10 20 30 40 50 60 70 80 3VK8 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER HYDROLASE/DNA 10-NOV-11 3VK8
TITLE CRYSTAL STRUCTURE OF DNA-GLYCOSYLASE BOUND TO DNA CONTAINING THYMINE TITLE 2 GLYCOL
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*CP*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*(CTG)P*GP*TP*CP*TP*AP*C)-3'); COMPND 16 CHAIN: D, F; COMPND 17 ENGINEERED: YES; COMPND 18 OTHER_DETAILS: DNA CONTAINING THYMINE GLYCOL
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, THYMINE GLYCOL, KEYWDS 2 ZINCLESS FINGER, DNA BINDING, HYDROLASE-DNA COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR K.IMAMURA,A.AVERILL,S.S.WALLACE,S.DOUBLIE
REVDAT 2 16-JAN-13 3VK8 1 JRNL REVDAT 1 14-DEC-11 3VK8 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. 2.00 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 14.96 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) (%) : 87.2 REMARK 3 NUMBER OF REFLECTIONS : 88772 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : FROM 3A46 REMARK 3 R VALUE (WORKING SET) : 0.200 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.200 REMARK 3 FREE R VALUE TEST SET COUNT : 8303 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.13 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 54.50 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2690 REMARK 3 BIN FREE R VALUE : 0.2970 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 831 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 : 4732 REMARK 3 NUCLEIC ACID ATOMS : 1054 REMARK 3 HETEROGEN ATOMS : 6 REMARK 3 SOLVENT ATOMS : 444 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.48 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 4.06200 REMARK 3 B22 (A**2) : -5.42400 REMARK 3 B33 (A**2) : 1.36200 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.58400 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.370 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.139 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.057 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.067 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 69.59 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 : CNS_TOPPAR:PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : DNA-RNA_REP-090403.PARAM REMARK 3 PARAMETER FILE 3 : CNS_TOPPAR:WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : CNS_TOPPAR:ION.PARAM REMARK 3 PARAMETER FILE 5 : GOL_XPLOR_PARAM REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : CNS_TOPPAR:PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : DNA-RNA-TEST.TOP REMARK 3 TOPOLOGY FILE 3 : CNS_TOPPAR:WATER.TOP REMARK 3 TOPOLOGY FILE 4 : CNS_TOPPAR:ION.TOP REMARK 3 TOPOLOGY FILE 5 : GOL_XPLOR_TOP REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE SF FILE CONTAINS FRIEDEL PAIRS
REMARK 4 REMARK 4 3VK8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-NOV-11. REMARK 100 THE RCSB ID CODE IS RCSB095148.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-OCT-08; 15-AUG-08 REMARK 200 TEMPERATURE (KELVIN) : 100; 100 REMARK 200 PH : 6.3 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; N REMARK 200 RADIATION SOURCE : APS; ROTATING ANODE REMARK 200 BEAMLINE : 23-ID-B; NULL REMARK 200 X-RAY GENERATOR MODEL : NULL; RIGAKU RUH3R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0332; 1.5418 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL CRYO-COOLED REMARK 200 SI(111); NULL REMARK 200 OPTICS : MIRRORS; XENOCS FOX 2D REMARK 200 MULTILAYER MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD; CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD; MAR REMARK 200 SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 96852 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 35.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.2 REMARK 200 DATA REDUNDANCY : 8.000 REMARK 200 R MERGE (I) : 0.13300 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 6.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 73.3 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : 0.37000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: THE SF FILE CONTAINS FRIEDEL PAIRS
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.18 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.29 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350, MG(NO3)2, 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 60.80850 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: 4480 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16120 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -23.0 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: 4120 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16400 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -24.0 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 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 HIS B 218 CG ND1 CD2 CE1 NE2 REMARK 470 ILE B 219 CG1 CG2 CD1 REMARK 470 TYR B 221 CG CD1 CD2 CE1 CE2 CZ OH
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 LYS A 72 CG CD CE NZ REMARK 480 SER A 73 CB OG REMARK 480 LYS A 75 CE NZ REMARK 480 GLU A 105 CG CD OE1 OE2 REMARK 480 GLU A 125 CD OE1 OE2 REMARK 480 ASP A 144 CB CG OD1 OD2 REMARK 480 LYS A 149 CD CE NZ REMARK 480 LYS A 151 CE NZ REMARK 480 LYS A 152 CD CE NZ REMARK 480 LYS A 154 CD CE NZ REMARK 480 GLN A 197 CD OE1 NE2 REMARK 480 GLU A 200 CD OE1 OE2 REMARK 480 VAL A 223 CB CG1 CG2 REMARK 480 GLU A 226 CB CG CD OE1 OE2 REMARK 480 ASN A 227 CG OD1 ND2 REMARK 480 LYS A 231 CD CE NZ REMARK 480 LYS A 246 CB CG CD CE NZ REMARK 480 LYS A 268 CE NZ REMARK 480 GLU A 289 CD OE1 OE2 REMARK 480 LYS B 35 CE NZ REMARK 480 LYS B 72 CG CD CE NZ REMARK 480 LYS B 129 CD CE NZ REMARK 480 ASP B 144 CB CG OD1 OD2 REMARK 480 LYS B 151 CD CE NZ REMARK 480 LYS B 152 CG CD CE NZ REMARK 480 LYS B 154 CD CE NZ REMARK 480 GLN B 155 CD OE1 NE2 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 ASN B 227 CG OD1 ND2 REMARK 480 LYS B 231 CD CE NZ REMARK 480 LYS B 246 CG CD CE NZ REMARK 480 GLU B 247 CG CD OE1 OE2 REMARK 480 LYS B 268 CD CE NZ REMARK 480 GLU B 289 CG CD OE1 OE2
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 61.22 -161.72 REMARK 500 LYS A 72 -27.65 -39.03 REMARK 500 GLU A 92 85.83 -69.56 REMARK 500 ASN A 104 33.41 74.57 REMARK 500 ASP A 112 95.98 -163.58 REMARK 500 HIS A 218 65.16 -157.21 REMARK 500 TYR A 221 45.63 -88.16 REMARK 500 MET A 222 35.03 -150.94 REMARK 500 ASP B 71 55.89 -162.73 REMARK 500 GLU B 105 15.21 55.79 REMARK 500 HIS B 218 61.10 -154.28 REMARK 500 MET B 222 34.10 -63.26 REMARK 500 REMARK 500 REMARK: NULL
REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A1442 DISTANCE = 6.94 ANGSTROMS
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 3001
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: 3VK7 RELATED DB: PDB REMARK 900 THE SAME PROTEIN BOUND TO DNA CONTAINING 5-HYDROXYURACIL
DBREF 3VK8 A 1 287 UNP Q5UQ00 FPG_MIMIV 1 287 DBREF 3VK8 B 1 287 UNP Q5UQ00 FPG_MIMIV 1 287 DBREF 3VK8 C 1 13 PDB 3VK8 3VK8 1 13 DBREF 3VK8 E 1 13 PDB 3VK8 3VK8 1 13 DBREF 3VK8 D 14 26 PDB 3VK8 3VK8 14 26 DBREF 3VK8 F 14 26 PDB 3VK8 3VK8 14 26
SEQADV 3VK8 GLN A 3 UNP Q5UQ00 GLU 3 ENGINEERED MUTATION SEQADV 3VK8 LEU A 288 UNP Q5UQ00 EXPRESSION TAG SEQADV 3VK8 GLU A 289 UNP Q5UQ00 EXPRESSION TAG SEQADV 3VK8 HIS A 290 UNP Q5UQ00 EXPRESSION TAG SEQADV 3VK8 HIS A 291 UNP Q5UQ00 EXPRESSION TAG SEQADV 3VK8 HIS A 292 UNP Q5UQ00 EXPRESSION TAG SEQADV 3VK8 HIS A 293 UNP Q5UQ00 EXPRESSION TAG SEQADV 3VK8 HIS A 294 UNP Q5UQ00 EXPRESSION TAG SEQADV 3VK8 HIS A 295 UNP Q5UQ00 EXPRESSION TAG SEQADV 3VK8 GLN B 3 UNP Q5UQ00 GLU 3 ENGINEERED MUTATION SEQADV 3VK8 LEU B 288 UNP Q5UQ00 EXPRESSION TAG SEQADV 3VK8 GLU B 289 UNP Q5UQ00 EXPRESSION TAG SEQADV 3VK8 HIS B 290 UNP Q5UQ00 EXPRESSION TAG SEQADV 3VK8 HIS B 291 UNP Q5UQ00 EXPRESSION TAG SEQADV 3VK8 HIS B 292 UNP Q5UQ00 EXPRESSION TAG SEQADV 3VK8 HIS B 293 UNP Q5UQ00 EXPRESSION TAG SEQADV 3VK8 HIS B 294 UNP Q5UQ00 EXPRESSION TAG SEQADV 3VK8 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 DC DT DG DG DA DC DG SEQRES 1 D 13 DC DG DT DC DC DA CTG DG DT DC DT DA DC SEQRES 1 E 13 DG DT DA DG DA DC DC DT DG DG DA DC DG SEQRES 1 F 13 DC DG DT DC DC DA CTG DG DT DC DT DA DC
MODRES 3VK8 CTG D 20 DT MODRES 3VK8 CTG F 20 DT
HET CTG D 20 22 HET CTG F 20 22 HET GOL A3001 6
HETNAM CTG (5R,6S)-5,6-DIHYDRO-5,6-DIHYDROXYTHYMIDINE-5'- HETNAM 2 CTG MONOPHOSPHATE HETNAM GOL GLYCEROL
HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL
FORMUL 4 CTG 2(C10 H17 N2 O10 P) FORMUL 7 GOL C3 H8 O3 FORMUL 8 HOH *444(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 ALA A 183 1 12 HELIX 8 8 LEU A 190 LEU A 194 5 5 HELIX 9 9 THR A 195 SER A 216 1 22 HELIX 10 10 MET A 222 ASN A 224 5 3 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 LYS B 35 5 5 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 GLY B 220 ASN B 224 5 5 HELIX 22 22 LEU B 225 LYS B 231 1 7
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 LYS A 268 0 SHEET 2 B 2 THR A 278 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 ARG B 97 O PHE B 110 SHEET 4 C 8 THR B 22 PHE B 28 -1 N GLU B 24 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 GLU B 65 N SER B 53 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 CTG D 20 1555 1555 1.61 LINK O3' CTG D 20 P DG D 21 1555 1555 1.60 LINK O3' DA F 19 P CTG F 20 1555 1555 1.61 LINK O3' CTG F 20 P DG F 21 1555 1555 1.60
CISPEP 1 LEU A 48 PRO A 49 0 0.28 CISPEP 2 LEU B 48 PRO B 49 0 0.01
SITE 1 AC1 7 LYS A 274 ARG A 277 HOH A1064 HOH A1356 SITE 2 AC1 7 HOH A1410 DC C 6 DG D 21
CRYST1 39.737 121.617 80.836 90.00 95.54 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 0.025165 0.000000 0.002441 0.00000
SCALE2 0.000000 0.008223 0.000000 0.00000
SCALE3 0.000000 0.000000 0.012429 0.00000