HEADER GLYCOSIDASE 27-MAY-97 1AKZ TITLE HUMAN URACIL-DNA GLYCOSYLASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: URACIL-DNA GLYCOSYLASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: UDG, UNG; COMPND 5 EC: 3.2.2.-; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 OTHER_DETAILS: STRUCTURE IS THAT OF RECOMBINANT HUMAN URACIL-DNA COMPND 9 GLYCOSYLASE IN WHICH THE 84 N-TERMINAL AMINO ACIDS CODED FOR BY THE COMPND 10 UNG GENE HAVE BEEN REPLACED BY THREE RESIDUES FROM THE EXPRESSION COMPND 11 VECTOR SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS GLYCOSYLASE, DNA REPAIR, URACIL REMOVAL FROM DNA, ALPHA/ BETA KEYWDS 2 PROTEIN, GLYCOSIDASE EXPDTA X-RAY DIFFRACTION AUTHOR J.A.TAINER,C.D.MOL REVDAT 4 07-FEB-24 1AKZ 1 REMARK REVDAT 3 30-MAR-11 1AKZ 1 AUTHOR REVDAT 2 24-FEB-09 1AKZ 1 VERSN REVDAT 1 20-AUG-97 1AKZ 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 2 REMARK 2 RESOLUTION. 1.57 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.8 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.57 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 100000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.1000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 94.5 REMARK 3 NUMBER OF REFLECTIONS : 30381 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) : 0.189 REMARK 3 FREE R VALUE : 0.224 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.490 REMARK 3 FREE R VALUE TEST SET COUNT : 3048 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) : 1.57 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.64 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.70 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3319 REMARK 3 BIN R VALUE (WORKING SET) : 0.3180 REMARK 3 BIN FREE R VALUE : 0.2860 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.85 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 390 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 : 1808 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 185 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) : 4.90220 REMARK 3 B22 (A**2) : 0.78850 REMARK 3 B33 (A**2) : -5.69080 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) : 1.154 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.96 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.949 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 0.958 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.649 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.746 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.812 ; 2.500 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 : PARAM19.SOL REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : TOPH19.SOL REMARK 3 TOPOLOGY FILE 3 : TOPH19.PEP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: AN OVERALL BULK SOLVENT CORRECTION WAS REMARK 3 APPLIED TO THE DATA. REMARK 4 REMARK 4 1AKZ 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_1000170946. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : FEB-95 REMARK 200 TEMPERATURE (KELVIN) : 275 REMARK 200 PH : 7.9 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) : 1.08 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 : 30433 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.570 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.5 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.04600 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.57 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.61 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.4 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.10600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 11.00 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MULTIPLE ISOMORPHOUS REMARK 200 REPLACEMENT REMARK 200 SOFTWARE USED: PHASES, SQUASH REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.25 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM IMIDAZOLE/MALEATE, PH 7.9, 1% REMARK 280 -4% SATURATED NACL, 1%-4% SATURATED AMMONIUM SULFATE, 16%-20% REMARK 280 PEG 4000, MIXED WITH EQUAL VOLUMES 30 MG/ML PROTEIN. REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 23.88000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 42.48500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.63500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 42.48500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.88000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 27.63500 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: 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 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 144 -71.94 -109.25 REMARK 500 HIS A 154 25.56 -140.45 REMARK 500 PHE A 158 -16.92 67.34 REMARK 500 REMARK 500 REMARK: NULL DBREF 1AKZ A 85 304 UNP P13051 UNG_HUMAN 85 304 SEQRES 1 A 223 MET GLU PHE PHE GLY GLU SER TRP LYS LYS HIS LEU SER SEQRES 2 A 223 GLY GLU PHE GLY LYS PRO TYR PHE ILE LYS LEU MET GLY SEQRES 3 A 223 PHE VAL ALA GLU GLU ARG LYS HIS TYR THR VAL TYR PRO SEQRES 4 A 223 PRO PRO HIS GLN VAL PHE THR TRP THR GLN MET CYS ASP SEQRES 5 A 223 ILE LYS ASP VAL LYS VAL VAL ILE LEU GLY GLN ASP PRO SEQRES 6 A 223 TYR HIS GLY PRO ASN GLN ALA HIS GLY LEU CYS PHE SER SEQRES 7 A 223 VAL GLN ARG PRO VAL PRO PRO PRO PRO SER LEU GLU ASN SEQRES 8 A 223 ILE TYR LYS GLU LEU SER THR ASP ILE GLU ASP PHE VAL SEQRES 9 A 223 HIS PRO GLY HIS GLY ASP LEU SER GLY TRP ALA LYS GLN SEQRES 10 A 223 GLY VAL LEU LEU LEU ASN ALA VAL LEU THR VAL ARG ALA SEQRES 11 A 223 HIS GLN ALA ASN SER HIS LYS GLU ARG GLY TRP GLU GLN SEQRES 12 A 223 PHE THR ASP ALA VAL VAL SER TRP LEU ASN GLN ASN SER SEQRES 13 A 223 ASN GLY LEU VAL PHE LEU LEU TRP GLY SER TYR ALA GLN SEQRES 14 A 223 LYS LYS GLY SER ALA ILE ASP ARG LYS ARG HIS HIS VAL SEQRES 15 A 223 LEU GLN THR ALA HIS PRO SER PRO LEU SER VAL TYR ARG SEQRES 16 A 223 GLY PHE PHE GLY CYS ARG HIS PHE SER LYS THR ASN GLU SEQRES 17 A 223 LEU LEU GLN LYS SER GLY LYS LYS PRO ILE ASP TRP LYS SEQRES 18 A 223 GLU LEU FORMUL 2 HOH *185(H2 O) HELIX 1 1 GLU A 87 GLY A 98 1 12 HELIX 2 2 PRO A 100 HIS A 115 1 16 HELIX 3 3 PRO A 122 GLN A 124 5 3 HELIX 4 4 THR A 127 THR A 129 5 3 HELIX 5 5 ILE A 134 ASP A 136 5 3 HELIX 6 6 PRO A 168 ASP A 180 1 13 HELIX 7 7 SER A 193 GLN A 198 1 6 HELIX 8 8 TRP A 222 ASN A 236 1 15 HELIX 9 9 SER A 247 ALA A 255 1 9 HELIX 10 10 VAL A 274 ARG A 276 5 3 HELIX 11 11 HIS A 283 SER A 294 1 12 SHEET 1 A 4 VAL A 200 ASN A 204 0 SHEET 2 A 4 VAL A 139 GLY A 143 1 N VAL A 139 O LEU A 201 SHEET 3 A 4 VAL A 241 TRP A 245 1 N VAL A 241 O VAL A 140 SHEET 4 A 4 HIS A 262 THR A 266 1 N HIS A 262 O PHE A 242 CISPEP 1 TYR A 119 PRO A 120 0 -1.36 CISPEP 2 ARG A 162 PRO A 163 0 0.54 CRYST1 47.760 55.270 84.970 90.00 90.00 90.00 P 21 21 21 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 0.020938 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018093 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011769 0.00000