PDB Short entry for 2SSP HEADER PROTEIN/DNA 28-APR-99 2SSP TITLE LEUCINE-272-ALANINE URACIL-DNA GLYCOSYLASE BOUND TO ABASIC SITE- TITLE 2 CONTAINING DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*CP*TP*GP*TP*(AAB)P*AP*TP*CP*TP*T)-3'); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'-D(*AP*AP*AP*GP*AP*TP*AP*AP*CP*AP*G)-3'); COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: PROTEIN (URACIL-DNA GLYCOSYLASE); COMPND 11 CHAIN: E; COMPND 12 FRAGMENT: MITOCHONDRIAL; COMPND 13 SYNONYM: UDG, UNG; COMPND 14 EC: 3.2.2.3; COMPND 15 ENGINEERED: YES; COMPND 16 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES; SOURCE 5 MOL_ID: 3; SOURCE 6 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 7 ORGANISM_COMMON: HUMAN; SOURCE 8 ORGANISM_TAXID: 9606; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DNA GLYCOSYLASE, DNA BASE EXCISION REPAIR, URACIL, DNA, PROTEIN/DNA, KEYWDS 2 ABASIC SITE, PROTEIN-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR S.S.PARIKH,C.D.MOL,G.SLUPPHAUG,S.BHARATI,H.E.KROKAN,J.A.TAINER REVDAT 4 02-AUG-23 2SSP 1 LINK REVDAT 3 09-JUL-14 2SSP 1 HETNAM VERSN REVDAT 2 24-FEB-09 2SSP 1 VERSN REVDAT 1 06-MAY-99 2SSP 0 JRNL AUTH S.S.PARIKH,C.D.MOL,G.SLUPPHAUG,S.BHARATI,H.E.KROKAN, JRNL AUTH 2 J.A.TAINER JRNL TITL BASE EXCISION REPAIR INITIATION REVEALED BY CRYSTAL JRNL TITL 2 STRUCTURES AND BINDING KINETICS OF HUMAN URACIL-DNA JRNL TITL 3 GLYCOSYLASE WITH DNA. JRNL REF EMBO J. V. 17 5214 1998 JRNL REFN ISSN 0261-4189 JRNL PMID 9724657 JRNL DOI 10.1093/EMBOJ/17.17.5214 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH G.SLUPPHAUG,C.D.MOL,B.KAVLI,A.S.ARVAI,H.E.KROKAN,J.A.TAINER REMARK 1 TITL A NUCLEOTIDE-FLIPPING MECHANISM FROM THE STRUCTURE OF HUMAN REMARK 1 TITL 2 URACIL-DNA GLYCOSYLASE BOUND TO DNA REMARK 1 REF NATURE V. 384 87 1996 REMARK 1 REFN ISSN 0028-0836 REMARK 1 DOI 10.1038/384087A0 REMARK 2 REMARK 2 RESOLUTION. 2.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 100000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.1000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.7 REMARK 3 NUMBER OF REFLECTIONS : 17195 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 SET) : 0.184 REMARK 3 FREE R VALUE : 0.257 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 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 : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.25 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.35 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 90.20 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1607 REMARK 3 BIN R VALUE (WORKING SET) : 0.2360 REMARK 3 BIN FREE R VALUE : 0.3070 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 : 1805 REMARK 3 NUCLEIC ACID ATOMS : 417 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 238 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) : -11.30000 REMARK 3 B22 (A**2) : 5.25000 REMARK 3 B33 (A**2) : 6.05000 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 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) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.410 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 : PARHCSDX.PRO REMARK 3 PARAMETER FILE 2 : PARAM_NDBX.DNA REMARK 3 PARAMETER FILE 3 : PARAM19.SOL REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : TOP_NDBX.DNA REMARK 3 TOPOLOGY FILE 3 : TOPH19.SOL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2SSP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY NDB. REMARK 100 THE DEPOSITION ID IS D_1000000969. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-AUG-96 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 6.5 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) : 1.080 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18564 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.250 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 (%) : 97.8 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08200 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.33 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.2 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.23100 REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1AKZ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 4000, 100 MM HEPES PH 6.5, 10% REMARK 280 DIOXANE, 1 MM DITHIOTHREITOL, VAPOR DIFFUSION, HANGING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z REMARK 290 4555 X+1/2,-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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 60.15000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.40000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 60.15000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 24.40000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, 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 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 GLU E 83 -145.59 -165.31 REMARK 500 GLN E 144 -62.24 -91.00 REMARK 500 ASN E 151 51.34 38.94 REMARK 500 GLN E 152 -65.14 -103.81 REMARK 500 HIS E 154 24.54 -150.33 REMARK 500 PHE E 158 -9.50 73.16 REMARK 500 LEU E 202 77.85 -102.17 REMARK 500 REMARK 500 REMARK: NULL DBREF 2SSP E 85 304 UNP P13051 UNG_HUMAN 94 313 DBREF 2SSP A 1 10 PDB 2SSP 2SSP 1 10 DBREF 2SSP B 21 31 PDB 2SSP 2SSP 21 31 SEQRES 1 A 10 DC DT DG DT AAB DA DT DC DT DT SEQRES 1 B 11 DA DA DA DG DA DT DA DA DC DA DG SEQRES 1 E 223 MET GLU PHE PHE GLY GLU SER TRP LYS LYS HIS LEU SER SEQRES 2 E 223 GLY GLU PHE GLY LYS PRO TYR PHE ILE LYS LEU MET GLY SEQRES 3 E 223 PHE VAL ALA GLU GLU ARG LYS HIS TYR THR VAL TYR PRO SEQRES 4 E 223 PRO PRO HIS GLN VAL PHE THR TRP THR GLN MET CYS ASP SEQRES 5 E 223 ILE LYS ASP VAL LYS VAL VAL ILE LEU GLY GLN ASP PRO SEQRES 6 E 223 TYR HIS GLY PRO ASN GLN ALA HIS GLY LEU CYS PHE SER SEQRES 7 E 223 VAL GLN ARG PRO VAL PRO PRO PRO PRO SER LEU GLU ASN SEQRES 8 E 223 ILE TYR LYS GLU LEU SER THR ASP ILE GLU ASP PHE VAL SEQRES 9 E 223 HIS PRO GLY HIS GLY ASP LEU SER GLY TRP ALA LYS GLN SEQRES 10 E 223 GLY VAL LEU LEU LEU ASN ALA VAL LEU THR VAL ARG ALA SEQRES 11 E 223 HIS GLN ALA ASN SER HIS LYS GLU ARG GLY TRP GLU GLN SEQRES 12 E 223 PHE THR ASP ALA VAL VAL SER TRP LEU ASN GLN ASN SER SEQRES 13 E 223 ASN GLY LEU VAL PHE LEU LEU TRP GLY SER TYR ALA GLN SEQRES 14 E 223 LYS LYS GLY SER ALA ILE ASP ARG LYS ARG HIS HIS VAL SEQRES 15 E 223 LEU GLN THR ALA HIS PRO SER PRO ALA SER VAL TYR ARG SEQRES 16 E 223 GLY PHE PHE GLY CYS ARG HIS PHE SER LYS THR ASN GLU SEQRES 17 E 223 LEU LEU GLN LYS SER GLY LYS LYS PRO ILE ASP TRP LYS SEQRES 18 E 223 GLU LEU HET AAB A 5 12 HETNAM AAB 2'-DEOXY-RIBOFURANOSE-5'-MONOPHOSPHATE HETSYN AAB ABASIC DEOXYRIBOSE FORMUL 1 AAB C5 H11 O7 P FORMUL 4 HOH *238(H2 O) HELIX 1 1 GLU E 87 PHE E 97 1 11 HELIX 2 2 PRO E 100 HIS E 115 1 16 HELIX 3 3 PRO E 122 GLN E 124 5 3 HELIX 4 4 THR E 127 GLN E 130 1 4 HELIX 5 5 ILE E 134 ASP E 136 5 3 HELIX 6 6 PRO E 168 ASP E 180 1 13 HELIX 7 7 SER E 193 GLN E 198 1 6 HELIX 8 8 TRP E 222 GLN E 235 1 14 HELIX 9 9 SER E 247 ALA E 255 1 9 HELIX 10 10 PRO E 271 ARG E 276 1 6 HELIX 11 11 HIS E 283 LYS E 293 1 11 SHEET 1 A 4 VAL E 200 ASN E 204 0 SHEET 2 A 4 VAL E 139 GLY E 143 1 N VAL E 139 O LEU E 201 SHEET 3 A 4 VAL E 241 TRP E 245 1 N VAL E 241 O VAL E 140 SHEET 4 A 4 HIS E 262 THR E 266 1 N HIS E 262 O PHE E 242 LINK O3' DT A 4 P AAB A 5 1555 1555 1.60 LINK O3' AAB A 5 P DA A 6 1555 1555 1.60 CISPEP 1 TYR E 119 PRO E 120 0 -0.29 CISPEP 2 ARG E 162 PRO E 163 0 0.74 CRYST1 120.300 48.800 65.600 90.00 90.00 90.00 P 21 21 2 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 0.008312 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020492 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015244 0.00000