PDB Short entry for 5L06 HEADER DNA 26-JUL-16 5L06 TITLE SOLUTION STRUCTURE OF A DNA DODECAMER WITH 5-METHYLCYTOSINE AT THE 3RD TITLE 2 POSITION COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*CP*GP*(5CM)P*GP*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, NON-CANONICAL, MODIFIED DNA, METHYLATED DNA, KEYWDS 2 EPIGENETICS, CPG SITE EXPDTA SOLUTION NMR NUMMDL 9 AUTHOR H.L.MIEARS,J.J.HOPPINS,D.R.GRUBER,R.D.KASYMOV,D.O.ZHARKOV,S.L.SMIRNOV REVDAT 5 01-MAY-24 5L06 1 REMARK REVDAT 4 27-NOV-19 5L06 1 REMARK REVDAT 3 19-DEC-18 5L06 1 JRNL REVDAT 2 20-SEP-17 5L06 1 COMPND REVDAT 1 21-DEC-16 5L06 0 JRNL AUTH D.R.GRUBER,J.J.TONER,H.L.MIEARS,A.V.SHERNYUKOV,A.S.KIRYUTIN, JRNL AUTH 2 A.A.LOMZOV,A.V.ENDUTKIN,I.R.GRIN,D.V.PETROVA, JRNL AUTH 3 M.S.KUPRYUSHKIN,A.V.YURKOVSKAYA,E.C.JOHNSON,M.OKON, JRNL AUTH 4 E.G.BAGRYANSKAYA,D.O.ZHARKOV,S.L.SMIRNOV JRNL TITL OXIDATIVE DAMAGE TO EPIGENETICALLY METHYLATED SITES AFFECTS JRNL TITL 2 DNA STABILITY, DYNAMICS AND ENZYMATIC DEMETHYLATION. JRNL REF NUCLEIC ACIDS RES. V. 46 10827 2018 JRNL REFN ESSN 1362-4962 JRNL PMID 30289469 JRNL DOI 10.1093/NAR/GKY893 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 12 REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, ... AND KOLLMAN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5L06 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-JUL-16. REMARK 100 THE DEPOSITION ID IS D_1000222513. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298; 278 REMARK 210 PH : 6.8; 6.8 REMARK 210 IONIC STRENGTH : 120; 120 REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 50 MM SODIUM CHLORIDE, 10 MM REMARK 210 POTASSIUM PHOSPHATE, 0.1 MM EDTA, 1 MM DNA (5'-D(*CP*GP*(DMC)P* REMARK 210 GP*AP*AP*TP*TP*CP*GP*CP*G)-3'), 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-1H TOCSY; REMARK 210 2D DQF-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRVIEW 9.0, NMRPIPE, CYANA 2.1, REMARK 210 AMBER 12 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 18 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 9 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 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. = 3.0 DEGREES REMARK 500 1 DC A 1 N1 - C2 - O2 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DC A 1 N3 - C2 - O2 ANGL. DEV. = -5.5 DEGREES REMARK 500 1 DG A 4 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 1 DA A 5 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 1 DA A 5 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES REMARK 500 1 DA A 5 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DA A 5 N1 - C6 - N6 ANGL. DEV. = -4.4 DEGREES REMARK 500 1 DA A 6 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES REMARK 500 1 DA A 6 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DA A 6 N1 - C6 - N6 ANGL. DEV. = -4.9 DEGREES REMARK 500 1 DC A 9 N3 - C2 - O2 ANGL. DEV. = -5.2 DEGREES REMARK 500 1 DG A 10 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 1 DC A 11 N3 - C2 - O2 ANGL. DEV. = -5.3 DEGREES REMARK 500 1 DG A 12 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DC B 13 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DC B 13 N1 - C2 - O2 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DC B 13 N3 - C2 - O2 ANGL. DEV. = -5.4 DEGREES REMARK 500 1 DG B 16 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DA B 17 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES REMARK 500 1 DA B 17 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DA B 17 N1 - C6 - N6 ANGL. DEV. = -4.4 DEGREES REMARK 500 1 DA B 18 C4 - C5 - C6 ANGL. DEV. = -3.3 DEGREES REMARK 500 1 DA B 18 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DA B 18 N1 - C6 - N6 ANGL. DEV. = -4.9 DEGREES REMARK 500 1 DT B 19 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 1 DC B 21 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 1 DC B 21 N3 - C2 - O2 ANGL. DEV. = -5.1 DEGREES REMARK 500 1 DG B 22 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 1 DC B 23 N3 - C2 - O2 ANGL. DEV. = -5.2 DEGREES REMARK 500 1 DG B 24 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 2 DC A 1 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 2 DC A 1 N3 - C2 - O2 ANGL. DEV. = -5.4 DEGREES REMARK 500 2 DG A 4 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 2 DA A 5 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 2 DA A 5 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES REMARK 500 2 DA A 5 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 2 DA A 5 N1 - C6 - N6 ANGL. DEV. = -4.4 DEGREES REMARK 500 2 DA A 6 C4 - C5 - C6 ANGL. DEV. = -3.3 DEGREES REMARK 500 2 DA A 6 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 2 DA A 6 N1 - C6 - N6 ANGL. DEV. = -5.0 DEGREES REMARK 500 2 DC A 9 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 2 DC A 9 N3 - C2 - O2 ANGL. DEV. = -5.1 DEGREES REMARK 500 2 DG A 10 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 2 DC A 11 N3 - C2 - O2 ANGL. DEV. = -5.2 DEGREES REMARK 500 2 DG A 12 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 2 DC B 13 N3 - C2 - O2 ANGL. DEV. = -5.2 DEGREES REMARK 500 2 DG B 16 O4' - C1' - N9 ANGL. DEV. = 1.8 DEGREES REMARK 500 2 DA B 17 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 2 DA B 17 C4 - C5 - C6 ANGL. DEV. = -3.3 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 271 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 5 DG B 16 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 30044 RELATED DB: BMRB REMARK 900 SAME SEQUENCE WITH A DIFFERENT, 8-OXOGUANINE, MODIFICATION REMARK 900 RELATED ID: 30038 RELATED DB: BMRB REMARK 900 SAME SEQUENCE WITH A DIFFERENT, 8-OXOGUANINE, MODIFICATION REMARK 900 RELATED ID: 5IZP RELATED DB: PDB REMARK 900 SAME SEQUENCE WITH A DIFFERENT, 8-OXOGUANINE, MODIFICATION REMARK 900 RELATED ID: 5IV1 RELATED DB: PDB REMARK 900 SAME SEQUENCE WITH A DIFFERENT, 8-OXOGUANINE, MODIFICATION REMARK 900 RELATED ID: 30148 RELATED DB: BMRB DBREF 5L06 A 1 12 PDB 5L06 5L06 1 12 DBREF 5L06 B 13 24 PDB 5L06 5L06 13 24 SEQRES 1 A 12 DC DG 5CM DG DA DA DT DT DC DG DC DG SEQRES 1 B 12 DC DG 5CM DG DA DA DT DT DC DG DC DG HET 5CM A 3 33 HET 5CM B 15 33 HETNAM 5CM 5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE FORMUL 1 5CM 2(C10 H16 N3 O7 P) LINK O3' DG A 2 P 5CM A 3 1555 1555 1.62 LINK O3' 5CM A 3 P DG A 4 1555 1555 1.62 LINK O3' DG B 14 P 5CM B 15 1555 1555 1.62 LINK O3' 5CM B 15 P DG B 16 1555 1555 1.62 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