HEADER TRANSFERASE/DNA 28-MAR-11 3RB3 TITLE DPO4 EXTENSION TERNARY COMPLEX WITH 3'-TERMINAL PRIMER A BASE OPPOSITE TITLE 2 THE 1-METHYLGUANINE (M1G) LESION COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE IV; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: POL IV; COMPND 5 EC: 2.7.7.7; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA (5'-D(*GP*TP*TP*GP*GP*AP*TP*GP*GP*TP*AP*GP*(2DA))-3'); COMPND 9 CHAIN: D; COMPND 10 ENGINEERED: YES; COMPND 11 OTHER_DETAILS: DNA PRIMER STRAND (DIDEOXY-TERMINATED AT THE 3-END); COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: DNA (5'-D(*C*CP*TP*AP*AP*CP*(MG1) COMPND 14 P*CP*TP*AP*CP*CP*AP*TP*CP*CP*AP*AP*CP*C)-3'); COMPND 15 CHAIN: E; COMPND 16 ENGINEERED: YES; COMPND 17 OTHER_DETAILS: DNA M1G-MODIFIED TEMPLATE STRAND SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SULFOLOBUS SOLFATARICUS; SOURCE 3 ORGANISM_TAXID: 273057; SOURCE 4 GENE: DBH, DPO4, SSO2448; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3) RIL CODON PLUS; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PET28A; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 OTHER_DETAILS: SYNTHETIC; SOURCE 12 MOL_ID: 3; SOURCE 13 SYNTHETIC: YES; SOURCE 14 OTHER_DETAILS: SYNTHETIC KEYWDS DNA DAMAGE, DNA REPAIR, DNA REPLICATION, DNA-BINDING, DNA-DIRECTED KEYWDS 2 DNA POLYMERASE, MAGNESIUM, METAL-BINDING, MUTATOR PROTEIN, KEYWDS 3 NUCLEOTIDYLTRANSFERASE, TRANSFERASE, TRANSFERASE-DNA COMPLEX, LESION KEYWDS 4 BYPASS, DNA POLYMERASE, Y-FAMILY POLYMERASE, DNTP-BINDING, 1- KEYWDS 5 METHYLGUANINE EXPDTA X-RAY DIFFRACTION AUTHOR O.RECHKOBLIT,D.J.PATEL REVDAT 3 22-NOV-17 3RB3 1 REMARK REVDAT 2 19-JUN-13 3RB3 1 JRNL VERSN REVDAT 1 15-JUN-11 3RB3 0 JRNL AUTH O.RECHKOBLIT,J.C.DELANEY,J.M.ESSIGMANN,D.J.PATEL JRNL TITL IMPLICATIONS FOR DAMAGE RECOGNITION DURING DPO4-MEDIATED JRNL TITL 2 MUTAGENIC BYPASS OF M1G AND M3C LESIONS. JRNL REF STRUCTURE V. 19 821 2011 JRNL REFN ISSN 0969-2126 JRNL PMID 21645853 JRNL DOI 10.1016/J.STR.2011.03.020 REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0102 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) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 3.500 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.4 REMARK 3 NUMBER OF REFLECTIONS : 12442 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) : 0.220 REMARK 3 R VALUE (WORKING SET) : 0.217 REMARK 3 FREE R VALUE : 0.264 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 641 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) : 2.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.87 REMARK 3 REFLECTION IN BIN (WORKING SET) : 791 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 84.37 REMARK 3 BIN R VALUE (WORKING SET) : 0.3060 REMARK 3 BIN FREE R VALUE SET COUNT : 40 REMARK 3 BIN FREE R VALUE : 0.3550 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2740 REMARK 3 NUCLEIC ACID ATOMS : 628 REMARK 3 HETEROGEN ATOMS : 49 REMARK 3 SOLVENT ATOMS : 35 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 71.39 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 10.20000 REMARK 3 B22 (A**2) : -5.10000 REMARK 3 B33 (A**2) : -5.09000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.403 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.355 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 39.115 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.935 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.920 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3553 ; 0.009 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4904 ; 1.585 ; 2.228 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 342 ; 5.610 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 122 ;35.125 ;23.607 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 561 ;18.940 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 24 ;17.326 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 556 ; 0.136 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2366 ; 0.004 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): 1715 ; 0.479 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2770 ; 0.694 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1838 ; 1.059 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2134 ; 1.839 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 341 REMARK 3 ORIGIN FOR THE GROUP (A): 20.5985 17.3163 12.2169 REMARK 3 T TENSOR REMARK 3 T11: 0.0669 T22: 0.1775 REMARK 3 T33: 0.1907 T12: -0.0032 REMARK 3 T13: -0.0673 T23: 0.0240 REMARK 3 L TENSOR REMARK 3 L11: 0.8717 L22: 3.1461 REMARK 3 L33: 4.4392 L12: -0.4011 REMARK 3 L13: 0.0831 L23: -1.2363 REMARK 3 S TENSOR REMARK 3 S11: -0.0365 S12: -0.1135 S13: 0.0011 REMARK 3 S21: 0.0816 S22: 0.1381 S23: 0.3202 REMARK 3 S31: -0.2919 S32: -0.5504 S33: -0.1016 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 3 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : D 802 D 813 REMARK 3 RESIDUE RANGE : E 901 E 918 REMARK 3 RESIDUE RANGE : A 414 A 414 REMARK 3 ORIGIN FOR THE GROUP (A): 10.7555 9.3513 20.9958 REMARK 3 T TENSOR REMARK 3 T11: 0.1050 T22: 0.6312 REMARK 3 T33: 0.3678 T12: -0.0491 REMARK 3 T13: 0.0222 T23: 0.1435 REMARK 3 L TENSOR REMARK 3 L11: 1.9760 L22: 2.6047 REMARK 3 L33: 1.6215 L12: -0.1800 REMARK 3 L13: 1.1719 L23: -0.5371 REMARK 3 S TENSOR REMARK 3 S11: 0.1431 S12: -0.4629 S13: 0.0668 REMARK 3 S21: 0.2296 S22: 0.1112 S23: 0.7158 REMARK 3 S31: 0.0460 S32: -0.9489 S33: -0.2543 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : 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 RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3RB3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-APR-11. REMARK 100 THE DEPOSITION ID IS D_1000064711. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-NOV-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97949 REMARK 200 MONOCHROMATOR : KOHZU HLD8-24 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13492 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.600 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.4 REMARK 200 DATA REDUNDANCY : 4.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.91 REMARK 200 COMPLETENESS FOR SHELL (%) : 83.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL 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 3RAQ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.81 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.72 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM HEPES, PH 7.0, 100 MM CALCIUM REMARK 280 ACETATE AND 10% PEG 4000, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K 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 46.59400 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 55.18300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 46.59400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 55.18300 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6990 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19760 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -49.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, D, 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 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 2DA D 814 REMARK 465 DC E 900 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 DC E 901 P OP1 OP2 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 DA E 904 O3' DA E 904 C3' -0.065 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 DG D 802 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 DT D 803 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DT D 804 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 DT D 808 C1' - O4' - C4' ANGL. DEV. = -6.8 DEGREES REMARK 500 DT D 811 O4' - C1' - N1 ANGL. DEV. = -6.0 DEGREES REMARK 500 DT D 811 C3' - O3' - P ANGL. DEV. = 7.2 DEGREES REMARK 500 DG D 813 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 DC E 901 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 DT E 902 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 DA E 903 O3' - P - O5' ANGL. DEV. = -20.8 DEGREES REMARK 500 DA E 903 O3' - P - OP2 ANGL. DEV. = -18.9 DEGREES REMARK 500 DA E 912 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 DC E 914 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 DC E 915 O4' - C1' - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 DC E 915 C3' - O3' - P ANGL. DEV. = 8.0 DEGREES REMARK 500 DA E 917 O4' - C1' - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 DC E 919 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES 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 TYR A 10 65.08 21.64 REMARK 500 SER A 22 10.19 -68.03 REMARK 500 LYS A 137 13.92 56.36 REMARK 500 LYS A 148 -70.94 -40.32 REMARK 500 LYS A 201 -156.33 -118.25 REMARK 500 VAL A 203 -63.95 -17.02 REMARK 500 ASP A 204 -5.87 -55.16 REMARK 500 MET A 216 -29.53 -176.19 REMARK 500 GLU A 232 -110.02 -81.62 REMARK 500 TYR A 233 102.43 43.13 REMARK 500 GLU A 235 117.70 -25.87 REMARK 500 ASP A 277 85.15 49.49 REMARK 500 LYS A 278 -16.46 72.54 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 416 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 7 OD1 REMARK 620 2 ASP A 105 OD2 61.8 REMARK 620 3 PHE A 8 O 94.7 99.4 REMARK 620 4 DGT A 414 O1G 114.9 155.5 105.1 REMARK 620 5 DGT A 414 O2A 91.4 65.0 157.7 91.6 REMARK 620 6 DGT A 414 O1B 153.8 92.3 85.2 90.2 79.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 417 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ALA A 181 O REMARK 620 2 ILE A 186 O 77.0 REMARK 620 3 HOH A 343 O 63.5 63.3 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 415 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 106 OE2 REMARK 620 2 ASP A 7 OD2 120.4 REMARK 620 3 DGT A 414 O2A 134.9 96.3 REMARK 620 4 HOH A 344 O 120.0 85.2 85.8 REMARK 620 5 ASP A 7 OD1 107.1 47.8 77.5 126.5 REMARK 620 6 ASP A 105 OD2 98.0 92.1 52.1 137.3 46.3 REMARK 620 7 ASP A 105 OD1 59.5 121.0 80.0 151.1 74.6 40.5 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DGT A 414 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 415 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 416 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 417 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EPE A 342 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3RAQ RELATED DB: PDB REMARK 900 DPO4 EXTENSION TERNARY COMPLEX WITH 3'-TERMINAL PRIMER C BASE REMARK 900 OPPOSITE THE 1-METHYLGUANINE (M1G) LESION REMARK 900 RELATED ID: 3RAX RELATED DB: PDB REMARK 900 DPO4 EXTENSION TERNARY COMPLEX WITH 3'-TERMINAL PRIMER T BASE REMARK 900 OPPOSITE THE 1-METHYLGUANINE (M1G) LESION REMARK 900 RELATED ID: 3RB0 RELATED DB: PDB REMARK 900 DPO4 EXTENSION TERNARY COMPLEX WITH 3'-TERMINAL PRIMER G BASE REMARK 900 OPPOSITE THE 1-METHYLGUANINE (M1G) LESION DBREF 3RB3 A 2 341 UNP Q97W02 DPO42_SULSO 2 341 DBREF 3RB3 D 802 814 PDB 3RB3 3RB3 802 814 DBREF 3RB3 E 900 919 PDB 3RB3 3RB3 900 919 SEQADV 3RB3 GLY A 1 UNP Q97W02 EXPRESSION TAG SEQRES 1 A 341 GLY ILE VAL LEU PHE VAL ASP PHE ASP TYR PHE TYR ALA SEQRES 2 A 341 GLN VAL GLU GLU VAL LEU ASN PRO SER LEU LYS GLY LYS SEQRES 3 A 341 PRO VAL VAL VAL CYS VAL PHE SER GLY ARG PHE GLU ASP SEQRES 4 A 341 SER GLY ALA VAL ALA THR ALA ASN TYR GLU ALA ARG LYS SEQRES 5 A 341 PHE GLY VAL LYS ALA GLY ILE PRO ILE VAL GLU ALA LYS SEQRES 6 A 341 LYS ILE LEU PRO ASN ALA VAL TYR LEU PRO MET ARG LYS SEQRES 7 A 341 GLU VAL TYR GLN GLN VAL SER SER ARG ILE MET ASN LEU SEQRES 8 A 341 LEU ARG GLU TYR SER GLU LYS ILE GLU ILE ALA SER ILE SEQRES 9 A 341 ASP GLU ALA TYR LEU ASP ILE SER ASP LYS VAL ARG ASP SEQRES 10 A 341 TYR ARG GLU ALA TYR ASN LEU GLY LEU GLU ILE LYS ASN SEQRES 11 A 341 LYS ILE LEU GLU LYS GLU LYS ILE THR VAL THR VAL GLY SEQRES 12 A 341 ILE SER LYS ASN LYS VAL PHE ALA LYS ILE ALA ALA ASP SEQRES 13 A 341 MET ALA LYS PRO ASN GLY ILE LYS VAL ILE ASP ASP GLU SEQRES 14 A 341 GLU VAL LYS ARG LEU ILE ARG GLU LEU ASP ILE ALA ASP SEQRES 15 A 341 VAL PRO GLY ILE GLY ASN ILE THR ALA GLU LYS LEU LYS SEQRES 16 A 341 LYS LEU GLY ILE ASN LYS LEU VAL ASP THR LEU SER ILE SEQRES 17 A 341 GLU PHE ASP LYS LEU LYS GLY MET ILE GLY GLU ALA LYS SEQRES 18 A 341 ALA LYS TYR LEU ILE SER LEU ALA ARG ASP GLU TYR ASN SEQRES 19 A 341 GLU PRO ILE ARG THR ARG VAL ARG LYS SER ILE GLY ARG SEQRES 20 A 341 ILE VAL THR MET LYS ARG ASN SER ARG ASN LEU GLU GLU SEQRES 21 A 341 ILE LYS PRO TYR LEU PHE ARG ALA ILE GLU GLU SER TYR SEQRES 22 A 341 TYR LYS LEU ASP LYS ARG ILE PRO LYS ALA ILE HIS VAL SEQRES 23 A 341 VAL ALA VAL THR GLU ASP LEU ASP ILE VAL SER ARG GLY SEQRES 24 A 341 ARG THR PHE PRO HIS GLY ILE SER LYS GLU THR ALA TYR SEQRES 25 A 341 SER GLU SER VAL LYS LEU LEU GLN LYS ILE LEU GLU GLU SEQRES 26 A 341 ASP GLU ARG LYS ILE ARG ARG ILE GLY VAL ARG PHE SER SEQRES 27 A 341 LYS PHE ILE SEQRES 1 D 13 DG DT DT DG DG DA DT DG DG DT DA DG 2DA SEQRES 1 E 20 DC DC DT DA DA DC MG1 DC DT DA DC DC DA SEQRES 2 E 20 DT DC DC DA DA DC DC MODRES 3RB3 MG1 E 906 DG HET MG1 E 906 23 HET DGT A 414 31 HET CA A 415 1 HET CA A 416 1 HET CA A 417 1 HET EPE A 342 15 HETNAM MG1 2'-DEOXY-1-METHYLGUANOSINE 5'-(DIHYDROGEN PHOSPHATE) HETNAM DGT 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE HETNAM CA CALCIUM ION HETNAM EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID HETSYN EPE HEPES FORMUL 3 MG1 C11 H16 N5 O7 P FORMUL 4 DGT C10 H16 N5 O13 P3 FORMUL 5 CA 3(CA 2+) FORMUL 8 EPE C8 H18 N2 O4 S FORMUL 9 HOH *35(H2 O) HELIX 1 1 TYR A 10 ASN A 20 1 11 HELIX 2 2 PRO A 21 LYS A 24 5 4 HELIX 3 3 ASN A 47 LYS A 52 1 6 HELIX 4 4 PRO A 60 LEU A 68 1 9 HELIX 5 5 ARG A 77 GLU A 94 1 18 HELIX 6 6 ASP A 117 GLU A 136 1 20 HELIX 7 7 ASN A 147 LYS A 159 1 13 HELIX 8 8 ASP A 167 LEU A 178 1 12 HELIX 9 9 ASP A 179 VAL A 183 5 5 HELIX 10 10 GLY A 187 LYS A 196 1 10 HELIX 11 11 VAL A 203 ILE A 208 1 6 HELIX 12 12 GLU A 209 ARG A 230 1 22 HELIX 13 13 ASN A 257 ASP A 277 1 21 HELIX 14 14 SER A 307 ASP A 326 1 20 SHEET 1 A 5 ILE A 99 ILE A 101 0 SHEET 2 A 5 GLU A 106 ASP A 110 -1 O TYR A 108 N GLU A 100 SHEET 3 A 5 VAL A 3 PHE A 8 -1 N LEU A 4 O LEU A 109 SHEET 4 A 5 VAL A 140 SER A 145 -1 O GLY A 143 N PHE A 5 SHEET 5 A 5 ILE A 163 ILE A 166 1 O LYS A 164 N ILE A 144 SHEET 1 B 3 GLY A 41 ALA A 46 0 SHEET 2 B 3 VAL A 28 PHE A 33 -1 N VAL A 32 O ALA A 42 SHEET 3 B 3 VAL A 72 PRO A 75 1 O LEU A 74 N CYS A 31 SHEET 1 C 4 SER A 244 SER A 255 0 SHEET 2 C 4 ILE A 330 PHE A 340 -1 O PHE A 337 N ILE A 245 SHEET 3 C 4 PRO A 281 THR A 290 -1 N VAL A 289 O ARG A 331 SHEET 4 C 4 ILE A 295 THR A 301 -1 O VAL A 296 N ALA A 288 LINK O3' DC E 905 P MG1 E 906 1555 1555 1.61 LINK O3' MG1 E 906 P DC E 907 1555 1555 1.60 LINK OD1 ASP A 7 CA CA A 416 1555 1555 2.30 LINK OD2 ASP A 105 CA CA A 416 1555 1555 2.30 LINK O PHE A 8 CA CA A 416 1555 1555 2.31 LINK O1G DGT A 414 CA CA A 416 1555 1555 2.31 LINK O ALA A 181 CA CA A 417 1555 1555 2.32 LINK O2A DGT A 414 CA CA A 416 1555 1555 2.33 LINK OE2 GLU A 106 CA CA A 415 1555 1555 2.33 LINK O1B DGT A 414 CA CA A 416 1555 1555 2.34 LINK OD2 ASP A 7 CA CA A 415 1555 1555 2.35 LINK O ILE A 186 CA CA A 417 1555 1555 2.35 LINK O2A DGT A 414 CA CA A 415 1555 1555 2.35 LINK CA CA A 417 O HOH A 343 1555 1555 2.43 LINK CA CA A 415 O HOH A 344 1555 1555 2.90 LINK OD1 ASP A 7 CA CA A 415 1555 1555 2.90 LINK OD2 ASP A 105 CA CA A 415 1555 1555 3.10 LINK OD1 ASP A 105 CA CA A 415 1555 1555 3.18 CISPEP 1 LYS A 159 PRO A 160 0 -0.99 SITE 1 AC1 18 ASP A 7 PHE A 8 ASP A 9 TYR A 10 SITE 2 AC1 18 PHE A 11 TYR A 12 VAL A 32 ALA A 44 SITE 3 AC1 18 THR A 45 TYR A 48 ARG A 51 ASP A 105 SITE 4 AC1 18 LYS A 159 HOH A 353 CA A 415 CA A 416 SITE 5 AC1 18 DC E 905 MG1 E 906 SITE 1 AC2 6 ASP A 7 ASP A 105 GLU A 106 HOH A 344 SITE 2 AC2 6 DGT A 414 CA A 416 SITE 1 AC3 5 ASP A 7 PHE A 8 ASP A 105 DGT A 414 SITE 2 AC3 5 CA A 415 SITE 1 AC4 4 ALA A 181 ILE A 186 HOH A 343 DG D 813 SITE 1 AC5 7 SER A 103 ILE A 104 ARG A 240 DG D 813 SITE 2 AC5 7 DC E 907 DT E 908 DA E 909 CRYST1 93.188 110.366 51.874 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 0.010731 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009061 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019277 0.00000