HEADER HYDROLASE 30-OCT-95 1UDH TITLE THE STRUCTURAL BASIS OF SPECIFIC BASE EXCISION REPAIR BY URACIL-DNA TITLE 2 GLYCOSYLASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: URACIL-DNA GLYCOSYLASE; COMPND 3 CHAIN: A; COMPND 4 EC: 3.2.2.3; COMPND 5 OTHER_DETAILS: ENCODED BY THE UL2 ORF OF HERPES SIMPLEX VIRUS TYPE 1 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HERPES SIMPLEX VIRUS (TYPE 1 / STRAIN 17); SOURCE 3 ORGANISM_TAXID: 10299; SOURCE 4 STRAIN: 17 KEYWDS HYDROLASE, DNA-N-GLYCOSIDASE EXPDTA X-RAY DIFFRACTION AUTHOR L.H.PEARL,R.SAVVA REVDAT 4 14-FEB-24 1UDH 1 REMARK REVDAT 3 24-FEB-09 1UDH 1 VERSN REVDAT 2 01-APR-03 1UDH 1 JRNL REVDAT 1 08-MAR-96 1UDH 0 JRNL AUTH R.SAVVA,K.MCAULEY-HECHT,T.BROWN,L.PEARL JRNL TITL THE STRUCTURAL BASIS OF SPECIFIC BASE-EXCISION REPAIR BY JRNL TITL 2 URACIL-DNA GLYCOSYLASE. JRNL REF NATURE V. 373 487 1995 JRNL REFN ISSN 0028-0836 JRNL PMID 7845459 JRNL DOI 10.1038/373487A0 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH R.SAVVA,L.H.PEARL REMARK 1 TITL CRYSTALLIZATION AND PRELIMINARY X-RAY ANALYSIS OF THE REMARK 1 TITL 2 URACIL-DNA GLYCOSYLASE DNA REPAIR ENZYME FROM HERPES SIMPLEX REMARK 1 TITL 3 VIRUS TYPE 1 REMARK 1 REF J.MOL.BIOL. V. 234 910 1993 REMARK 1 REFN ISSN 0022-2836 REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 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) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 21818 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.237 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL 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) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL 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 : 1826 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 18 REMARK 3 SOLVENT ATOMS : 94 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 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) : 0.014 REMARK 3 BOND ANGLES (DEGREES) : 1.860 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) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1UDH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000176921. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.87 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21944 REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.2 REMARK 200 DATA REDUNDANCY : 2.100 REMARK 200 R MERGE (I) : 0.02900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.05 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 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 16.38667 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 32.77333 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 ASP A 2 REMARK 465 LEU A 3 REMARK 465 THR A 4 REMARK 465 ASN A 5 REMARK 465 GLY A 6 REMARK 465 GLY A 7 REMARK 465 VAL A 8 REMARK 465 SER A 9 REMARK 465 PRO A 10 REMARK 465 ALA A 11 REMARK 465 ALA A 12 REMARK 465 THR A 13 REMARK 465 SER A 14 REMARK 465 ALA A 15 REMARK 465 PRO A 16 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 ARG A 73 NE - CZ - NH2 ANGL. DEV. = -3.4 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 GLN A 87 -84.35 -93.33 REMARK 500 HIS A 97 21.38 -146.10 REMARK 500 PHE A 101 -25.60 70.83 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 SO4 A 245 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 246 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE URA A 247 DBREF 1UDH A 1 244 UNP P10186 UNG_HHV11 91 334 SEQRES 1 A 244 MET ASP LEU THR ASN GLY GLY VAL SER PRO ALA ALA THR SEQRES 2 A 244 SER ALA PRO LEU ASP TRP THR THR PHE ARG ARG VAL PHE SEQRES 3 A 244 LEU ILE ASP ASP ALA TRP ARG PRO LEU MET GLU PRO GLU SEQRES 4 A 244 LEU ALA ASN PRO LEU THR ALA HIS LEU LEU ALA GLU TYR SEQRES 5 A 244 ASN ARG ARG CYS GLN THR GLU GLU VAL LEU PRO PRO ARG SEQRES 6 A 244 GLU ASP VAL PHE SER TRP THR ARG TYR CYS THR PRO ASP SEQRES 7 A 244 GLU VAL ARG VAL VAL ILE ILE GLY GLN ASP PRO TYR HIS SEQRES 8 A 244 HIS PRO GLY GLN ALA HIS GLY LEU ALA PHE SER VAL ARG SEQRES 9 A 244 ALA ASN VAL PRO PRO PRO PRO SER LEU ARG ASN VAL LEU SEQRES 10 A 244 ALA ALA VAL LYS ASN CYS TYR PRO GLU ALA ARG MET SER SEQRES 11 A 244 GLY HIS GLY CYS LEU GLU LYS TRP ALA ARG ASP GLY VAL SEQRES 12 A 244 LEU LEU LEU ASN THR THR LEU THR VAL LYS ARG GLY ALA SEQRES 13 A 244 ALA ALA SER HIS SER ARG ILE GLY TRP ASP ARG PHE VAL SEQRES 14 A 244 GLY GLY VAL ILE ARG ARG LEU ALA ALA ARG ARG PRO GLY SEQRES 15 A 244 LEU VAL PHE MET LEU TRP GLY THR HIS ALA GLN ASN ALA SEQRES 16 A 244 ILE ARG PRO ASP PRO ARG VAL HIS CYS VAL LEU LYS PHE SEQRES 17 A 244 SER HIS PRO SER PRO LEU SER LYS VAL PRO PHE GLY THR SEQRES 18 A 244 CYS GLN HIS PHE LEU VAL ALA ASN ARG TYR LEU GLU THR SEQRES 19 A 244 ARG SER ILE SER PRO ILE ASP TRP SER VAL HET SO4 A 245 5 HET SO4 A 246 5 HET URA A 247 8 HETNAM SO4 SULFATE ION HETNAM URA URACIL FORMUL 2 SO4 2(O4 S 2-) FORMUL 4 URA C4 H4 N2 O2 FORMUL 5 HOH *94(H2 O) HELIX 1 1 ASP A 18 PHE A 26 1 9 HELIX 2 2 ASP A 30 LEU A 40 5 11 HELIX 3 3 PRO A 43 THR A 58 1 16 HELIX 4 4 ARG A 65 ASP A 67 5 3 HELIX 5 5 SER A 70 THR A 72 5 3 HELIX 6 6 PRO A 77 GLU A 79 5 3 HELIX 7 7 PRO A 111 CYS A 123 1 13 HELIX 8 8 GLU A 136 ARG A 140 1 5 HELIX 9 9 TRP A 165 ARG A 179 1 15 HELIX 10 10 THR A 190 ALA A 195 1 6 HELIX 11 11 PHE A 219 THR A 221 5 3 HELIX 12 12 HIS A 224 ARG A 235 1 12 SHEET 1 A 4 VAL A 143 ASN A 147 0 SHEET 2 A 4 VAL A 82 GLY A 86 1 N VAL A 82 O LEU A 144 SHEET 3 A 4 VAL A 184 TRP A 188 1 N VAL A 184 O VAL A 83 SHEET 4 A 4 CYS A 204 PHE A 208 1 N CYS A 204 O PHE A 185 CISPEP 1 LEU A 62 PRO A 63 0 -0.69 SITE 1 AC1 7 ARG A 54 GLN A 57 GLY A 189 THR A 190 SITE 2 AC1 7 SER A 209 HIS A 210 SER A 215 SITE 1 AC2 7 PRO A 111 SER A 112 URA A 247 HOH A 265 SITE 2 AC2 7 HOH A 290 HOH A 322 HOH A 341 SITE 1 AC3 10 GLY A 86 GLN A 87 ASP A 88 TYR A 90 SITE 2 AC3 10 ALA A 100 PHE A 101 ASN A 147 SO4 A 246 SITE 3 AC3 10 HOH A 303 HOH A 339 CRYST1 65.140 65.140 49.160 90.00 90.00 120.00 P 31 3 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 0.015352 0.008863 0.000000 0.00000 SCALE2 0.000000 0.017726 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020342 0.00000