PDB Short entry for 1OE5 HEADER HYDROLASE/DNA 19-MAR-03 1OE5 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*3DRP*GP*GP*AP*CP*TP*3DRP*AP*CP*GP*GP*GP)-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, DNA GLYCOSYLASE, SINGLE STRANDED EXPDTA X-RAY DIFFRACTION AUTHOR J.E.A.WIBLEY,L.H.PEARL REVDAT 3 17-JUL-13 1OE5 1 HEADER COMPND KEYWDS JRNL REVDAT 3 2 REMARK VERSN DBREF SEQRES REVDAT 3 3 HETSYN FORMUL LINK SITE REVDAT 3 4 SCALE1 ATOM HETATM TER REVDAT 3 5 CONECT MASTER REVDAT 2 24-FEB-09 1OE5 1 VERSN REVDAT 1 11-JUL-03 1OE5 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. 2.3 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 69.01 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 95.8 REMARK 3 NUMBER OF REFLECTIONS : 28407 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) : 0.166 REMARK 3 R VALUE (WORKING SET) : 0.163 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1512 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) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.36 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1576 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.1830 REMARK 3 BIN FREE R VALUE SET COUNT : 88 REMARK 3 BIN FREE R VALUE : 0.2600 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3873 REMARK 3 NUCLEIC ACID ATOMS : 467 REMARK 3 HETEROGEN ATOMS : 90 REMARK 3 SOLVENT ATOMS : 227 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.23 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.49000 REMARK 3 B22 (A**2) : -0.20000 REMARK 3 B33 (A**2) : 0.70000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 1.04000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.267 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.221 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.148 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.049 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.956 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.912 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4596 ; 0.031 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6328 ; 2.590 ; 2.109 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 489 ; 7.637 ; 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): 661 ; 0.163 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3306 ; 0.012 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2035 ; 0.242 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 288 ; 0.186 ; 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): 73 ; 0.196 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 21 ; 0.209 ; 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): 2448 ; 1.477 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3967 ; 2.634 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2148 ; 4.192 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2359 ; 6.489 ; 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: NULL REMARK 4 REMARK 4 1OE5 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-12402. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JUL-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 : 29920 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 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 (%) : 95.8 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.06600 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 6.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.42 REMARK 200 COMPLETENESS FOR SHELL (%) : 77.1 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : 0.22200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.000 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 (%): 54.5 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.83 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 60.29800 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 42.82650 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 60.29800 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 42.82650 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: PQS REMARK 350 TOTAL BURIED SURFACE AREA: 9340 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 31040 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -2.7 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 SER A 37 N CA CB OG 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 ASP A 60 CB ASP A 60 CG 0.127 REMARK 500 ASP A 60 C ASP A 60 O 0.116 REMARK 500 MET A 95 CG MET A 95 SD 0.167 REMARK 500 ALA A 212 CA ALA A 212 CB 0.168 REMARK 500 VAL A 245 CB VAL A 245 CG1 0.156 REMARK 500 ALA B 212 CA ALA B 212 CB 0.145 REMARK 500 ARG B 254 CG ARG B 254 CD 0.181 REMARK 500 DC E 282 C2 DC E 282 N3 0.049 REMARK 500 DC E 282 C5' DC E 282 C4' 0.064 REMARK 500 DC E 282 O5' DC E 282 C5' 0.157 REMARK 500 DC E 282 P DC E 282 O5' 0.073 REMARK 500 DC E 290 P DC E 290 O5' 0.073 REMARK 500 DC E 291 O5' DC E 291 C5' -0.154 REMARK 500 DG E 292 C5 DG E 292 C4 -0.043 REMARK 500 DC F 392 N3 DC F 392 C4 0.050 REMARK 500 DG F 394 C8 DG F 394 N7 0.046 REMARK 500 DG F 395 C6 DG F 395 N1 0.044 REMARK 500 DG F 395 C8 DG F 395 N7 0.036 REMARK 500 DT F 398 C1' DT F 398 N1 0.081 REMARK 500 DG F 402 C3' DG F 402 O3' 0.103 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 LEU A 93 CB - CG - CD2 ANGL. DEV. = 10.9 DEGREES REMARK 500 ASP A 192 CB - CG - OD2 ANGL. DEV. = 7.9 DEGREES REMARK 500 ARG A 198 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG A 198 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 CYS A 210 CA - CB - SG ANGL. DEV. = -7.7 DEGREES REMARK 500 ARG B 136 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 LYS B 260 CD - CE - NZ ANGL. DEV. = -14.4 DEGREES REMARK 500 DC E 281 C4 - C5 - C6 ANGL. DEV. = -7.5 DEGREES REMARK 500 DC E 281 C5 - C4 - N4 ANGL. DEV. = -6.2 DEGREES REMARK 500 DC E 281 C5' - C4' - O4' ANGL. DEV. = 8.7 DEGREES REMARK 500 DC E 281 C5 - C6 - N1 ANGL. DEV. = 5.9 DEGREES REMARK 500 DC E 281 N1 - C2 - N3 ANGL. DEV. = -4.5 DEGREES REMARK 500 DC E 281 N3 - C4 - C5 ANGL. DEV. = 4.4 DEGREES REMARK 500 DC E 282 C5' - C4' - O4' ANGL. DEV. = 8.0 DEGREES REMARK 500 DC E 282 N1 - C2 - O2 ANGL. DEV. = -3.8 DEGREES REMARK 500 DC E 282 O4' - C1' - N1 ANGL. DEV. = 6.2 DEGREES REMARK 500 DC E 282 O4' - C4' - C3' ANGL. DEV. = -3.8 DEGREES REMARK 500 DC E 282 O5' - P - OP1 ANGL. DEV. = -7.6 DEGREES REMARK 500 DC E 282 O5' - P - OP2 ANGL. DEV. = 9.6 DEGREES REMARK 500 DC E 282 OP1 - P - OP2 ANGL. DEV. = 10.8 DEGREES REMARK 500 DC E 282 C3' - O3' - P ANGL. DEV. = -7.3 DEGREES REMARK 500 DC E 283 O4' - C1' - C2' ANGL. DEV. = -5.7 DEGREES REMARK 500 DC E 283 O4' - C1' - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 DG E 284 N3 - C2 - N2 ANGL. DEV. = 6.9 DEGREES REMARK 500 DT E 285 C5 - C4 - O4 ANGL. DEV. = -6.2 DEGREES REMARK 500 DT E 285 N3 - C4 - O4 ANGL. DEV. = 4.2 DEGREES REMARK 500 DT E 285 O4' - C1' - N1 ANGL. DEV. = 5.8 DEGREES REMARK 500 DG E 286 C5 - C6 - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 DG E 286 O4' - C1' - N9 ANGL. DEV. = 6.3 DEGREES REMARK 500 DG E 288 O4' - C1' - N9 ANGL. DEV. = -4.4 DEGREES REMARK 500 DG E 288 O5' - C5' - C4' ANGL. DEV. = -6.2 DEGREES REMARK 500 DT E 289 C6 - C5 - C7 ANGL. DEV. = -4.0 DEGREES REMARK 500 DC E 290 O4' - C1' - N1 ANGL. DEV. = -6.1 DEGREES REMARK 500 DC E 291 C5' - C4' - C3' ANGL. DEV. = -19.5 DEGREES REMARK 500 DC E 291 C6 - N1 - C2 ANGL. DEV. = 2.5 DEGREES REMARK 500 DC E 291 O4' - C1' - C2' ANGL. DEV. = 6.8 DEGREES REMARK 500 DC E 291 O4' - C1' - N1 ANGL. DEV. = 7.0 DEGREES REMARK 500 DC E 291 O4' - C4' - C3' ANGL. DEV. = 4.9 DEGREES REMARK 500 DC E 291 O5' - C5' - C4' ANGL. DEV. = -6.0 DEGREES REMARK 500 DC E 291 O5' - P - OP1 ANGL. DEV. = -13.1 DEGREES REMARK 500 DC E 291 O5' - P - OP2 ANGL. DEV. = 10.0 DEGREES REMARK 500 DC E 291 OP1 - P - OP2 ANGL. DEV. = 13.8 DEGREES REMARK 500 DG E 292 C5 - C6 - O6 ANGL. DEV. = -4.2 DEGREES REMARK 500 DG E 292 N1 - C2 - N2 ANGL. DEV. = 7.2 DEGREES REMARK 500 DG E 292 N3 - C2 - N2 ANGL. DEV. = -4.9 DEGREES REMARK 500 DC F 392 C5 - C4 - N4 ANGL. DEV. = -5.6 DEGREES REMARK 500 DC F 392 N3 - C4 - N4 ANGL. DEV. = 5.7 DEGREES REMARK 500 DC F 392 O4' - C1' - N1 ANGL. DEV. = 8.5 DEGREES REMARK 500 DG F 394 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 DG F 394 C6 - N1 - C2 ANGL. DEV. = -5.3 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 80 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 ASP A 60 -101.23 106.92 REMARK 500 VAL A 70 -64.66 -95.81 REMARK 500 MET A 95 -62.35 -92.24 REMARK 500 SER A 126 -144.48 -97.61 REMARK 500 SER A 277 -68.52 -25.75 REMARK 500 ASP B 60 -71.55 92.12 REMARK 500 SER B 126 -153.04 -102.55 REMARK 500 LYS B 195 107.98 -47.18 REMARK 500 ALA B 196 -69.79 154.00 REMARK 500 LYS B 246 -158.24 -120.12 REMARK 500 LEU B 279 67.03 -116.67 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 ASN A 259 LYS A 260 146.67 REMARK 500 GLN B 59 ASP B 60 132.61 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 40 24.6 L L OUTSIDE RANGE REMARK 500 VAL A 215 24.1 L L OUTSIDE RANGE REMARK 500 ASN A 259 23.2 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 URA A1282 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EPE A1285 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EPE B1282 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DUR F1405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A1283 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IPA A1284 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IPA B1281 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1OE4 RELATED DB: PDB REMARK 900 XENOPUS SMUG1, AN ANTI-MUTATOR URACIL-DNA GLYCOSYLASE REMARK 900 RELATED ID: 1OE6 RELATED DB: PDB REMARK 900 XENOPUS SMUG1, AN ANTI-MUTATOR URACIL-DNA GLYCOSYLASE REMARK 999 REMARK 999 SEQUENCE REMARK 999 RESIDUES 3DR IN CHAIN F IS THE RESULT OF DEGLYCOSYLATION REMARK 999 OF DEOXYURACIL DBREF 1OE5 A 35 281 UNP Q9YGN6 Q9YGN6 1 247 DBREF 1OE5 B 35 281 UNP Q9YGN6 Q9YGN6 1 247 DBREF 1OE5 E 281 292 PDB 1OE5 1OE5 281 292 DBREF 1OE5 F 392 404 PDB 1OE5 1OE5 392 404 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 13 DC 3DR DG DG DA DC DT 3DR DA DC DG DG DG HET 3DR F 393 11 HET 3DR F 399 11 HET URA A1282 8 HET EPE A1285 15 HET EPE B1282 15 HET DUR F1405 16 HET GOL A1283 6 HET IPA A1284 4 HET IPA B1281 4 HETNAM 3DR 1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE HETNAM URA URACIL HETNAM EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE HETNAM 2 EPE ETHANESULFONIC ACID HETNAM DUR 2'-DEOXYURIDINE HETNAM GOL GLYCEROL HETNAM IPA ISOPROPYL ALCOHOL HETSYN 3DR ABASIC DIDEOXYRIBOSE HETSYN EPE HEPES HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN IPA 2-PROPANOL FORMUL 2 3DR 2(C5 H11 O6 P) FORMUL 5 URA C4 H4 N2 O2 FORMUL 6 EPE 2(C8 H18 N2 O4 S) FORMUL 8 DUR C9 H12 N2 O5 FORMUL 9 GOL C3 H8 O3 FORMUL 10 IPA 2(C3 H8 O) FORMUL 12 HOH *227(H2 O) HELIX 1 1 PRO A 38 ASN A 55 1 18 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 THR A 189 LEU A 193 5 5 HELIX 10 10 PRO A 194 GLY A 217 1 24 HELIX 11 11 GLY A 225 GLU A 239 1 15 HELIX 12 12 GLY A 261 LEU A 273 1 13 HELIX 13 13 LEU A 276 THR A 280 5 5 HELIX 14 14 PRO B 38 ASN B 55 1 18 HELIX 15 15 ASN B 67 ALA B 72 1 6 HELIX 16 16 ALA B 72 CYS B 84 1 13 HELIX 17 17 GLY B 101 GLY B 106 1 6 HELIX 18 18 GLU B 111 TRP B 118 1 8 HELIX 19 19 HIS B 132 ARG B 136 5 5 HELIX 20 20 ARG B 138 CYS B 142 5 5 HELIX 21 21 GLU B 146 GLY B 161 1 16 HELIX 22 22 GLN B 162 LYS B 168 1 7 HELIX 23 23 THR B 189 LEU B 193 5 5 HELIX 24 24 ALA B 196 GLY B 217 1 22 HELIX 25 25 GLY B 225 ALA B 238 1 14 HELIX 26 26 ASN B 255 LEU B 273 1 19 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 P 3DR F 393 O3' DC F 392 1555 1555 1.64 LINK O3' 3DR F 393 P DG F 394 1555 1555 1.60 LINK O3' 3DR F 399 P DA F 400 1555 1555 1.63 LINK P 3DR F 399 O3' DT F 398 1555 1555 1.61 SITE 1 AC1 10 GLY A 94 MET A 95 ASN A 96 GLY A 98 SITE 2 AC1 10 PHE A 109 ASN A 174 HIS A 250 HOH A2031 SITE 3 AC1 10 HOH A2035 HOH A2120 SITE 1 AC2 8 SER A 54 TYR A 66 ASN A 67 TYR A 71 SITE 2 AC2 8 PRO A 128 GLU A 129 HOH A2049 HOH A2123 SITE 1 AC3 7 SER B 54 TYR B 66 ASN B 67 TYR B 71 SITE 2 AC3 7 PRO B 128 GLU B 129 HOH B2082 SITE 1 AC4 10 ASN B 96 PHE B 109 GLU B 146 SER B 148 SITE 2 AC4 10 HIS B 250 SER B 252 HOH B2017 DC F 392 SITE 3 AC4 10 3DR F 393 DG F 394 SITE 1 AC5 5 PRO A 99 GLU A 146 HOH A2099 HOH A2119 SITE 2 AC5 5 HOH A2120 SITE 1 AC6 3 ASP A 117 HOH A2122 ARG B 151 SITE 1 AC7 6 ALA A 150 ARG A 151 SER A 154 ASN B 113 SITE 2 AC7 6 ASP B 117 HOH B2081 CRYST1 120.596 85.653 78.467 90.00 118.56 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 0.008292 0.000000 0.004514 0.00000 SCALE2 0.000000 0.011675 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014510 0.00000