HEADER HYDROLASE/DNA 10-NOV-11 3VK7 TITLE CRYSTAL STRUCTURE OF DNA-GLYCOSYLASE BOUND TO DNA CONTAINING 5- TITLE 2 HYDROXYURACIL COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROBABLE FORMAMIDOPYRIMIDINE-DNA GLYCOSYLASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: FAPY-DNA GLYCOSYLASE, DNA-(APURINIC OR APYRIMIDINIC SITE) COMPND 5 LYASE, AP LYASE; COMPND 6 EC: 3.2.2.23, 4.2.99.18; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: DNA (5'-D(*GP*TP*AP*GP*AP*CP*GP*TP*GP*GP*AP*CP*G)-3'); COMPND 11 CHAIN: C, E; COMPND 12 ENGINEERED: YES; COMPND 13 OTHER_DETAILS: COMPLEMENTARY DNA; COMPND 14 MOL_ID: 3; COMPND 15 MOLECULE: DNA (5'-D(*CP*GP*TP*CP*CP*AP*(OHU)P*GP*TP*CP*TP*AP*C)-3'); COMPND 16 CHAIN: D, F; COMPND 17 ENGINEERED: YES; COMPND 18 OTHER_DETAILS: DNA CONTAINING 5-HYDROXYURACIL SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ACANTHAMOEBA POLYPHAGA MIMIVIRUS; SOURCE 3 ORGANISM_COMMON: APMV; SOURCE 4 ORGANISM_TAXID: 212035; SOURCE 5 GENE: MIMI_L315; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA(DE3)PLYS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET22B; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 MOL_ID: 3; SOURCE 14 SYNTHETIC: YES KEYWDS DNA GLYCOSYLASE, HNEIL1 ORTHOLOG, DNA LESION, 5-HYDROXYURACIL, KEYWDS 2 ZINCLESS FINGER, DNA BINDING, HYDROLASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR K.IMAMURA,A.AVERILL,S.S.WALLACE,S.DOUBLIE REVDAT 3 08-NOV-23 3VK7 1 REMARK SEQADV LINK REVDAT 2 16-JAN-13 3VK7 1 JRNL REVDAT 1 14-DEC-11 3VK7 0 JRNL AUTH K.IMAMURA,A.AVERILL,S.S.WALLACE,S.DOUBLIE JRNL TITL STRUCTURAL CHARACTERIZATION OF VIRAL ORTHOLOG OF HUMAN DNA JRNL TITL 2 GLYCOSYLASE NEIL1 BOUND TO THYMINE GLYCOL OR JRNL TITL 3 5-HYDROXYURACIL-CONTAINING DNA JRNL REF J.BIOL.CHEM. V. 287 4288 2012 JRNL REFN ISSN 0021-9258 JRNL PMID 22170059 JRNL DOI 10.1074/JBC.M111.315309 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH K.IMAMURA,S.S.WALLACE,S.DOUBLIE REMARK 1 TITL STRUCTURAL CHARACTERIZATION OF A VIRAL NEIL1 ORTHOLOG REMARK 1 TITL 2 UNLIGANDED AND BOUND TO ABASIC SITE-CONTAINING DNA REMARK 1 REF J.BIOL.CHEM. V. 284 26174 2009 REMARK 1 REFN ISSN 0021-9258 REMARK 1 PMID 19625256 REMARK 1 DOI 10.1074/JBC.M109.021907 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.30 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.1 REMARK 3 NUMBER OF REFLECTIONS : 40659 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.218 REMARK 3 R VALUE (WORKING SET) : 0.213 REMARK 3 FREE R VALUE : 0.266 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.270 REMARK 3 FREE R VALUE TEST SET COUNT : 3770 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 28.2985 - 6.2778 0.97 1491 155 0.1935 0.2183 REMARK 3 2 6.2778 - 4.9918 1.00 1475 179 0.1898 0.2255 REMARK 3 3 4.9918 - 4.3634 0.99 1486 157 0.1717 0.2135 REMARK 3 4 4.3634 - 3.9656 0.94 1410 136 0.1775 0.2155 REMARK 3 5 3.9656 - 3.6821 0.32 487 53 0.1814 0.1547 REMARK 3 6 3.6821 - 3.4654 0.20 318 22 0.1628 0.2178 REMARK 3 7 3.4654 - 3.2921 0.94 1391 151 0.1779 0.2268 REMARK 3 8 3.2921 - 3.1490 0.99 1500 171 0.1999 0.2639 REMARK 3 9 3.1490 - 3.0279 0.99 1436 173 0.1981 0.2297 REMARK 3 10 3.0279 - 2.9235 1.00 1499 166 0.2195 0.2862 REMARK 3 11 2.9235 - 2.8322 0.99 1433 170 0.2293 0.3173 REMARK 3 12 2.8322 - 2.7513 0.99 1513 163 0.2235 0.2988 REMARK 3 13 2.7513 - 2.6789 0.99 1458 162 0.2217 0.2620 REMARK 3 14 2.6789 - 2.6136 0.99 1472 140 0.2010 0.2991 REMARK 3 15 2.6136 - 2.5542 0.98 1479 166 0.2026 0.2636 REMARK 3 16 2.5542 - 2.4999 0.98 1441 147 0.2134 0.2790 REMARK 3 17 2.4999 - 2.4499 0.98 1473 162 0.2234 0.2943 REMARK 3 18 2.4499 - 2.4037 0.98 1467 166 0.2196 0.3043 REMARK 3 19 2.4037 - 2.3608 0.97 1441 149 0.2169 0.2731 REMARK 3 20 2.3608 - 2.3208 0.95 1404 166 0.2235 0.3089 REMARK 3 21 2.3208 - 2.2834 0.92 1376 112 0.2359 0.3030 REMARK 3 22 2.2834 - 2.2483 0.82 1277 96 0.2710 0.3182 REMARK 3 23 2.2483 - 2.2152 0.93 1474 43 0.2541 0.2509 REMARK 3 24 2.2152 - 2.1841 0.94 1446 109 0.2311 0.2942 REMARK 3 25 2.1841 - 2.1545 0.94 1404 174 0.2382 0.3406 REMARK 3 26 2.1545 - 2.1266 0.95 1396 143 0.2427 0.2972 REMARK 3 27 2.1266 - 2.1000 0.97 1442 139 0.2387 0.3588 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.36 REMARK 3 B_SOL : 52.30 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 1.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.030 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.45 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.22510 REMARK 3 B22 (A**2) : -3.09740 REMARK 3 B33 (A**2) : 5.32250 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -1.52550 REMARK 3 B23 (A**2) : 0.00000 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 : 0.005 6116 REMARK 3 ANGLE : 0.989 8485 REMARK 3 CHIRALITY : 0.067 889 REMARK 3 PLANARITY : 0.004 890 REMARK 3 DIHEDRAL : 20.224 2354 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 : 2 REMARK 3 NCS GROUP : 1 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: CHAIN A AND (RESSEQ 7:200 ) REMARK 3 SELECTION : CHAIN B AND (RESSEQ 7:200 ) REMARK 3 ATOM PAIRS NUMBER : 1577 REMARK 3 RMSD : 0.023 REMARK 3 NCS GROUP : 2 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: CHAIN A AND (RESSEQ 230:270 ) REMARK 3 SELECTION : CHAIN B AND (RESSEQ 230:270 ) REMARK 3 ATOM PAIRS NUMBER : 337 REMARK 3 RMSD : 0.019 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3VK7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 22-NOV-11. REMARK 100 THE DEPOSITION ID IS D_1000095147. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-OCT-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.3 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 23-ID-B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0332 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL CRYO-COOLED REMARK 200 SI(111) REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 41763 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.6 REMARK 200 DATA REDUNDANCY : 2.800 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.9 REMARK 200 DATA REDUNDANCY IN SHELL : 2.70 REMARK 200 R MERGE FOR SHELL (I) : 0.23200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: PDB ENTRY 3A46 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.31 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.29 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350, HCOONA, PH 6.3, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 285K 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 60.79700 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3970 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16340 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C, D REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3980 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16300 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, E, F 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 HIS A 290 REMARK 465 HIS A 291 REMARK 465 HIS A 292 REMARK 465 HIS A 293 REMARK 465 HIS A 294 REMARK 465 HIS A 295 REMARK 465 MET B 1 REMARK 465 LEU B 288 REMARK 465 GLU B 289 REMARK 465 HIS B 290 REMARK 465 HIS B 291 REMARK 465 HIS B 292 REMARK 465 HIS B 293 REMARK 465 HIS B 294 REMARK 465 HIS B 295 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 TYR A 221 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 TYR B 221 CG CD1 CD2 CE1 CE2 CZ OH REMARK 475 REMARK 475 ZERO OCCUPANCY RESIDUES REMARK 475 THE FOLLOWING RESIDUES WERE MODELED WITH ZERO OCCUPANCY. REMARK 475 THE LOCATION AND PROPERTIES OF THESE RESIDUES MAY NOT REMARK 475 BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 475 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE) REMARK 475 M RES C SSEQI REMARK 475 GLU A 289 REMARK 475 LYS B 287 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 ASP A 27 CG OD1 OD2 REMARK 480 GLU A 37 CB CG CD OE1 OE2 REMARK 480 LYS A 72 CG CD CE NZ REMARK 480 SER A 73 CB OG REMARK 480 ASN A 74 CB CG OD1 ND2 REMARK 480 LYS A 75 CE NZ REMARK 480 GLU A 125 CD OE1 OE2 REMARK 480 LYS A 152 CG CD CE NZ REMARK 480 GLN A 197 CG CD OE1 NE2 REMARK 480 ILE A 219 CB CG1 CG2 CD1 REMARK 480 VAL A 223 CB CG1 CG2 REMARK 480 LYS A 246 CG CD CE NZ REMARK 480 ASP A 249 CG OD1 OD2 REMARK 480 LYS B 35 CE NZ REMARK 480 ASN B 54 CB CG OD1 ND2 REMARK 480 ASP B 71 CB CG OD1 OD2 REMARK 480 LYS B 72 CG CD CE NZ REMARK 480 LYS B 75 CE NZ REMARK 480 LYS B 129 CG CD CE NZ REMARK 480 LYS B 149 CB CG CD CE NZ REMARK 480 LYS B 151 NZ REMARK 480 LYS B 154 CD CE NZ REMARK 480 LYS B 184 CD CE NZ REMARK 480 GLU B 200 CG CD OE1 OE2 REMARK 480 VAL B 223 CB CG1 CG2 REMARK 480 GLU B 226 CB CG CD OE1 OE2 REMARK 480 LYS B 231 CB CG CD CE NZ REMARK 480 LYS B 246 CG CD CE NZ REMARK 480 ASP B 249 CG OD1 OD2 REMARK 480 LYS B 268 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 DT C 2 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DT C 8 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 DC C 12 C3' - C2' - C1' ANGL. DEV. = -5.3 DEGREES REMARK 500 DT D 16 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 DA D 19 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 DT D 22 C1' - O4' - C4' ANGL. DEV. = -6.3 DEGREES REMARK 500 DT D 22 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 DT E 8 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 DC E 12 C3' - C2' - C1' ANGL. DEV. = -6.5 DEGREES REMARK 500 DC E 12 O4' - C1' - N1 ANGL. DEV. = 4.1 DEGREES REMARK 500 DG F 15 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 DT F 16 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DA F 19 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 DT F 22 O4' - C1' - N1 ANGL. DEV. = 2.3 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 ASP A 71 58.99 -157.30 REMARK 500 ASP A 112 91.38 -161.98 REMARK 500 ASP A 144 55.97 -148.03 REMARK 500 HIS A 218 68.85 -153.70 REMARK 500 HIS A 218 67.75 -153.38 REMARK 500 MET A 222 40.04 -73.83 REMARK 500 HIS A 238 71.72 35.27 REMARK 500 LEU A 288 67.72 -102.31 REMARK 500 ASP B 71 59.58 -157.58 REMARK 500 ASP B 112 92.50 -162.77 REMARK 500 ASP B 144 56.67 -147.07 REMARK 500 HIS B 238 71.99 35.76 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT B 296 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT D 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3A46 RELATED DB: PDB REMARK 900 THE SAME PROTEIN IN COMPLEX WITH THF REMARK 900 RELATED ID: 3VK8 RELATED DB: PDB REMARK 900 SAME PROTEIN BOUND TO DNA CONTAINING THYMINE GLYCOL DBREF 3VK7 A 1 287 UNP Q5UQ00 FPG_MIMIV 1 287 DBREF 3VK7 B 1 287 UNP Q5UQ00 FPG_MIMIV 1 287 DBREF 3VK7 C 1 13 PDB 3VK7 3VK7 1 13 DBREF 3VK7 E 1 13 PDB 3VK7 3VK7 1 13 DBREF 3VK7 D 14 26 PDB 3VK7 3VK7 14 26 DBREF 3VK7 F 14 26 PDB 3VK7 3VK7 14 26 SEQADV 3VK7 GLN A 3 UNP Q5UQ00 GLU 3 ENGINEERED MUTATION SEQADV 3VK7 LEU A 288 UNP Q5UQ00 EXPRESSION TAG SEQADV 3VK7 GLU A 289 UNP Q5UQ00 EXPRESSION TAG SEQADV 3VK7 HIS A 290 UNP Q5UQ00 EXPRESSION TAG SEQADV 3VK7 HIS A 291 UNP Q5UQ00 EXPRESSION TAG SEQADV 3VK7 HIS A 292 UNP Q5UQ00 EXPRESSION TAG SEQADV 3VK7 HIS A 293 UNP Q5UQ00 EXPRESSION TAG SEQADV 3VK7 HIS A 294 UNP Q5UQ00 EXPRESSION TAG SEQADV 3VK7 HIS A 295 UNP Q5UQ00 EXPRESSION TAG SEQADV 3VK7 GLN B 3 UNP Q5UQ00 GLU 3 ENGINEERED MUTATION SEQADV 3VK7 LEU B 288 UNP Q5UQ00 EXPRESSION TAG SEQADV 3VK7 GLU B 289 UNP Q5UQ00 EXPRESSION TAG SEQADV 3VK7 HIS B 290 UNP Q5UQ00 EXPRESSION TAG SEQADV 3VK7 HIS B 291 UNP Q5UQ00 EXPRESSION TAG SEQADV 3VK7 HIS B 292 UNP Q5UQ00 EXPRESSION TAG SEQADV 3VK7 HIS B 293 UNP Q5UQ00 EXPRESSION TAG SEQADV 3VK7 HIS B 294 UNP Q5UQ00 EXPRESSION TAG SEQADV 3VK7 HIS B 295 UNP Q5UQ00 EXPRESSION TAG SEQRES 1 A 295 MET PRO GLN GLY PRO GLU VAL ALA LEU THR ALA ASP ILE SEQRES 2 A 295 LEU GLU LYS TYR PHE LYS GLY LYS THR LEU GLU TYR ILE SEQRES 3 A 295 ASP PHE ILE SER GLY ARG TYR SER LYS SER GLU PRO GLU SEQRES 4 A 295 GLY TYR ASP ASP PHE ILE ALA ASN LEU PRO LEU LYS VAL SEQRES 5 A 295 SER ASN VAL ASP THR LYS GLY LYS PHE LEU TRP PHE GLU SEQRES 6 A 295 LEU PHE ASP PRO ASN ASP LYS SER ASN LYS TRP TYR ILE SEQRES 7 A 295 TRP ASN THR PHE GLY LEU THR GLY MET TRP SER LEU PHE SEQRES 8 A 295 GLU ALA LYS TYR THR ARG ALA VAL LEU SER PHE ASP ASN SEQRES 9 A 295 GLU LEU MET ALA TYR PHE SER ASP MET ARG ASN PHE GLY SEQRES 10 A 295 THR PHE LYS PHE SER ASN SER GLU LYS GLU LEU LYS ARG SEQRES 11 A 295 LYS LEU ASN GLU LEU GLY PRO ASP PHE LEU LYS ASN ASP SEQRES 12 A 295 ASP ILE ASP ILE SER LYS ILE LYS LYS TYR LYS GLN PRO SEQRES 13 A 295 ILE VAL ALA LEU LEU MET ASP GLN LYS LYS ILE GLY SER SEQRES 14 A 295 GLY LEU GLY ASN TYR LEU VAL ALA GLU ILE LEU TYR ARG SEQRES 15 A 295 ALA LYS ILE ASP PRO HIS LYS LEU GLY SER ASN LEU THR SEQRES 16 A 295 ASP GLN GLU ILE GLU ASN LEU TRP TYR TRP ILE LYS TYR SEQRES 17 A 295 GLU THR LYS LEU ALA TYR ASP SER ASN HIS ILE GLY TYR SEQRES 18 A 295 MET VAL ASN LEU GLU ASN GLU SER SER LYS ILE GLY ARG SEQRES 19 A 295 LYS ASN TYR HIS PRO ASN ILE HIS PRO THR GLU LYS GLU SEQRES 20 A 295 PHE ASP PHE LEU VAL TYR ARG LYS LYS LYS ASP PRO ASN SEQRES 21 A 295 GLY ASN LYS VAL ILE ALA ASP LYS ILE ILE GLY SER GLY SEQRES 22 A 295 LYS ASN LYS ARG THR THR TYR TRP ALA PRO ALA ILE GLN SEQRES 23 A 295 LYS LEU GLU HIS HIS HIS HIS HIS HIS SEQRES 1 B 295 MET PRO GLN GLY PRO GLU VAL ALA LEU THR ALA ASP ILE SEQRES 2 B 295 LEU GLU LYS TYR PHE LYS GLY LYS THR LEU GLU TYR ILE SEQRES 3 B 295 ASP PHE ILE SER GLY ARG TYR SER LYS SER GLU PRO GLU SEQRES 4 B 295 GLY TYR ASP ASP PHE ILE ALA ASN LEU PRO LEU LYS VAL SEQRES 5 B 295 SER ASN VAL ASP THR LYS GLY LYS PHE LEU TRP PHE GLU SEQRES 6 B 295 LEU PHE ASP PRO ASN ASP LYS SER ASN LYS TRP TYR ILE SEQRES 7 B 295 TRP ASN THR PHE GLY LEU THR GLY MET TRP SER LEU PHE SEQRES 8 B 295 GLU ALA LYS TYR THR ARG ALA VAL LEU SER PHE ASP ASN SEQRES 9 B 295 GLU LEU MET ALA TYR PHE SER ASP MET ARG ASN PHE GLY SEQRES 10 B 295 THR PHE LYS PHE SER ASN SER GLU LYS GLU LEU LYS ARG SEQRES 11 B 295 LYS LEU ASN GLU LEU GLY PRO ASP PHE LEU LYS ASN ASP SEQRES 12 B 295 ASP ILE ASP ILE SER LYS ILE LYS LYS TYR LYS GLN PRO SEQRES 13 B 295 ILE VAL ALA LEU LEU MET ASP GLN LYS LYS ILE GLY SER SEQRES 14 B 295 GLY LEU GLY ASN TYR LEU VAL ALA GLU ILE LEU TYR ARG SEQRES 15 B 295 ALA LYS ILE ASP PRO HIS LYS LEU GLY SER ASN LEU THR SEQRES 16 B 295 ASP GLN GLU ILE GLU ASN LEU TRP TYR TRP ILE LYS TYR SEQRES 17 B 295 GLU THR LYS LEU ALA TYR ASP SER ASN HIS ILE GLY TYR SEQRES 18 B 295 MET VAL ASN LEU GLU ASN GLU SER SER LYS ILE GLY ARG SEQRES 19 B 295 LYS ASN TYR HIS PRO ASN ILE HIS PRO THR GLU LYS GLU SEQRES 20 B 295 PHE ASP PHE LEU VAL TYR ARG LYS LYS LYS ASP PRO ASN SEQRES 21 B 295 GLY ASN LYS VAL ILE ALA ASP LYS ILE ILE GLY SER GLY SEQRES 22 B 295 LYS ASN LYS ARG THR THR TYR TRP ALA PRO ALA ILE GLN SEQRES 23 B 295 LYS LEU GLU HIS HIS HIS HIS HIS HIS SEQRES 1 C 13 DG DT DA DG DA DC DG DT DG DG DA DC DG SEQRES 1 D 13 DC DG DT DC DC DA OHU DG DT DC DT DA DC SEQRES 1 E 13 DG DT DA DG DA DC DG DT DG DG DA DC DG SEQRES 1 F 13 DC DG DT DC DC DA OHU DG DT DC DT DA DC MODRES 3VK7 OHU D 20 DU MODRES 3VK7 OHU F 20 DU HET OHU D 20 40 HET OHU F 20 40 HET FMT B 296 3 HET FMT D 1 3 HETNAM OHU 2'-DEOXY-5-HYDROXYURIDINE 5'-(DIHYDROGEN PHOSPHATE) HETNAM FMT FORMIC ACID FORMUL 4 OHU 2(C9 H13 N2 O9 P) FORMUL 7 FMT 2(C H2 O2) FORMUL 9 HOH *456(H2 O) HELIX 1 1 GLN A 3 LYS A 19 1 17 HELIX 2 2 GLY A 31 SER A 36 1 6 HELIX 3 3 GLY A 40 ALA A 46 1 7 HELIX 4 4 SER A 124 ASN A 133 1 10 HELIX 5 5 ASP A 146 TYR A 153 5 8 HELIX 6 6 PRO A 156 ASP A 163 1 8 HELIX 7 7 GLY A 172 LYS A 184 1 13 HELIX 8 8 LEU A 190 LEU A 194 5 5 HELIX 9 9 THR A 195 ASP A 215 1 21 HELIX 10 10 GLY A 220 ASN A 224 5 5 HELIX 11 11 LEU A 225 SER A 230 1 6 HELIX 12 12 GLN B 3 LYS B 19 1 17 HELIX 13 13 GLY B 31 SER B 36 1 6 HELIX 14 14 GLY B 40 ALA B 46 1 7 HELIX 15 15 SER B 124 ASN B 133 1 10 HELIX 16 16 ASP B 146 TYR B 153 5 8 HELIX 17 17 PRO B 156 ASP B 163 1 8 HELIX 18 18 GLY B 172 ALA B 183 1 12 HELIX 19 19 LEU B 190 LEU B 194 5 5 HELIX 20 20 THR B 195 SER B 216 1 22 HELIX 21 21 MET B 222 ASN B 224 5 3 HELIX 22 22 LEU B 225 SER B 230 1 6 SHEET 1 A 8 GLY A 86 SER A 89 0 SHEET 2 A 8 MET A 107 ASP A 112 -1 O SER A 111 N MET A 87 SHEET 3 A 8 THR A 96 PHE A 102 -1 N LEU A 100 O ALA A 108 SHEET 4 A 8 THR A 22 PHE A 28 -1 N TYR A 25 O SER A 101 SHEET 5 A 8 LEU A 50 LYS A 58 -1 O LEU A 50 N LEU A 23 SHEET 6 A 8 PHE A 61 ASP A 68 -1 O PHE A 67 N LYS A 51 SHEET 7 A 8 ASP A 71 THR A 81 -1 O TRP A 76 N LEU A 66 SHEET 8 A 8 THR A 118 SER A 122 -1 O LYS A 120 N TRP A 79 SHEET 1 B 2 ILE A 265 ASP A 267 0 SHEET 2 B 2 THR A 279 TRP A 281 -1 O THR A 279 N ASP A 267 SHEET 1 C 8 GLY B 86 SER B 89 0 SHEET 2 C 8 MET B 107 ASP B 112 -1 O SER B 111 N MET B 87 SHEET 3 C 8 THR B 96 PHE B 102 -1 N LEU B 100 O ALA B 108 SHEET 4 C 8 THR B 22 PHE B 28 -1 N TYR B 25 O SER B 101 SHEET 5 C 8 LEU B 50 LYS B 58 -1 O LEU B 50 N LEU B 23 SHEET 6 C 8 PHE B 61 ASP B 68 -1 O PHE B 67 N LYS B 51 SHEET 7 C 8 ASP B 71 THR B 81 -1 O TRP B 76 N LEU B 66 SHEET 8 C 8 THR B 118 SER B 122 -1 O LYS B 120 N TRP B 79 SHEET 1 D 2 ILE B 265 ASP B 267 0 SHEET 2 D 2 THR B 279 TRP B 281 -1 O THR B 279 N ASP B 267 LINK O3' DA D 19 P AOHU D 20 1555 1555 1.60 LINK O3' DA D 19 P BOHU D 20 1555 1555 1.60 LINK O3' DA F 19 P AOHU F 20 1555 1555 1.61 LINK O3' DA F 19 P BOHU F 20 1555 1555 1.61 CISPEP 1 LEU A 48 PRO A 49 0 5.59 CISPEP 2 LEU B 48 PRO B 49 0 4.39 SITE 1 AC1 5 LYS B 274 ASN B 275 ARG B 277 DG F 21 SITE 2 AC1 5 DT F 22 SITE 1 AC2 5 LYS A 274 ARG A 277 DG D 21 DT D 22 SITE 2 AC2 5 HOH D 56 CRYST1 39.703 121.594 81.121 90.00 95.49 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 0.025187 0.000000 0.002421 0.00000 SCALE2 0.000000 0.008224 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012384 0.00000