASFP4 1 296 DBREF 6KI3 C 1 9 PDB 6KI3 6KI3 1 9 DBREF 6KI3 D 10 17 PDB 6KI3 6KI3 10 17 DBREF 6KI3 E 1 17 PDB 6KI3 6KI3 1 17 DBREF 6KI3 B 1 296 UNP P0C9C6 APE_ASFP4 1 296 DBREF 6KI3 F 1 9 PDB 6KI3 6KI3 1 9 DBREF 6KI3 G 10 17 PDB 6KI3 6KI3 10 17 DBREF 6KI3 H 1 17 PDB 6KI3 6KI3 1 17 SEQADV 6KI3 GLY A -4 UNP P0C9C6 EXPRESSION TAG SEQADV 6KI3 SER A -3 UNP P0C9C6 EXPRESSION TAG SEQADV 6KI3 GLY A -2 UNP P0C9C6 EXPRESSION TAG SEQADV 6KI3 GLY A -1 UNP P0C9C6 EXPRESSION TAG SEQADV 6KI3 GLY A 0 UNP P0C9C6 EXPRESSION TAG SEQADV 6KI3 GLY B -4 UNP P0C9C6 EXPRESSION TAG SEQADV 6KI3 SER B -3 UNP P0C9C6 EXPRESSION TAG SEQADV 6KI3 GLY B -2 UNP P0C9C6 EXPRESSION TAG SEQADV 6KI3 GLY B -1 UNP P0C9C6 EXPRESSION TAG SEQADV 6KI3 GLY B 0 UNP P0C9C6 EXPRESSION TAG SEQRES 1 A 301 GLY SER GLY GLY GLY MET PHE GLY ALA PHE VAL SER HIS SEQRES 2 A 301 ARG LEU TRP SER ASP SER GLY CYS THR THR THR CYS ILE SEQRES 3 A 301 THR ASN SER ILE ALA ASN TYR VAL ALA PHE GLY GLU GLN SEQRES 4 A 301 ILE GLY PHE PRO PHE LYS SER ALA GLN VAL PHE ILE ALA SEQRES 5 A 301 GLY PRO ARG LYS ALA VAL ILE ASN ILE GLN GLU ASP ASP SEQRES 6 A 301 LYS VAL GLU LEU LEU LYS MET ILE VAL LYS HIS ASN LEU SEQRES 7 A 301 TRP VAL VAL ALA HIS GLY THR TYR LEU ASP VAL PRO TRP SEQRES 8 A 301 SER ARG ARG SER ALA PHE VAL THR HIS PHE ILE GLN GLN SEQRES 9 A 301 GLU LEU LEU ILE CYS LYS GLU VAL GLY ILE LYS GLY LEU SEQRES 10 A 301 VAL LEU HIS LEU GLY ALA VAL GLU PRO GLU LEU ILE VAL SEQRES 11 A 301 GLU GLY LEU LYS LYS ILE LYS PRO VAL GLU GLY VAL VAL SEQRES 12 A 301 ILE TYR LEU GLU THR PRO HIS ASN LYS HIS HIS THR TYR SEQRES 13 A 301 LYS TYR SER THR MET GLU GLN ILE LYS GLU LEU PHE LEU SEQRES 14 A 301 ARG ILE ARG ASN THR ARG LEU LYS GLN ILE GLY LEU CYS SEQRES 15 A 301 ILE ASP THR ALA HIS ILE TRP SER SER GLY VAL ASN ILE SEQRES 16 A 301 SER SER TYR ASN ASP ALA GLY GLN TRP LEU ARG SER LEU SEQRES 17 A 301 GLU ASN ILE HIS SER VAL ILE PRO PRO SER HIS ILE MET SEQRES 18 A 301 PHE HIS LEU ASN ASP ALA ALA THR GLU CYS GLY SER GLY SEQRES 19 A 301 ILE ASP ARG HIS ALA SER LEU PHE GLU GLY MET ILE TRP SEQRES 20 A 301 LYS SER TYR SER HIS LYS ILE LYS GLN SER GLY LEU TYR SEQRES 21 A 301 CYS PHE VAL GLU TYR ILE THR ARG HIS GLN CYS PRO ALA SEQRES 22 A 301 ILE LEU GLU ARG ASN LEU GLY SER SER MET GLN LEU GLN SEQRES 23 A 301 THR ALA LEU THR ALA GLU PHE THR THR LEU LYS SER LEU SEQRES 24 A 301 LEU LYS SEQRES 1 C 9 DG DC DA DG DC DG DT DC DC SEQRES 1 D 8 3DR DC DG DA DC DG DA DG SEQRES 1 E 17 DC DC DT DC DG DT DC DG DG DG DG DA DC SEQRES 2 E 17 DG DC DT DG SEQRES 1 B 301 GLY SER GLY GLY GLY MET PHE GLY ALA PHE VAL SER HIS SEQRES 2 B 301 ARG LEU TRP SER ASP SER GLY CYS THR THR THR CYS ILE SEQRES 3 B 301 THR ASN SER ILE ALA ASN TYR VAL ALA PHE GLY GLU GLN SEQRES 4 B 301 ILE GLY PHE PRO PHE LYS SER ALA GLN VAL PHE ILE ALA SEQRES 5 B 301 GLY PRO ARG LYS ALA VAL ILE ASN ILE GLN GLU ASP ASP SEQRES 6 B 301 LYS VAL GLU LEU LEU LYS MET ILE VAL LYS HIS ASN LEU SEQRES 7 B 301 TRP VAL VAL ALA HIS GLY THR TYR LEU ASP VAL PRO TRP SEQRES 8 B 301 SER ARG ARG SER ALA PHE VAL THR HIS PHE ILE GLN GLN SEQRES 9 B 301 GLU LEU LEU ILE CYS LYS GLU VAL GLY ILE LYS GLY LEU SEQRES 10 B 301 VAL LEU HIS LEU GLY ALA VAL GLU PRO GLU LEU ILE VAL SEQRES 11 B 301 GLU GLY LEU LYS LYS ILE LYS PRO VAL GLU GLY VAL VAL SEQRES 12 B 301 ILE TYR LEU GLU THR PRO HIS ASN LYS HIS HIS THR TYR SEQRES 13 B 301 LYS TYR SER THR MET GLU GLN ILE LYS GLU LEU PHE LEU SEQRES 14 B 301 ARG ILE ARG ASN THR ARG LEU LYS GLN ILE GLY LEU CYS SEQRES 15 B 301 ILE ASP THR ALA HIS ILE TRP SER SER GLY VAL ASN ILE SEQRES 16 B 301 SER SER TYR ASN ASP ALA GLY GLN TRP LEU ARG SER LEU SEQRES 17 B 301 GLU ASN ILE HIS SER VAL ILE PRO PRO SER HIS ILE MET SEQRES 18 B 301 PHE HIS LEU ASN ASP ALA ALA THR GLU CYS GLY SER GLY SEQRES 19 B 301 ILE ASP ARG HIS ALA SER LEU PHE GLU GLY MET ILE TRP SEQRES 20 B 301 LYS SER TYR SER HIS LYS ILE LYS GLN SER GLY LEU TYR SEQRES 21 B 301 CYS PHE VAL GLU TYR ILE THR ARG HIS GLN CYS PRO ALA SEQRES 22 B 301 ILE LEU GLU ARG ASN LEU GLY SER SER MET GLN LEU GLN SEQRES 23 B 301 THR ALA LEU THR ALA GLU PHE THR THR LEU LYS SER LEU SEQRES 24 B 301 LEU LYS SEQRES 1 F 9 DG DC DA DG DC DG DT DC DC SEQRES 1 G 8 3DR DC DG DA DC DG DA DG SEQRES 1 H 17 DC DC DT DC DG DT DC DG DG DG DG DA DC SEQRES 2 H 17 DG DC DT DG HET 3DR D 10 12 HET 3DR G 10 12 HET ZN A 301 1 HET ZN A 302 1 HET ZN A 303 1 HET ZN B 301 1 HET ZN B 302 1 HET ZN B 303 1 HETNAM 3DR 1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE HETNAM ZN ZINC ION HETSYN 3DR ABASIC DIDEOXYRIBOSE FORMUL 3 3DR 2(C5 H11 O6 P) FORMUL 9 ZN 6(ZN 2+) FORMUL 15 HOH *89(H2 O) HELIX 1 AA1 SER A 7 SER A 12 1 6 HELIX 2 AA2 THR A 19 ILE A 35 1 17 HELIX 3 AA3 GLN A 57 ASN A 72 1 16 HELIX 4 AA4 SER A 90 GLY A 108 1 19 HELIX 5 AA5 GLU A 120 LYS A 130 1 11 HELIX 6 AA6 THR A 155 ARG A 170 1 16 HELIX 7 AA7 THR A 180 SER A 186 1 7 HELIX 8 AA8 SER A 192 ASN A 205 1 14 HELIX 9 AA9 PRO A 211 SER A 213 5 3 HELIX 10 AB1 TRP A 242 SER A 246 5 5 HELIX 11 AB2 LYS A 248 GLN A 251 5 4 HELIX 12 AB3 SER A 252 GLN A 265 1 14 HELIX 13 AB4 SER A 276 LYS A 296 1 21 HELIX 14 AB5 SER B 7 SER B 12 1 6 HELIX 15 AB6 THR B 19 ILE B 35 1 17 HELIX 16 AB7 GLN B 57 ASN B 72 1 16 HELIX 17 AB8 ARG B 89 GLY B 108 1 20 HELIX 18 AB9 GLU B 120 LYS B 130 1 11 HELIX 19 AC1 THR B 155 THR B 169 1 15 HELIX 20 AC2 THR B 180 SER B 186 1 7 HELIX 21 AC3 SER B 192 ASN B 205 1 14 HELIX 22 AC4 PRO B 211 SER B 213 5 3 HELIX 23 AC5 TRP B 242 SER B 246 5 5 HELIX 24 AC6 LYS B 248 GLN B 251 5 4 HELIX 25 AC7 SER B 252 GLN B 265 1 14 HELIX 26 AC8 SER B 276 LYS B 296 1 21 SHEET 1 AA1 9 MET A 1 PHE A 5 0 SHEET 2 AA1 9 SER A 41A VAL A 44 1 O GLN A 43 N ALA A 4 SHEET 3 AA1 9 TRP A 74 HIS A 78 1 O HIS A 78 N VAL A 44 SHEET 4 AA1 9 GLY A 111 HIS A 115 1 O GLY A 111 N ALA A 77 SHEET 5 AA1 9 VAL A 138 GLU A 142 1 O GLU A 142 N LEU A 114 SHEET 6 AA1 9 ILE A 174 ASP A 179 1 O GLY A 175 N ILE A 139 SHEET 7 AA1 9 ILE A 215 HIS A 218 1 O MET A 216 N ILE A 178 SHEET 8 AA1 9 PRO A 267 LEU A 270 1 O ILE A 269 N PHE A 217 SHEET 9 AA1 9 MET A 1 PHE A 5 1 N MET A 1 O ALA A 268 SHEET 1 AA2 2 ASP A 221 ALA A 222 0 SHEET 2 AA2 2 HIS A 233 ALA A 234 -1 O ALA A 234 N ASP A 221 SHEET 1 AA3 9 MET B 1 PHE B 5 0 SHEET 2 AA3 9 SER B 41A VAL B 44 1 O GLN B 43 N ALA B 4 SHEET 3 AA3 9 TRP B 74 HIS B 78 1 O HIS B 78 N VAL B 44 SHEET 4 AA3 9 GLY B 111 HIS B 115 1 O GLY B 111 N ALA B 77 SHEET 5 AA3 9 VAL B 138 GLU B 142 1 O TYR B 140 N LEU B 114 SHEET 6 AA3 9 ILE B 174 ASP B 179 1 O GLY B 175 N ILE B 139 SHEET 7 AA3 9 ILE B 215 HIS B 218 1 O MET B 216 N ILE B 178 SHEET 8 AA3 9 PRO B 267 LEU B 270 1 O ILE B 269 N PHE B 217 SHEET 9 AA3 9 MET B 1 PHE B 5 1 N PHE B 5 O LEU B 270 SHEET 1 AA4 2 ASP B 221 ALA B 222 0 SHEET 2 AA4 2 HIS B 233 ALA B 234 -1 O ALA B 234 N ASP B 221 SSBOND 1 CYS A 16 CYS A 20 1555 1555 2.03 SSBOND 2 CYS B 16 CYS B 20 1555 1555 2.03 LINK NE2 HIS A 78 ZN ZN A 303 1555 1555 2.17 LINK NE2 HIS A 115 ZN ZN A 303 1555 1555 2.14 LINK OE1 GLU A 142 ZN ZN A 302 1555 1555 2.15 LINK OE2 GLU A 142 ZN ZN A 303 1555 1555 2.14 LINK OD2 ASP A 179 ZN ZN A 302 1555 1555 2.12 LINK NE2 HIS A 182 ZN ZN A 301 1555 1555 2.08 LINK ND1 HIS A 218 ZN ZN A 302 1555 1555 2.34 LINK OD2 ASP A 231 ZN ZN A 301 1555 1555 2.01 LINK NE2 HIS A 233 ZN ZN A 301 1555 1555 2.07 LINK OE2 GLU A 271 ZN ZN A 302 1555 1555 2.29 LINK OP1 3DR D 10 ZN ZN A 303 1555 1555 2.02 LINK OP2 3DR D 10 ZN ZN A 301 1555 1555 2.47 LINK OP2 3DR D 10 ZN ZN A 302 1555 1555 2.12 LINK OP3 3DR D 10 ZN ZN A 301 1555 1555 2.17 LINK O3' 3DR D 10 P DC D 11 1555 1555 1.61 LINK NE2 HIS B 78 ZN ZN B 303 1555 1555 2.15 LINK NE2 HIS B 115 ZN ZN B 303 1555 1555 2.20 LINK OE1 GLU B 142 ZN ZN B 302 1555 1555 2.00 LINK OE2 GLU B 142 ZN ZN B 303 1555 1555 1.94 LINK OD2 ASP B 179 ZN ZN B 302 1555 1555 2.20 LINK NE2 HIS B 182 ZN ZN B 301 1555 1555 2.00 LINK ND1 HIS B 218 ZN ZN B 302 1555 1555 2.32 LINK OD2 ASP B 231 ZN ZN B 301 1555 1555 2.03 LINK NE2 HIS B 233 ZN ZN B 301 1555 1555 2.10 LINK OE2 GLU B 271 ZN ZN B 302 1555 1555 2.08 LINK OP1 3DR G 10 ZN ZN B 303 1555 1555 2.11 LINK OP2 3DR G 10 ZN ZN B 302 1555 1555 2.02 LINK OP2 3DR G 10 ZN ZN B 301 1555 1555 2.67 LINK OP3 3DR G 10 ZN ZN B 301 1555 1555 2.04 LINK O3' 3DR G 10 P DC G 11 1555 1555 1.61 CISPEP 1 GLY A 48 PRO A 49 0 0.87 CISPEP 2 GLY B 48 PRO B 49 0 2.84 SITE 1 AC1 5 HIS A 182 ASP A 231 HIS A 233 DC C 9 SITE 2 AC1 5 3DR D 10 SITE 1 AC2 6 GLU A 142 ASP A 179 HIS A 218 GLU A 271 SITE 2 AC2 6 ZN A 303 3DR D 10 SITE 1 AC3 5 HIS A 78 HIS A 115 GLU A 142 ZN A 302 SITE 2 AC3 5 3DR D 10 SITE 1 AC4 4 HIS B 182 ASP B 231 HIS B 233 3DR G 10 SITE 1 AC5 6 GLU B 142 ASP B 179 HIS B 218 GLU B 271 SITE 2 AC5 6 ZN B 303 3DR G 10 SITE 1 AC6 5 HIS B 78 HIS B 115 GLU B 142 ZN B 302 SITE 2 AC6 5 3DR G 10 SITE 1 AC7 23 PHE B 5 PHE B 45 PRO B 49 ARG B 50 SITE 2 AC7 23 HIS B 78 TYR B 81 HIS B 115 GLU B 142 SITE 3 AC7 23 ASP B 179 HIS B 182 ASP B 231 HIS B 233 SITE 4 AC7 23 GLU B 271 ASN B 273 ZN B 301 ZN B 302 SITE 5 AC7 23 ZN B 303 HOH B 406 DC F 9 DG G 12 SITE 6 AC7 23 HOH G 103 DC H 7 DG H 8 CRYST1 50.637 84.698 98.585 90.00 93.66 90.00 P 1 21 1 4 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 0.019748 0.000000 0.001263 0.00000 SCALE2 0.000000 0.011807 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010164 0.00000