HEADER DNA 09-MAR-15 2N0L OBSLTE 27-JUL-16 2N0L 5IV1 TITLE SOLUTION STRUCTURE OF DNA DODECAMER WITH 8-OXOGUANINE AT 4TH POSITION COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA_(5'-D(*CP*GP*CP*(8OG)P*AP*AP*TP*TP*CP*GP*CP*G)-3'); COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS DREW-DICKERSON, DNA, DODECAMER, NON-CANONICAL, 8-OXOGUANINE, 8-OXO-7, KEYWDS 2 8-DIHYDROGUANINE, 8-OXO, DOUBLE-HELIX, MODIFIED DNA, OXIDIZED DNA, KEYWDS 3 DNA DAMAGE, DNA ADDUCT, NUCLEIC ACID, CPG SITE, LESION EXPDTA SOLUTION NMR NUMMDL 11 MDLTYP MINIMIZED AVERAGE AUTHOR H.L.MIEARS,D.R.GRUBER,J.J.HOPPINS,A.S.KIRYUTIN,R.D.KASYMOV, AUTHOR 2 A.V.YURKOVSKAYA,D.O.ZHARKOV,S.L.SMIRNOV REVDAT 2 27-JUL-16 2N0L 1 OBSLTE REVDAT 1 09-MAR-16 2N0L 0 JRNL AUTH H.L.MIEARS,D.R.GRUBER,J.J.HOPPINS,D.O.ZHARKOV,S.L.SMIRNOV JRNL TITL SOLUTION STRUCTURE OF DNA DODECAMER WITH 8-OXOGUANINE AT 4TH JRNL TITL 2 POSITION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR_NIH 2.37 REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: USED A/B DNA FROM AMBER TO GENERATE REMARK 3 STARTING STRUCTURES. REMARK 4 REMARK 4 2N0L COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-MAR-15. REMARK 100 THE RCSB ID CODE IS RCSB104270. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.8 REMARK 210 IONIC STRENGTH : 120 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.2 MM DNA (5'-D(*CP*GP*CP*(8OG) REMARK 210 P*AP*AP*TP*TP*CP*GP*CP*G)-3'), 50 MM SODIUM CHLORIDE, 10 MM REMARK 210 POTASSIUM PHOSPHATE, 1 MM EDTA, 100 % D2O, 100% D2O; 0.2 MM DNA REMARK 210 (5'-D(*CP*GP*CP*(8OG)P*AP*AP*TP*TP*CP*GP*CP*G)-3'), 50 MM SODIUM REMARK 210 CHLORIDE, 10 MM POTASSIUM PHOSPHATE, 1 MM EDTA, 10 % D2O, 90% REMARK 210 H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-1H TOCSY; REMARK 210 2D 1H-1H COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRVIEW 9.0.0-B77, X-PLOR_NIH REMARK 210 2.37, CYANA 2.1, NMRPIPE 7.9 REV REMARK 210 2013.021.23.09, AMBER REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 24 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 11 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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: 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 1 DC A 1 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 1 DG A 2 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 1 DC A 3 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 1 DA A 5 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 1 DA A 6 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 1 DT A 7 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 1 DT A 8 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 1 DC A 9 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DG A 10 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 1 DC A 11 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DG A 12 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 1 DC B 13 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 1 DG B 14 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 1 DC B 15 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DA B 17 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DA B 18 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DT B 19 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 DT B 20 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 DC B 21 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 1 DG B 22 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 1 DC B 23 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 DG B 24 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 2 DC A 1 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 2 DG A 2 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 2 DC A 3 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 2 DA A 5 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 2 DA A 6 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 2 DT A 7 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 2 DT A 8 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 2 DC A 9 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 2 DG A 10 O4' - C1' - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 2 DC A 11 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 2 DG A 12 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 2 DC B 13 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 2 DG B 14 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 2 DC B 15 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 2 DA B 17 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 2 DA B 18 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 2 DT B 19 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 2 DT B 20 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 2 DC B 21 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 2 DG B 22 O4' - C1' - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 2 DC B 23 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 2 DG B 24 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 3 DC A 1 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 3 DG A 2 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 3 DC A 3 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 3 DA A 5 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 3 DA A 6 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 3 DT A 7 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 242 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2MWU RELATED DB: PDB REMARK 900 RELATED ID: 25369 RELATED DB: BMRB REMARK 900 RELATED ID: 25528 RELATED DB: BMRB DBREF 2N0L A 1 12 PDB 2N0L 2N0L 1 12 DBREF 2N0L B 13 24 PDB 2N0L 2N0L 13 24 SEQRES 1 A 12 DC DG DC 8OG DA DA DT DT DC DG DC DG SEQRES 1 B 12 DC DG DC 8OG DA DA DT DT DC DG DC DG MODRES 2N0L 8OG A 4 DG MODRES 2N0L 8OG B 16 DG HET 8OG A 4 34 HET 8OG B 16 34 HETNAM 8OG 8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE HETSYN 8OG 8-OXO-7,8-DIHYDRO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE FORMUL 1 8OG 2(C10 H14 N5 O8 P) LINK O3' DC A 3 P 8OG A 4 1555 1555 1.61 LINK O3' 8OG A 4 P DA A 5 1555 1555 1.61 LINK O3' DC B 15 P 8OG B 16 1555 1555 1.61 LINK O3' 8OG B 16 P DA B 17 1555 1555 1.61 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1