HEADER HYDROLASE/DNA 20-FEB-99 4SKN TITLE A NUCLEOTIDE-FLIPPING MECHANISM FROM THE STRUCTURE OF HUMAN URACIL-DNA TITLE 2 GLYCOSYLASE BOUND TO DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*TP*GP*GP*GP*(D1P)P*GP*GP*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*CP*CP*GP*CP*CP*C)-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 SYNONYM: UDG, UNG; COMPND 13 EC: 3.2.2.3; COMPND 14 ENGINEERED: YES; COMPND 15 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, HYDROLASE-DNA KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR G.SLUPPHAUG,C.D.MOL,B.KAVLI,A.S.ARVAI,H.E.KROKAN,J.A.TAINER REVDAT 5 20-SEP-23 4SKN 1 REMARK REVDAT 4 03-NOV-21 4SKN 1 REMARK SEQADV LINK REVDAT 3 24-FEB-09 4SKN 1 VERSN REVDAT 2 14-JUN-00 4SKN 3 ATOM DBREF HEADER REVDAT 1 26-FEB-99 4SKN 0 JRNL AUTH G.SLUPPHAUG,C.D.MOL,B.KAVLI,A.S.ARVAI,H.E.KROKAN,J.A.TAINER JRNL TITL A NUCLEOTIDE-FLIPPING MECHANISM FROM THE STRUCTURE OF HUMAN JRNL TITL 2 URACIL-DNA GLYCOSYLASE BOUND TO DNA. JRNL REF NATURE V. 384 87 1996 JRNL REFN ISSN 0028-0836 JRNL PMID 8900285 JRNL DOI 10.1038/384087A0 REMARK 2 REMARK 2 RESOLUTION. 2.90 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) : 2.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.900 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 100000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.1000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 93.8 REMARK 3 NUMBER OF REFLECTIONS : 6861 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 : 0.273 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 711 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) : 2.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.03 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 6150 REMARK 3 BIN R VALUE (WORKING SET) : 0.3566 REMARK 3 BIN FREE R VALUE : 0.3960 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.60 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 87 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 : 1811 REMARK 3 NUCLEIC ACID ATOMS : 397 REMARK 3 HETEROGEN ATOMS : 8 REMARK 3 SOLVENT ATOMS : 75 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) : 30.49000 REMARK 3 B22 (A**2) : 26.58000 REMARK 3 B33 (A**2) : 3.67000 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) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.392 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.66 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.391 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: REMARK 3 THE ELECTRON DENSITY FOR THE DNA 5' OF THE URACIL-CONTAINING REMARK 3 NUCLEOTIDE IS POOR. REMARK 3 REMARK 3 THE COBALAMIN HAS BEEN MODELLED AS THE 5-COORDINATES REMARK 3 REDUCED COB(II)ALAMIN (B12R), SINCE THERE IS NO ELECTRON REMARK 3 DENSITY FOR AN ADENOSYL GROUP LINKED TO THE COBALT ATOM. REMARK 3 HOWEVER, A HALF-OCCUPIED 5'-DEOXYADENOSINE HAS BEEN BUILT REMARK 3 INTO ELECTRON DENSITY IN THE ACTIVE SITE (RESIDUES A803 AND REMARK 3 AND C803). REMARK 3 REMARK 3 RESIDUES A801 AND A802 (AND C801, C802) REPRESENT AN REMARK 3 EQUIMOLAR MIXTURE OF SUBSTRATE AND PRODUCT, SUCCINYL- AND REMARK 3 METHYLMALONYL-COENZYME A. REMARK 4 REMARK 4 4SKN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-FEB-99. REMARK 100 THE DEPOSITION ID IS D_1000000519. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-APR-96 REMARK 200 TEMPERATURE (KELVIN) : 100 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) : 1.08 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 : 7140 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.900 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 200 DATA REDUNDANCY : 3.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.10800 REMARK 200 FOR THE DATA SET : 7.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.39800 REMARK 200 FOR SHELL : NULL 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 (%): 49.68 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.44 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 6.5 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 24.41500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 48.57500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.83000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 48.57500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.41500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.83000 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 87 -70.74 -40.27 REMARK 500 PRO E 121 159.51 -48.43 REMARK 500 GLN E 144 -81.99 -91.00 REMARK 500 HIS E 148 24.08 -79.22 REMARK 500 GLN E 152 -64.09 -96.21 REMARK 500 ARG E 162 153.11 -49.00 REMARK 500 PRO E 163 31.26 -90.64 REMARK 500 PRO E 168 -57.51 -26.10 REMARK 500 HIS E 186 107.77 -50.96 REMARK 500 HIS E 212 17.87 52.52 REMARK 500 THR E 266 169.81 176.52 REMARK 500 PRO E 269 -0.14 -56.36 REMARK 500 ARG E 276 34.41 -83.48 REMARK 500 ASP E 300 75.62 -104.28 REMARK 500 TRP E 301 -14.47 -49.74 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 URA E 305 DBREF 4SKN E 85 304 UNP P13051 UNG_HUMAN 94 313 DBREF 4SKN A 1 10 PDB 4SKN 4SKN 1 10 DBREF 4SKN B 21 30 PDB 4SKN 4SKN 21 30 SEQADV 4SKN MET E 82 UNP P13051 CLONING ARTIFACT SEQADV 4SKN GLU E 83 UNP P13051 CLONING ARTIFACT SEQADV 4SKN PHE E 84 UNP P13051 CLONING ARTIFACT SEQADV 4SKN ASN E 145 UNP P13051 ASP 145 ENGINEERED MUTATION SEQADV 4SKN ARG E 272 UNP P13051 LEU 272 ENGINEERED MUTATION SEQRES 1 A 10 DT DG DG DG ORP DG DG DC DT DT SEQRES 1 B 10 DA DA DA DG DC DC DG DC DC DC 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 ASN 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 ARG 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 ORP A 5 12 HET URA E 305 8 HETNAM ORP 2-DEOXY-5-PHOSPHONO-RIBOSE HETNAM URA URACIL FORMUL 1 ORP C5 H11 O7 P FORMUL 4 URA C4 H4 N2 O2 FORMUL 5 HOH *75(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' DG A 4 P ORP A 5 1555 1555 1.61 LINK O3 ORP A 5 P DG A 6 1555 1555 1.62 CISPEP 1 TYR E 119 PRO E 120 0 -0.53 CISPEP 2 ARG E 162 PRO E 163 0 0.18 SITE 1 AC1 9 ORP A 5 GLY E 143 GLN E 144 ASN E 145 SITE 2 AC1 9 TYR E 147 CYS E 157 PHE E 158 ASN E 204 SITE 3 AC1 9 HIS E 268 CRYST1 48.830 65.660 97.150 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 0.020479 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015230 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010293 0.00000