PDB Short entry for 3UFJ HEADER HYDROLASE/DNA 01-NOV-11 3UFJ TITLE HUMAN THYMINE DNA GLYCOSYLASE BOUND TO SUBSTRATE ANALOG 2'-FLUORO-2'- TITLE 2 DEOXYURIDINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: G/T MISMATCH-SPECIFIC THYMINE DNA GLYCOSYLASE; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: CORE DOMAIN (UNP RESIDUES 111-308); COMPND 5 SYNONYM: THYMINE-DNA GLYCOSYLASE; COMPND 6 EC: 3.2.2.29; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: 5'-D(*CP*AP*GP*CP*TP*CP*TP*GP*TP*AP*CP*GP*TP*GP*AP*GP*CP*AP COMPND 10 *GP*TP*GP*GP*A)-3'; COMPND 11 CHAIN: C, E; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: 5'-D(*CP*CP*AP*CP*TP*GP*CP*TP*CP*AP*(UF2) COMPND 15 P*GP*TP*AP*CP*AP*GP*AP*GP*CP*TP*GP*T)-3'; COMPND 16 CHAIN: D, F; COMPND 17 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: TDG; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET-28; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 MOL_ID: 3; SOURCE 14 SYNTHETIC: YES KEYWDS DNA DAMAGE, DNA REPAIR, DNA BINDING, GLYCOSIDASE, NUCLEUS, HYDROLASE- KEYWDS 2 DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR E.POZHARSKI,A.MAITI,A.C.DROHAT REVDAT 4 13-SEP-23 3UFJ 1 SEQADV LINK REVDAT 3 06-JUN-12 3UFJ 1 JRNL REVDAT 2 23-MAY-12 3UFJ 1 JRNL REVDAT 1 25-APR-12 3UFJ 0 JRNL AUTH A.MAITI,M.S.NOON,A.D.MACKERELL,E.POZHARSKI,A.C.DROHAT JRNL TITL LESION PROCESSING BY A REPAIR ENZYME IS SEVERELY CURTAILED JRNL TITL 2 BY RESIDUES NEEDED TO PREVENT ABERRANT ACTIVITY ON UNDAMAGED JRNL TITL 3 DNA. JRNL REF PROC.NATL.ACAD.SCI.USA V. 109 8091 2012 JRNL REFN ISSN 0027-8424 JRNL PMID 22573813 JRNL DOI 10.1073/PNAS.1201010109 REMARK 2 REMARK 2 RESOLUTION. 2.97 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.97 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.63 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 17438 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 + TEST SET) : 0.265 REMARK 3 R VALUE (WORKING SET) : 0.263 REMARK 3 FREE R VALUE : 0.304 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 881 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.97 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.04 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1167 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.92 REMARK 3 BIN R VALUE (WORKING SET) : 0.3840 REMARK 3 BIN FREE R VALUE SET COUNT : 57 REMARK 3 BIN FREE R VALUE : 0.4800 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2629 REMARK 3 NUCLEIC ACID ATOMS : 1876 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 1 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 102.2 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 104.4 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -52.00000 REMARK 3 B22 (A**2) : -52.00000 REMARK 3 B33 (A**2) : 104.01000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.102 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.581 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 38.948 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.921 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.891 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4805 ; 0.007 ; 0.016 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6932 ; 1.106 ; 1.682 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 367 ; 5.613 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 105 ;35.467 ;23.524 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 338 ;18.577 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 10 ;11.768 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 685 ; 0.068 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3102 ; 0.005 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : 3 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 124 A 154 2 REMARK 3 1 B 124 B 154 2 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 MEDIUM POSITIONAL 1 A (A): 107 ; 0.070 ; 0.500 REMARK 3 TIGHT THERMAL 1 A (A**2): 124 ;10.720 ; 0.500 REMARK 3 MEDIUM THERMAL 1 A (A**2): 107 ;10.490 ; 2.000 REMARK 3 REMARK 3 NCS GROUP NUMBER : 2 REMARK 3 CHAIN NAMES : C E REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 C 1 C 25 1 REMARK 3 1 E 1 E 25 1 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 TIGHT THERMAL 2 C (A**2): 473 ;13.000 ; 0.500 REMARK 3 REMARK 3 NCS GROUP NUMBER : 3 REMARK 3 CHAIN NAMES : D F REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 D 1 D 25 1 REMARK 3 1 F 1 F 25 1 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 TIGHT THERMAL 3 D (A**2): 465 ;15.590 ; 0.500 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT REMARK 3 U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 3UFJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-NOV-11. REMARK 100 THE DEPOSITION ID IS D_1000068690. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-MAY-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.3 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL7-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : SIDE SCATTERING I-BEAM BENT REMARK 200 SINGLE CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17456 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.967 REMARK 200 RESOLUTION RANGE LOW (A) : 140.761 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 11.00 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.97 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.04 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 11.30 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.100 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: PDB ENTRY 2RBA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.32 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.82 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG3350, 0.2 M POTASSIUM SODIUM REMARK 280 TARTRATE TETRAHYDRATE, PH 7.3, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 36.63933 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 18.31967 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 27.47950 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 9.15983 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 45.79917 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 APPLY THE FOLLOWING TO CHAINS: A, B, 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 GLY A 105 REMARK 465 SER A 106 REMARK 465 HIS A 107 REMARK 465 MET A 108 REMARK 465 ALA A 109 REMARK 465 SER A 110 REMARK 465 PHE A 111 REMARK 465 ASN A 112 REMARK 465 GLY A 113 REMARK 465 VAL A 114 REMARK 465 SER A 115 REMARK 465 GLU A 116 REMARK 465 ALA A 117 REMARK 465 GLU A 118 REMARK 465 LEU A 119 REMARK 465 ASN A 305 REMARK 465 MET A 306 REMARK 465 ASP A 307 REMARK 465 VAL A 308 REMARK 465 GLY B 105 REMARK 465 SER B 106 REMARK 465 HIS B 107 REMARK 465 MET B 108 REMARK 465 ALA B 109 REMARK 465 SER B 110 REMARK 465 PHE B 111 REMARK 465 ASN B 112 REMARK 465 GLY B 113 REMARK 465 VAL B 114 REMARK 465 SER B 115 REMARK 465 GLU B 116 REMARK 465 ALA B 117 REMARK 465 GLU B 118 REMARK 465 LEU B 119 REMARK 465 LEU B 120 REMARK 465 THR B 121 REMARK 465 LYS B 122 REMARK 465 ASN B 305 REMARK 465 MET B 306 REMARK 465 ASP B 307 REMARK 465 VAL B 308 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 LEU A 120 CG CD1 CD2 REMARK 470 THR A 121 OG1 CG2 REMARK 470 LYS A 122 CG CD CE NZ REMARK 470 LYS A 148 CD CE NZ REMARK 470 LYS A 161 CG CD CE NZ REMARK 470 MET A 165 CG SD CE REMARK 470 LYS A 184 CE NZ REMARK 470 LYS A 201 CG CD CE NZ REMARK 470 LYS A 206 CG CD CE NZ REMARK 470 ARG A 209 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 210 CG CD OE1 OE2 REMARK 470 LYS A 232 CG CD CE NZ REMARK 470 GLU A 236 CG CD OE1 OE2 REMARK 470 ILE A 237 CG1 CG2 CD1 REMARK 470 SER A 239 OG REMARK 470 LYS A 240 CG CD CE NZ REMARK 470 GLU A 241 CG CD OE1 OE2 REMARK 470 VAL A 242 CG1 CG2 REMARK 470 VAL A 245 CG1 CG2 REMARK 470 LYS A 246 CG CD CE NZ REMARK 470 VAL A 247 CG1 CG2 REMARK 470 LYS A 248 CG CD CE NZ REMARK 470 ASN A 249 CG OD1 ND2 REMARK 470 GLU A 251 CG CD OE1 OE2 REMARK 470 GLN A 278 CG CD OE1 NE2 REMARK 470 PHE A 279 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ARG A 281 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 283 CG CD OE1 NE2 REMARK 470 LYS A 285 CG CD CE NZ REMARK 470 ILE A 290 CG1 CG2 CD1 REMARK 470 LYS A 291 CG CD CE NZ REMARK 470 LYS A 300 CG CD CE NZ REMARK 470 ILE A 302 CG1 CG2 CD1 REMARK 470 THR B 123 OG1 CG2 REMARK 470 ILE B 134 CG1 CG2 CD1 REMARK 470 LYS B 148 CE NZ REMARK 470 LYS B 161 CG CD CE NZ REMARK 470 MET B 165 CG SD CE REMARK 470 SER B 166 OG REMARK 470 LEU B 168 CD1 CD2 REMARK 470 VAL B 171 CG1 CG2 REMARK 470 HIS B 179 CG ND1 CD2 CE1 NE2 REMARK 470 THR B 180 OG1 CG2 REMARK 470 LEU B 181 CG CD1 CD2 REMARK 470 LYS B 184 CG CD CE NZ REMARK 470 ILE B 187 CG1 CG2 CD1 REMARK 470 GLU B 194 CG CD OE1 OE2 REMARK 470 LYS B 201 CG CD CE NZ REMARK 470 ASP B 202 CG OD1 OD2 REMARK 470 LYS B 206 CG CD CE NZ REMARK 470 ARG B 209 CD NE CZ NH1 NH2 REMARK 470 GLU B 210 CG CD OE1 OE2 REMARK 470 ARG B 213 CG CD NE CZ NH1 NH2 REMARK 470 ILE B 214 CG1 CG2 CD1 REMARK 470 LEU B 215 CD1 CD2 REMARK 470 VAL B 216 CG1 CG2 REMARK 470 GLN B 217 CG CD OE1 NE2 REMARK 470 LYS B 218 CG CD CE NZ REMARK 470 LEU B 219 CG CD1 CD2 REMARK 470 LYS B 221 CG CD CE NZ REMARK 470 LYS B 232 CG CD CE NZ REMARK 470 ILE B 237 CG1 CG2 CD1 REMARK 470 SER B 239 OG REMARK 470 LYS B 240 CG CD CE NZ REMARK 470 GLU B 241 CG CD OE1 OE2 REMARK 470 VAL B 242 CG1 CG2 REMARK 470 VAL B 245 CG1 CG2 REMARK 470 LYS B 246 CG CD CE NZ REMARK 470 LYS B 248 CG CD CE NZ REMARK 470 LEU B 250 CD1 CD2 REMARK 470 GLU B 251 CG CD OE1 OE2 REMARK 470 THR B 262 OG1 CG2 REMARK 470 GLU B 263 CD OE1 OE2 REMARK 470 MET B 269 SD CE REMARK 470 SER B 272 OG REMARK 470 GLN B 278 CG CD OE1 NE2 REMARK 470 PHE B 279 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ARG B 281 NE CZ NH1 NH2 REMARK 470 ASP B 284 CG OD1 OD2 REMARK 470 LYS B 285 CG CD CE NZ REMARK 470 VAL B 286 CG1 CG2 REMARK 470 HIS B 287 CG ND1 CD2 CE1 NE2 REMARK 470 ILE B 290 CG1 CG2 CD1 REMARK 470 LYS B 291 CG CD CE NZ REMARK 470 LYS B 293 CG CD CE NZ REMARK 470 ASP B 294 CG OD1 OD2 REMARK 470 ARG B 296 CG CD NE CZ NH1 NH2 REMARK 470 GLN B 298 CG CD OE1 NE2 REMARK 470 LYS B 300 CG CD CE NZ REMARK 470 ILE B 302 CG1 CG2 CD1 REMARK 470 GLU B 303 CG CD OE1 OE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 N GLY A 156 OP1 DC F 9 1.81 REMARK 500 O PRO A 155 OP1 DC F 9 1.82 REMARK 500 C PRO A 155 OP1 DC F 9 1.98 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 TRP B 160 CE2 TRP B 160 CD2 0.077 REMARK 500 REMARK 500 REMARK: NULL 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 DC F 9 O5' - P - OP1 ANGL. DEV. = -5.4 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 LYS A 122 -32.13 -141.82 REMARK 500 ASN A 131 74.78 55.72 REMARK 500 ASP A 133 -70.09 -70.97 REMARK 500 PRO A 153 -100.54 -74.33 REMARK 500 PRO A 198 -74.97 -32.14 REMARK 500 VAL A 216 -53.79 -28.65 REMARK 500 GLN A 223 66.73 35.00 REMARK 500 ASN A 249 70.55 24.15 REMARK 500 SER A 273 178.24 -49.57 REMARK 500 PHE A 279 68.16 -110.69 REMARK 500 GLU A 303 47.87 -75.59 REMARK 500 ASN B 131 75.53 51.02 REMARK 500 ASP B 133 -77.45 -67.82 REMARK 500 ILE B 139 -70.45 -65.18 REMARK 500 PRO B 153 -99.24 -74.03 REMARK 500 PRO B 155 49.49 -89.59 REMARK 500 PHE B 164 -80.13 -63.64 REMARK 500 THR B 190 -176.55 -171.75 REMARK 500 PRO B 198 -74.99 -33.93 REMARK 500 LYS B 201 -2.52 -58.33 REMARK 500 LEU B 203 -65.88 -92.36 REMARK 500 SER B 204 -120.13 138.28 REMARK 500 SER B 205 -67.83 -170.22 REMARK 500 GLN B 223 74.08 29.64 REMARK 500 GLU B 236 -71.80 -30.73 REMARK 500 ASN B 249 77.26 23.03 REMARK 500 ALA B 274 37.35 -84.16 REMARK 500 ILE B 302 13.02 -69.43 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2RBA RELATED DB: PDB REMARK 900 COMPLEX WITH ABASIC DNA DBREF 3UFJ A 111 308 UNP Q13569 TDG_HUMAN 111 308 DBREF 3UFJ B 111 308 UNP Q13569 TDG_HUMAN 111 308 DBREF 3UFJ C 1 23 PDB 3UFJ 3UFJ 1 23 DBREF 3UFJ E 1 23 PDB 3UFJ 3UFJ 1 23 DBREF 3UFJ D 1 23 PDB 3UFJ 3UFJ 1 23 DBREF 3UFJ F 1 23 PDB 3UFJ 3UFJ 1 23 SEQADV 3UFJ GLY A 105 UNP Q13569 EXPRESSION TAG SEQADV 3UFJ SER A 106 UNP Q13569 EXPRESSION TAG SEQADV 3UFJ HIS A 107 UNP Q13569 EXPRESSION TAG SEQADV 3UFJ MET A 108 UNP Q13569 EXPRESSION TAG SEQADV 3UFJ ALA A 109 UNP Q13569 EXPRESSION TAG SEQADV 3UFJ SER A 110 UNP Q13569 EXPRESSION TAG SEQADV 3UFJ GLY B 105 UNP Q13569 EXPRESSION TAG SEQADV 3UFJ SER B 106 UNP Q13569 EXPRESSION TAG SEQADV 3UFJ HIS B 107 UNP Q13569 EXPRESSION TAG SEQADV 3UFJ MET B 108 UNP Q13569 EXPRESSION TAG SEQADV 3UFJ ALA B 109 UNP Q13569 EXPRESSION TAG SEQADV 3UFJ SER B 110 UNP Q13569 EXPRESSION TAG SEQRES 1 A 204 GLY SER HIS MET ALA SER PHE ASN GLY VAL SER GLU ALA SEQRES 2 A 204 GLU LEU LEU THR LYS THR LEU PRO ASP ILE LEU THR PHE SEQRES 3 A 204 ASN LEU ASP ILE VAL ILE ILE GLY ILE ASN PRO GLY LEU SEQRES 4 A 204 MET ALA ALA TYR LYS GLY HIS HIS TYR PRO GLY PRO GLY SEQRES 5 A 204 ASN HIS PHE TRP LYS CYS LEU PHE MET SER GLY LEU SER SEQRES 6 A 204 GLU VAL GLN LEU ASN HIS MET ASP ASP HIS THR LEU PRO SEQRES 7 A 204 GLY LYS TYR GLY ILE GLY PHE THR ASN MET VAL GLU ARG SEQRES 8 A 204 THR THR PRO GLY SER LYS ASP LEU SER SER LYS GLU PHE SEQRES 9 A 204 ARG GLU GLY GLY ARG ILE LEU VAL GLN LYS LEU GLN LYS SEQRES 10 A 204 TYR GLN PRO ARG ILE ALA VAL PHE ASN GLY LYS CYS ILE SEQRES 11 A 204 TYR GLU ILE PHE SER LYS GLU VAL PHE GLY VAL LYS VAL SEQRES 12 A 204 LYS ASN LEU GLU PHE GLY LEU GLN PRO HIS LYS ILE PRO SEQRES 13 A 204 ASP THR GLU THR LEU CYS TYR VAL MET PRO SER SER SER SEQRES 14 A 204 ALA ARG CYS ALA GLN PHE PRO ARG ALA GLN ASP LYS VAL SEQRES 15 A 204 HIS TYR TYR ILE LYS LEU LYS ASP LEU ARG ASP GLN LEU SEQRES 16 A 204 LYS GLY ILE GLU ARG ASN MET ASP VAL SEQRES 1 B 204 GLY SER HIS MET ALA SER PHE ASN GLY VAL SER GLU ALA SEQRES 2 B 204 GLU LEU LEU THR LYS THR LEU PRO ASP ILE LEU THR PHE SEQRES 3 B 204 ASN LEU ASP ILE VAL ILE ILE GLY ILE ASN PRO GLY LEU SEQRES 4 B 204 MET ALA ALA TYR LYS GLY HIS HIS TYR PRO GLY PRO GLY SEQRES 5 B 204 ASN HIS PHE TRP LYS CYS LEU PHE MET SER GLY LEU SER SEQRES 6 B 204 GLU VAL GLN LEU ASN HIS MET ASP ASP HIS THR LEU PRO SEQRES 7 B 204 GLY LYS TYR GLY ILE GLY PHE THR ASN MET VAL GLU ARG SEQRES 8 B 204 THR THR PRO GLY SER LYS ASP LEU SER SER LYS GLU PHE SEQRES 9 B 204 ARG GLU GLY GLY ARG ILE LEU VAL GLN LYS LEU GLN LYS SEQRES 10 B 204 TYR GLN PRO ARG ILE ALA VAL PHE ASN GLY LYS CYS ILE SEQRES 11 B 204 TYR GLU ILE PHE SER LYS GLU VAL PHE GLY VAL LYS VAL SEQRES 12 B 204 LYS ASN LEU GLU PHE GLY LEU GLN PRO HIS LYS ILE PRO SEQRES 13 B 204 ASP THR GLU THR LEU CYS TYR VAL MET PRO SER SER SER SEQRES 14 B 204 ALA ARG CYS ALA GLN PHE PRO ARG ALA GLN ASP LYS VAL SEQRES 15 B 204 HIS TYR TYR ILE LYS LEU LYS ASP LEU ARG ASP GLN LEU SEQRES 16 B 204 LYS GLY ILE GLU ARG ASN MET ASP VAL SEQRES 1 C 23 DC DA DG DC DT DC DT DG DT DA DC DG DT SEQRES 2 C 23 DG DA DG DC DA DG DT DG DG DA SEQRES 1 D 23 DC DC DA DC DT DG DC DT DC DA UF2 DG DT SEQRES 2 D 23 DA DC DA DG DA DG DC DT DG DT SEQRES 1 E 23 DC DA DG DC DT DC DT DG DT DA DC DG DT SEQRES 2 E 23 DG DA DG DC DA DG DT DG DG DA SEQRES 1 F 23 DC DC DA DC DT DG DC DT DC DA UF2 DG DT SEQRES 2 F 23 DA DC DA DG DA DG DC DT DG DT MODRES 3UFJ UF2 D 11 DU MODRES 3UFJ UF2 F 11 DU HET UF2 D 11 20 HET UF2 F 11 20 HETNAM UF2 1-(2-DEOXY-2-FLUORO-5-O-PHOSPHONO-BETA-D- HETNAM 2 UF2 ARABINOFURANOSYL)PYRIMIDINE-2,4(1H,3H)-DIONE HETSYN UF2 2'-FLUORO-2'-DEOXYURIDINE FORMUL 4 UF2 2(C9 H12 F N2 O8 P) FORMUL 7 HOH *(H2 O) HELIX 1 1 GLY A 142 GLY A 149 1 8 HELIX 2 2 HIS A 158 SER A 166 1 9 HELIX 3 3 ASN A 174 HIS A 179 5 6 HELIX 4 4 THR A 180 GLY A 186 1 7 HELIX 5 5 SER A 204 GLN A 223 1 20 HELIX 6 6 GLY A 231 PHE A 243 1 13 HELIX 7 7 VAL A 286 ILE A 302 1 17 HELIX 8 8 GLY B 142 GLY B 149 1 8 HELIX 9 9 HIS B 158 SER B 166 1 9 HELIX 10 10 ASN B 174 HIS B 179 5 6 HELIX 11 11 THR B 180 GLY B 186 1 7 HELIX 12 12 SER B 205 GLN B 223 1 19 HELIX 13 13 GLY B 231 PHE B 243 1 13 HELIX 14 14 VAL B 286 ILE B 302 1 17 SHEET 1 A 5 ILE A 187 ASN A 191 0 SHEET 2 A 5 ILE A 134 GLY A 138 1 N ILE A 134 O GLY A 188 SHEET 3 A 5 ILE A 226 ASN A 230 1 O VAL A 228 N VAL A 135 SHEET 4 A 5 LEU A 265 MET A 269 1 O LEU A 265 N ALA A 227 SHEET 5 A 5 GLY A 253 GLN A 255 -1 N GLY A 253 O VAL A 268 SHEET 1 B 5 ILE B 187 ASN B 191 0 SHEET 2 B 5 ILE B 134 GLY B 138 1 N GLY B 138 O THR B 190 SHEET 3 B 5 ILE B 226 ASN B 230 1 O VAL B 228 N VAL B 135 SHEET 4 B 5 LEU B 265 MET B 269 1 O LEU B 265 N ALA B 227 SHEET 5 B 5 GLY B 253 LYS B 258 -1 N GLY B 253 O VAL B 268 LINK O3' DA D 10 P UF2 D 11 1555 1555 1.60 LINK O3' DA F 10 P UF2 F 11 1555 1555 1.59 CISPEP 1 THR A 121 LYS A 122 0 -3.50 CISPEP 2 GLY A 154 PRO A 155 0 -13.70 CISPEP 3 PRO A 155 GLY A 156 0 12.33 CISPEP 4 PRO A 198 GLY A 199 0 4.31 CISPEP 5 GLY B 154 PRO B 155 0 2.97 CISPEP 6 PRO B 198 GLY B 199 0 -0.44 CRYST1 162.537 162.537 54.959 90.00 90.00 120.00 P 65 12 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 0.006152 0.003552 0.000000 0.00000 SCALE2 0.000000 0.007104 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018195 0.00000 MTRIX1 1 1.000000 0.000000 0.000000 0.00000 1 MTRIX2 1 0.000000 1.000000 0.000000 0.00000 1 MTRIX3 1 0.000000 0.000000 1.000000 0.00000 1 MTRIX1 2 -0.378435 -0.924920 0.036192 0.21862 1 MTRIX2 2 -0.923551 0.374680 -0.081667 -0.77200 1 MTRIX3 2 0.061975 -0.064331 -0.996002 -17.42732 1