HEADER HYDROLASE/DNA 19-MAR-03 1OE6 TITLE XENOPUS SMUG1, AN ANTI-MUTATOR URACIL-DNA GLYCOSYLASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: SINGLE-STRAND SELECTIVE MONOFUNCTIONAL URACIL DNA COMPND 3 GLYCOSYLASE; COMPND 4 CHAIN: A, B; COMPND 5 FRAGMENT: RESIDUES 1-247; COMPND 6 SYNONYM: SMUG1; COMPND 7 EC: 3.2.2.-; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: 5'-D(*CP*CP*CP*GP*TP*GP*AP*GP*TP*CP*CP*G)-3'; COMPND 11 CHAIN: E; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: 5'-D(*CP*GP*GP*AP*CP*TP*3DRP*AP*CP*GP*GP*G)-3'; COMPND 14 CHAIN: F SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: XENOPUS LAEVIS; SOURCE 3 ORGANISM_COMMON: AFRICAN CLAWED FROG; SOURCE 4 ORGANISM_TAXID: 8355; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 SYNTHETIC: YES; SOURCE 9 MOL_ID: 3; SOURCE 10 SYNTHETIC: YES KEYWDS HYDROLASE-DNA COMPLEX, HYDROLASE, DNA GLYCOSYLASE, SINGLE STRANDED EXPDTA X-RAY DIFFRACTION AUTHOR J.E.A.WIBLEY,L.H.PEARL REVDAT 4 17-JUL-13 1OE6 1 HEADER COMPND KEYWDS JRNL REVDAT 4 2 REMARK VERSN DBREF SEQRES REVDAT 4 3 HETSYN FORMUL LINK SITE REVDAT 4 4 ATOM HETATM TER CONECT REVDAT 4 5 MASTER REVDAT 3 03-NOV-09 1OE6 1 VERSN REVDAT 2 24-FEB-09 1OE6 1 VERSN REVDAT 1 11-JUL-03 1OE6 0 JRNL AUTH J.E.A.WIBLEY,T.R.WATERS,K.HAUSHALTER,G.L.VERDINE,L.H.PEARL JRNL TITL STRUCTURE AND SPECIFICITY OF THE VERTEBRATE ANTI-MUTATOR JRNL TITL 2 URACIL-DNA GLYCOSYLASE SMUG1 JRNL REF MOL.CELL V. 11 1647 2003 JRNL REFN ISSN 1097-2765 JRNL PMID 12820976 JRNL DOI 10.1016/S1097-2765(03)00235-1 REMARK 2 REMARK 2 RESOLUTION. 2.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.24 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 69.01 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 19561 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) : 0.157 REMARK 3 R VALUE (WORKING SET) : 0.154 REMARK 3 FREE R VALUE : 0.218 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 1063 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) : 2.65 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.72 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1330 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2440 REMARK 3 BIN FREE R VALUE SET COUNT : 73 REMARK 3 BIN FREE R VALUE : 0.3360 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3877 REMARK 3 NUCLEIC ACID ATOMS : 467 REMARK 3 HETEROGEN ATOMS : 45 REMARK 3 SOLVENT ATOMS : 110 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 44.55 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.72000 REMARK 3 B22 (A**2) : -0.08000 REMARK 3 B33 (A**2) : 0.56000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 2.30000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.716 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.283 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.179 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.562 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.961 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.924 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4562 ; 0.051 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 3889 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6290 ; 4.073 ; 2.102 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9193 ; 3.405 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 490 ; 9.143 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 658 ; 0.212 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4673 ; 0.018 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 801 ; 0.012 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1087 ; 0.315 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 4565 ; 0.298 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 2696 ; 0.127 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 153 ; 0.296 ; 0.200 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): 11 ; 0.162 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 63 ; 0.277 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 3 ; 0.095 ; 0.200 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): 2453 ; 1.836 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3976 ; 3.316 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2109 ; 5.112 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2300 ; 8.203 ; 4.500 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 : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE REMARK 3 RIDING POSITIONS REMARK 4 REMARK 4 1OE6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 17-JUN-03. REMARK 100 THE PDBE ID CODE IS EBI-12403. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-NOV-02 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.934 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20624 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.650 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : 0.09200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.79 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.90 REMARK 200 R MERGE FOR SHELL (I) : 0.43800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: OTHER REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NATIVE STRUCTURE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.6 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.88 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 60.48450 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 43.25900 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 60.48450 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 43.25900 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4680 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25000 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -4.0 KCAL/MOL 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 THR A 35 REMARK 465 GLU A 36 REMARK 465 GLY A 281 REMARK 465 THR B 35 REMARK 465 GLY B 281 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 SER A 37 O HOH A 2001 2.02 REMARK 500 C CYS A 205 C1 A IPA A 1285 2.18 REMARK 500 N ASP A 206 C1 A IPA A 1285 2.11 REMARK 500 N ASP A 206 C1 B IPA A 1285 2.12 REMARK 500 C ASP A 206 O2 A IPA A 1285 1.97 REMARK 500 N GLU A 207 O2 A IPA A 1285 1.52 REMARK 500 N GLU A 207 C2 A IPA A 1285 1.65 REMARK 500 N GLU A 207 C2 B IPA A 1285 1.66 REMARK 500 N GLU A 207 O2 B IPA A 1285 1.99 REMARK 500 O LEU B 51 OG SER B 54 2.13 REMARK 500 O HOH A 2016 O HOH A 2051 1.58 REMARK 500 O HOH B 2007 O HOH B 2019 1.86 REMARK 500 O HOH B 2007 O HOH B 2045 1.29 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 ALA A 39 CA ALA A 39 CB -0.153 REMARK 500 GLU A 46 CD GLU A 46 OE2 0.173 REMARK 500 GLU A 48 CD GLU A 48 OE1 0.074 REMARK 500 GLU A 48 CD GLU A 48 OE2 0.131 REMARK 500 GLU A 48 CG GLU A 48 CD 0.092 REMARK 500 ASP A 60 CB ASP A 60 CG 0.185 REMARK 500 VAL A 62 CB VAL A 62 CG1 0.143 REMARK 500 TYR A 66 CD2 TYR A 66 CE2 -0.122 REMARK 500 PRO A 68 CA PRO A 68 C -0.129 REMARK 500 TYR A 79 CD2 TYR A 79 CE2 -0.103 REMARK 500 TYR A 79 CG TYR A 79 CD1 -0.125 REMARK 500 LYS A 87 CD LYS A 87 CE 0.209 REMARK 500 VAL A 90 CA VAL A 90 CB -0.146 REMARK 500 MET A 95 CG MET A 95 SD 0.168 REMARK 500 VAL A 112 CA VAL A 112 CB -0.149 REMARK 500 VAL A 115 CB VAL A 115 CG1 -0.213 REMARK 500 ARG A 116 CA ARG A 116 CB -0.152 REMARK 500 LYS A 127 CD LYS A 127 CE 0.216 REMARK 500 GLU A 129 CD GLU A 129 OE1 0.067 REMARK 500 GLU A 129 CD GLU A 129 OE2 0.098 REMARK 500 GLU A 129 CG GLU A 129 CD 0.097 REMARK 500 VAL A 130 CB VAL A 130 CG2 -0.148 REMARK 500 ARG A 136 C ARG A 136 O -0.117 REMARK 500 GLU A 141 CD GLU A 141 OE2 -0.076 REMARK 500 GLU A 146 CD GLU A 146 OE1 0.171 REMARK 500 GLU A 146 CG GLU A 146 CD 0.090 REMARK 500 PHE A 152 N PHE A 152 CA -0.134 REMARK 500 GLU A 164 CD GLU A 164 OE1 0.112 REMARK 500 CYS A 170 CB CYS A 170 SG -0.111 REMARK 500 PHE A 180 CE2 PHE A 180 CZ 0.122 REMARK 500 GLU A 203 CD GLU A 203 OE1 0.075 REMARK 500 GLU A 203 CD GLU A 203 OE2 0.080 REMARK 500 ASP A 206 C ASP A 206 O -0.122 REMARK 500 ASP A 206 N ASP A 206 CA 0.123 REMARK 500 GLU A 207 CD GLU A 207 OE1 0.138 REMARK 500 GLU A 207 CG GLU A 207 CD 0.142 REMARK 500 GLU A 207 N GLU A 207 CA 0.176 REMARK 500 GLN A 211 CG GLN A 211 CD 0.164 REMARK 500 VAL A 218 CB VAL A 218 CG2 0.153 REMARK 500 SER A 228 CB SER A 228 OG -0.080 REMARK 500 GLU A 229 C GLU A 229 O 0.136 REMARK 500 ARG A 233 NE ARG A 233 CZ 0.099 REMARK 500 MET A 237 CG A MET A 237 SD A 0.192 REMARK 500 MET A 237 SD A MET A 237 CE A 0.363 REMARK 500 VAL A 245 C VAL A 245 O -0.119 REMARK 500 LYS A 260 CD LYS A 260 CE 0.164 REMARK 500 GLU A 272 CD GLU A 272 OE1 0.080 REMARK 500 GLU A 272 CD GLU A 272 OE2 0.136 REMARK 500 GLU B 36 CB GLU B 36 CG 0.157 REMARK 500 GLU B 36 CD GLU B 36 OE1 0.112 REMARK 500 REMARK 500 THIS ENTRY HAS 190 BOND DEVIATIONS. 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 VAL A 45 CB - CA - C ANGL. DEV. = -12.5 DEGREES REMARK 500 GLU A 46 OE1 - CD - OE2 ANGL. DEV. = 8.1 DEGREES REMARK 500 LYS A 52 CD - CE - NZ ANGL. DEV. = -18.8 DEGREES REMARK 500 ASP A 60 CB - CG - OD2 ANGL. DEV. = 8.2 DEGREES REMARK 500 PRO A 61 N - CD - CG ANGL. DEV. = 9.4 DEGREES REMARK 500 PRO A 68 N - CD - CG ANGL. DEV. = -9.3 DEGREES REMARK 500 GLU A 77 OE1 - CD - OE2 ANGL. DEV. = 7.8 DEGREES REMARK 500 MET A 95 CG - SD - CE ANGL. DEV. = 13.1 DEGREES REMARK 500 SER A 126 CB - CA - C ANGL. DEV. = 12.9 DEGREES REMARK 500 GLU A 146 CA - CB - CG ANGL. DEV. = 13.6 DEGREES REMARK 500 GLU A 146 CG - CD - OE1 ANGL. DEV. = 13.6 DEGREES REMARK 500 GLU A 146 CG - CD - OE2 ANGL. DEV. = -12.6 DEGREES REMARK 500 ARG A 151 NE - CZ - NH1 ANGL. DEV. = 6.1 DEGREES REMARK 500 ARG A 151 NE - CZ - NH2 ANGL. DEV. = -6.7 DEGREES REMARK 500 CYS A 160 CB - CA - C ANGL. DEV. = -10.6 DEGREES REMARK 500 GLY A 161 N - CA - C ANGL. DEV. = 19.1 DEGREES REMARK 500 CYS A 170 CA - CB - SG ANGL. DEV. = -7.5 DEGREES REMARK 500 CYS A 170 CB - CA - C ANGL. DEV. = -8.2 DEGREES REMARK 500 ASP A 192 CB - CG - OD2 ANGL. DEV. = 8.1 DEGREES REMARK 500 ASP A 199 CB - CG - OD2 ANGL. DEV. = 7.3 DEGREES REMARK 500 CYS A 205 CA - CB - SG ANGL. DEV. = -7.0 DEGREES REMARK 500 CYS A 205 CB - CA - C ANGL. DEV. = -8.2 DEGREES REMARK 500 ASP A 206 CB - CG - OD1 ANGL. DEV. = 6.8 DEGREES REMARK 500 GLU A 207 CA - CB - CG ANGL. DEV. = 14.6 DEGREES REMARK 500 GLU A 207 C - N - CA ANGL. DEV. = 17.9 DEGREES REMARK 500 VAL A 224 N - CA - C ANGL. DEV. = -19.2 DEGREES REMARK 500 ARG A 233 NE - CZ - NH2 ANGL. DEV. = 5.4 DEGREES REMARK 500 LYS A 234 CD - CE - NZ ANGL. DEV. = 15.6 DEGREES REMARK 500 MET A 249 CG - SD - CE ANGL. DEV. = -10.0 DEGREES REMARK 500 ARG A 267 NE - CZ - NH2 ANGL. DEV. = -4.0 DEGREES REMARK 500 THR A 280 CA - CB - CG2 ANGL. DEV. = 12.8 DEGREES REMARK 500 THR A 280 CA - C - O ANGL. DEV. = 16.2 DEGREES REMARK 500 THR A 280 CB - CA - C ANGL. DEV. = 18.3 DEGREES REMARK 500 VAL B 45 CB - CA - C ANGL. DEV. = -12.6 DEGREES REMARK 500 LYS B 52 CD - CE - NZ ANGL. DEV. = -15.7 DEGREES REMARK 500 LEU B 56 CA - CB - CG ANGL. DEV. = 20.0 DEGREES REMARK 500 VAL B 57 CB - CA - C ANGL. DEV. = 11.6 DEGREES REMARK 500 ASP B 60 CB - CG - OD2 ANGL. DEV. = 5.8 DEGREES REMARK 500 VAL B 130 CG1 - CB - CG2 ANGL. DEV. = 9.8 DEGREES REMARK 500 ARG B 138 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 LEU B 155 CA - CB - CG ANGL. DEV. = 15.2 DEGREES REMARK 500 CYS B 170 CB - CA - C ANGL. DEV. = -8.0 DEGREES REMARK 500 ASP B 192 CB - CG - OD2 ANGL. DEV. = 6.3 DEGREES REMARK 500 GLN B 197 N - CA - CB ANGL. DEV. = 11.8 DEGREES REMARK 500 ARG B 198 NE - CZ - NH1 ANGL. DEV. = 5.3 DEGREES REMARK 500 GLU B 203 CA - CB - CG ANGL. DEV. = 13.2 DEGREES REMARK 500 ASP B 206 CB - CG - OD1 ANGL. DEV. = 6.4 DEGREES REMARK 500 ARG B 226 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ASP B 242 CB - CG - OD2 ANGL. DEV. = 6.3 DEGREES REMARK 500 PRO B 251 N - CD - CG ANGL. DEV. = 10.4 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 258 ANGLE DEVIATIONS. 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 59 -163.59 -170.17 REMARK 500 ASP A 60 -96.40 101.95 REMARK 500 VAL A 70 -65.99 -96.75 REMARK 500 MET A 95 -61.20 -94.77 REMARK 500 PHE A 109 37.41 37.91 REMARK 500 SER A 126 -146.24 -94.06 REMARK 500 ARG A 135 48.77 -141.26 REMARK 500 CYS A 142 115.82 -37.92 REMARK 500 ASP A 206 -63.37 -26.43 REMARK 500 GLU A 207 -79.37 -41.31 REMARK 500 ALA A 208 -59.70 -28.46 REMARK 500 LYS A 246 -166.38 -129.41 REMARK 500 LEU A 276 -29.25 -39.60 REMARK 500 ASN B 55 7.34 -69.10 REMARK 500 ASP B 60 -82.44 95.30 REMARK 500 PRO B 68 1.79 -62.83 REMARK 500 VAL B 70 -75.59 -87.03 REMARK 500 SER B 86 170.72 169.35 REMARK 500 MET B 95 -78.11 -78.42 REMARK 500 SER B 126 -143.00 -111.35 REMARK 500 PHE B 140 2.18 -69.98 REMARK 500 LYS B 195 101.62 1.16 REMARK 500 ALA B 196 -86.66 136.73 REMARK 500 ALA B 238 9.07 -65.19 REMARK 500 GLU B 239 31.33 -148.36 REMARK 500 LYS B 246 -160.53 -104.71 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLN A 59 ASP A 60 141.73 REMARK 500 GLN B 59 ASP B 60 135.23 REMARK 500 LEU B 279 THR B 280 -145.91 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 ASP A 206 24.8 L L OUTSIDE RANGE REMARK 500 ALA A 208 24.9 L L OUTSIDE RANGE REMARK 500 VAL A 215 17.9 L L OUTSIDE RANGE REMARK 500 THR A 280 20.7 L L OUTSIDE RANGE REMARK 500 GLN B 197 18.9 L L OUTSIDE RANGE REMARK 500 CYS B 205 24.6 L L OUTSIDE RANGE REMARK 500 ASP B 242 23.5 L L OUTSIDE RANGE REMARK 500 LEU B 279 46.4 L L OUTSIDE RANGE 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 HMU A1282 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HMU A1283 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A1284 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IPA A1285 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1OE4 RELATED DB: PDB REMARK 900 XENOPUS SMUG1, AN ANTI-MUTATOR URACIL-DNA REMARK 900 GLYCOSYLASE REMARK 900 RELATED ID: 1OE5 RELATED DB: PDB REMARK 900 XENOPUS SMUG1, AN ANTI-MUTATOR URACIL-DNA REMARK 900 GLYCOSYLASE REMARK 999 REMARK 999 SEQUENCE REMARK 999 RESIDUES 3DR IN CHAIN F IS THE RESULT OF DEGLYCOSYLATION REMARK 999 OF DEOXYURACIL DBREF 1OE6 A 35 281 UNP Q9YGN6 Q9YGN6 1 247 DBREF 1OE6 B 35 281 UNP Q9YGN6 Q9YGN6 1 247 DBREF 1OE6 E 281 292 PDB 1OE6 1OE6 281 292 DBREF 1OE6 F 293 304 PDB 1OE6 1OE6 293 304 SEQRES 1 A 247 THR GLU SER PRO ALA ASP SER PHE LEU LYS VAL GLU LEU SEQRES 2 A 247 GLU LEU ASN LEU LYS LEU SER ASN LEU VAL PHE GLN ASP SEQRES 3 A 247 PRO VAL GLN TYR VAL TYR ASN PRO LEU VAL TYR ALA TRP SEQRES 4 A 247 ALA PRO HIS GLU ASN TYR VAL GLN THR TYR CYS LYS SER SEQRES 5 A 247 LYS LYS GLU VAL LEU PHE LEU GLY MET ASN PRO GLY PRO SEQRES 6 A 247 PHE GLY MET ALA GLN THR GLY VAL PRO PHE GLY GLU VAL SEQRES 7 A 247 ASN HIS VAL ARG ASP TRP LEU GLN ILE GLU GLY PRO VAL SEQRES 8 A 247 SER LYS PRO GLU VAL GLU HIS PRO LYS ARG ARG ILE ARG SEQRES 9 A 247 GLY PHE GLU CYS PRO GLN SER GLU VAL SER GLY ALA ARG SEQRES 10 A 247 PHE TRP SER LEU PHE LYS SER LEU CYS GLY GLN PRO GLU SEQRES 11 A 247 THR PHE PHE LYS HIS CYS PHE VAL HIS ASN HIS CYS PRO SEQRES 12 A 247 LEU ILE PHE MET ASN HIS SER GLY LYS ASN LEU THR PRO SEQRES 13 A 247 THR ASP LEU PRO LYS ALA GLN ARG ASP THR LEU LEU GLU SEQRES 14 A 247 ILE CYS ASP GLU ALA LEU CYS GLN ALA VAL ARG VAL LEU SEQRES 15 A 247 GLY VAL LYS LEU VAL ILE GLY VAL GLY ARG PHE SER GLU SEQRES 16 A 247 GLN ARG ALA ARG LYS ALA LEU MET ALA GLU GLY ILE ASP SEQRES 17 A 247 VAL THR VAL LYS GLY ILE MET HIS PRO SER PRO ARG ASN SEQRES 18 A 247 PRO GLN ALA ASN LYS GLY TRP GLU GLY ILE VAL ARG GLY SEQRES 19 A 247 GLN LEU LEU GLU LEU GLY VAL LEU SER LEU LEU THR GLY SEQRES 1 B 247 THR GLU SER PRO ALA ASP SER PHE LEU LYS VAL GLU LEU SEQRES 2 B 247 GLU LEU ASN LEU LYS LEU SER ASN LEU VAL PHE GLN ASP SEQRES 3 B 247 PRO VAL GLN TYR VAL TYR ASN PRO LEU VAL TYR ALA TRP SEQRES 4 B 247 ALA PRO HIS GLU ASN TYR VAL GLN THR TYR CYS LYS SER SEQRES 5 B 247 LYS LYS GLU VAL LEU PHE LEU GLY MET ASN PRO GLY PRO SEQRES 6 B 247 PHE GLY MET ALA GLN THR GLY VAL PRO PHE GLY GLU VAL SEQRES 7 B 247 ASN HIS VAL ARG ASP TRP LEU GLN ILE GLU GLY PRO VAL SEQRES 8 B 247 SER LYS PRO GLU VAL GLU HIS PRO LYS ARG ARG ILE ARG SEQRES 9 B 247 GLY PHE GLU CYS PRO GLN SER GLU VAL SER GLY ALA ARG SEQRES 10 B 247 PHE TRP SER LEU PHE LYS SER LEU CYS GLY GLN PRO GLU SEQRES 11 B 247 THR PHE PHE LYS HIS CYS PHE VAL HIS ASN HIS CYS PRO SEQRES 12 B 247 LEU ILE PHE MET ASN HIS SER GLY LYS ASN LEU THR PRO SEQRES 13 B 247 THR ASP LEU PRO LYS ALA GLN ARG ASP THR LEU LEU GLU SEQRES 14 B 247 ILE CYS ASP GLU ALA LEU CYS GLN ALA VAL ARG VAL LEU SEQRES 15 B 247 GLY VAL LYS LEU VAL ILE GLY VAL GLY ARG PHE SER GLU SEQRES 16 B 247 GLN ARG ALA ARG LYS ALA LEU MET ALA GLU GLY ILE ASP SEQRES 17 B 247 VAL THR VAL LYS GLY ILE MET HIS PRO SER PRO ARG ASN SEQRES 18 B 247 PRO GLN ALA ASN LYS GLY TRP GLU GLY ILE VAL ARG GLY SEQRES 19 B 247 GLN LEU LEU GLU LEU GLY VAL LEU SER LEU LEU THR GLY SEQRES 1 E 12 DC DC DC DG DT DG DA DG DT DC DC DG SEQRES 1 F 12 DC DG DG DA DC DT 3DR DA DC DG DG DG HET 3DR F 299 11 HET HMU A1282 10 HET HMU A1283 10 HET GOL A1284 6 HET IPA A1285 8 HETNAM 3DR 1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE HETNAM HMU 5-HYDROXYMETHYL URACIL HETNAM GOL GLYCEROL HETNAM IPA ISOPROPYL ALCOHOL HETSYN 3DR ABASIC DIDEOXYRIBOSE HETSYN HMU 5-(HYDROXYMETHYL)PYRIMIDINE-2,4(1H,3H)-DIONE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN IPA 2-PROPANOL FORMUL 5 3DR C5 H11 O6 P FORMUL 6 HMU 2(C5 H6 N2 O3) FORMUL 7 GOL C3 H8 O3 FORMUL 8 IPA C3 H8 O FORMUL 9 HOH *110(H2 O) HELIX 1 1 PRO A 38 LEU A 56 1 19 HELIX 2 2 ASN A 67 ALA A 72 1 6 HELIX 3 3 ALA A 72 CYS A 84 1 13 HELIX 4 4 GLY A 101 GLY A 106 1 6 HELIX 5 5 GLU A 111 TRP A 118 1 8 HELIX 6 6 ARG A 138 CYS A 142 5 5 HELIX 7 7 GLU A 146 GLY A 161 1 16 HELIX 8 8 GLN A 162 LYS A 168 1 7 HELIX 9 9 PRO A 194 GLY A 217 1 24 HELIX 10 10 GLY A 225 GLU A 239 1 15 HELIX 11 11 GLY A 261 LEU A 273 1 13 HELIX 12 12 PRO B 38 ASN B 55 1 18 HELIX 13 13 ASN B 67 ALA B 72 1 6 HELIX 14 14 ALA B 72 CYS B 84 1 13 HELIX 15 15 GLY B 101 GLY B 106 1 6 HELIX 16 16 GLU B 111 TRP B 118 1 8 HELIX 17 17 ARG B 138 CYS B 142 5 5 HELIX 18 18 GLU B 146 GLY B 161 1 16 HELIX 19 19 GLN B 162 LYS B 168 1 7 HELIX 20 20 THR B 189 LEU B 193 5 5 HELIX 21 21 ALA B 196 GLY B 217 1 22 HELIX 22 22 GLY B 225 ALA B 238 1 14 HELIX 23 23 GLN B 257 LEU B 273 1 17 SHEET 1 AA 3 TYR A 64 TYR A 66 0 SHEET 2 AA 3 ILE A 179 MET A 181 -1 O ILE A 179 N TYR A 66 SHEET 3 AA 3 ASN A 187 LEU A 188 -1 O LEU A 188 N PHE A 180 SHEET 1 AB 4 CYS A 170 ASN A 174 0 SHEET 2 AB 4 VAL A 90 GLY A 94 1 O VAL A 90 N PHE A 171 SHEET 3 AB 4 LEU A 220 VAL A 224 1 O LEU A 220 N LEU A 91 SHEET 4 AB 4 THR A 244 ILE A 248 1 O THR A 244 N VAL A 221 SHEET 1 BA 3 TYR B 64 TYR B 66 0 SHEET 2 BA 3 ILE B 179 MET B 181 -1 O ILE B 179 N TYR B 66 SHEET 3 BA 3 ASN B 187 LEU B 188 -1 O LEU B 188 N PHE B 180 SHEET 1 BB 4 CYS B 170 ASN B 174 0 SHEET 2 BB 4 VAL B 90 GLY B 94 1 O VAL B 90 N PHE B 171 SHEET 3 BB 4 LEU B 220 VAL B 224 1 O LEU B 220 N LEU B 91 SHEET 4 BB 4 THR B 244 ILE B 248 1 O THR B 244 N VAL B 221 LINK O3' 3DR F 299 P DA F 300 1555 1555 1.65 LINK P 3DR F 299 O3' DT F 298 1555 1555 1.66 CISPEP 1 SER A 37 PRO A 38 0 21.66 SITE 1 AC1 11 MET A 95 ASN A 96 GLY A 98 GLY A 101 SITE 2 AC1 11 MET A 102 PHE A 109 GLU A 146 ASN A 174 SITE 3 AC1 11 HIS A 250 GOL A1284 HOH A2024 SITE 1 AC2 7 PRO A 99 SER A 145 GLU A 146 VAL A 147 SITE 2 AC2 7 GOL A1284 HOH A2052 HOH A2053 SITE 1 AC3 7 MET A 95 ASN A 96 GLU A 146 SER A 252 SITE 2 AC3 7 HMU A1282 HMU A1283 DC E 281 SITE 1 AC4 7 GLU A 203 ILE A 204 CYS A 205 ASP A 206 SITE 2 AC4 7 GLU A 207 ALA A 208 LEU A 209 CRYST1 120.969 86.518 78.456 90.00 118.53 90.00 C 1 2 1 8 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 0.008267 0.000000 0.004494 0.00000 SCALE2 0.000000 0.011558 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014508 0.00000