HEADER DNA 08-AUG-17 6ALT TITLE SOLUTION STRUCTURE OF A DNA DODECAMER WITH 5-METHYLCYTOSINE AT THE 3RD TITLE 2 AND 9TH POSITION COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*(DC5)P*GP*(DMC)P*GP*AP*AP*TP*TP*(DMC) COMPND 3 P*GP*CP*(DG3))-3'); COMPND 4 CHAIN: A, B; COMPND 5 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, EPIGENETICS EXPDTA SOLUTION NMR NUMMDL 11 AUTHOR D.R.GRUBER,J.J.HOPPINS,H.L.MIEARS,D.O.ZHARKOV,S.L.SMIRNOV REVDAT 4 27-NOV-19 6ALT 1 REMARK REVDAT 3 19-DEC-18 6ALT 1 JRNL REVDAT 2 27-SEP-17 6ALT 1 REMARK REVDAT 1 20-SEP-17 6ALT 0 SPRSDE 20-SEP-17 6ALT 5TMI 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 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 6ALT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-AUG-17. REMARK 100 THE DEPOSITION ID IS D_1000229436. 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(*(DC5)P*GP*(DMC) REMARK 210 P*GP*AP*AP*TP*TP*(DMC)P*GP*CP*(DG3))-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 : AMBER, NMRVIEW, NMRPIPE, CYANA REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 18 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 11 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 DG A 2 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 1 DG A 4 O4' - C1' - N9 ANGL. DEV. = 4.0 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. = -4.7 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. = -4.7 DEGREES REMARK 500 1 DT A 7 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 1 DT A 7 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 1 DG A 10 O4' - C1' - N9 ANGL. DEV. = 2.4 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. = 3.8 DEGREES REMARK 500 1 DG B 16 O4' - C1' - N9 ANGL. DEV. = 3.5 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. = 3.7 DEGREES REMARK 500 1 DA B 17 N1 - C6 - N6 ANGL. DEV. = -4.6 DEGREES REMARK 500 1 DA B 18 C4 - C5 - C6 ANGL. DEV. = -3.2 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. = -4.7 DEGREES REMARK 500 1 DT B 19 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 1 DT B 19 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 DG B 22 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DC B 23 N3 - C2 - O2 ANGL. DEV. = -5.3 DEGREES REMARK 500 1 DG B 24 O4' - C1' - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 DG A 2 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 2 DG A 4 O4' - C1' - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 2 DA A 5 O4' - C1' - N9 ANGL. DEV. = 1.9 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. = 3.7 DEGREES REMARK 500 2 DA A 5 N1 - C6 - N6 ANGL. DEV. = -4.7 DEGREES REMARK 500 2 DA A 6 C4 - C5 - C6 ANGL. DEV. = -3.2 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. = -4.8 DEGREES REMARK 500 2 DT A 7 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 2 DT A 7 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 2 DG A 10 O4' - C1' - N9 ANGL. DEV. = 2.2 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. = 3.6 DEGREES REMARK 500 2 DG B 16 O4' - C1' - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 2 DA B 17 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 2 DA B 17 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 2 DA B 17 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 2 DA B 17 N1 - C6 - N6 ANGL. DEV. = -4.6 DEGREES REMARK 500 2 DA B 18 C4 - C5 - C6 ANGL. DEV. = -3.3 DEGREES REMARK 500 2 DA B 18 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 2 DA B 18 N1 - C6 - N6 ANGL. DEV. = -4.7 DEGREES REMARK 500 2 DT B 19 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 2 DT B 19 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 2 DG B 22 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 304 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 30191 RELATED DB: BMRB DBREF 6ALT A 1 12 PDB 6ALT 6ALT 1 12 DBREF 6ALT B 13 24 PDB 6ALT 6ALT 13 24 SEQRES 1 A 12 DCZ DG 5CM DG DA DA DT DT 5CM DG DC DG SEQRES 1 B 12 DCZ DG 5CM DG DA DA DT DT 5CM DG DC DG HET DCZ A 1 28 HET 5CM A 3 33 HET 5CM A 9 33 HET DCZ B 13 28 HET 5CM B 15 33 HET 5CM B 21 33 HETNAM DCZ 2'-DEOXYCYTIDINE HETNAM 5CM 5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE FORMUL 1 DCZ 2(C9 H13 N3 O4) FORMUL 1 5CM 4(C10 H16 N3 O7 P) LINK O3' DCZ A 1 P DG A 2 1555 1555 1.62 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' DT A 8 P 5CM A 9 1555 1555 1.62 LINK O3' 5CM A 9 P DG A 10 1555 1555 1.61 LINK O3' DCZ B 13 P DG B 14 1555 1555 1.62 LINK O3' DG B 14 P 5CM B 15 1555 1555 1.61 LINK O3' 5CM B 15 P DG B 16 1555 1555 1.62 LINK O3' DT B 20 P 5CM B 21 1555 1555 1.62 LINK O3' 5CM B 21 P DG B 22 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 HETATM 1 N1 DCZ A 1 1.443 -2.323 -2.679 1.00 0.00 N HETATM 2 C2 DCZ A 1 1.724 -0.949 -2.720 1.00 0.00 C HETATM 3 N3 DCZ A 1 0.784 -0.032 -2.388 1.00 0.00 N HETATM 4 C4 DCZ A 1 -0.391 -0.465 -1.979 1.00 0.00 C HETATM 5 C5 DCZ A 1 -0.733 -1.841 -1.879 1.00 0.00 C HETATM 6 C6 DCZ A 1 0.212 -2.748 -2.237 1.00 0.00 C HETATM 7 O2 DCZ A 1 2.825 -0.513 -3.061 1.00 0.00 O HETATM 8 N4 DCZ A 1 -1.273 0.457 -1.715 1.00 0.00 N HETATM 9 C1' DCZ A 1 2.482 -3.294 -3.133 1.00 0.00 C HETATM 10 C2' DCZ A 1 2.900 -4.328 -2.087 1.00 0.00 C HETATM 11 C3' DCZ A 1 3.293 -5.561 -2.915 1.00 0.00 C HETATM 12 C4' DCZ A 1 2.819 -5.202 -4.336 1.00 0.00 C HETATM 13 O4' DCZ A 1 1.996 -4.049 -4.225 1.00 0.00 O HETATM 14 O3' DCZ A 1 4.696 -5.812 -2.926 1.00 0.00 O HETATM 15 C5' DCZ A 1 2.068 -6.344 -5.044 1.00 0.00 C HETATM 16 O5' DCZ A 1 0.880 -6.740 -4.358 1.00 0.00 O HETATM 17 H5 DCZ A 1 -1.705 -2.175 -1.550 1.00 0.00 H HETATM 18 H6 DCZ A 1 -0.007 -3.810 -2.208 1.00 0.00 H HETATM 19 HN41 DCZ A 1 -0.992 1.426 -1.817 1.00 0.00 H HETATM 20 HN42 DCZ A 1 -2.190 0.195 -1.402 1.00 0.00 H HETATM 21 H1' DCZ A 1 3.383 -2.756 -3.451 1.00 0.00 H HETATM 22 H2'1 DCZ A 1 2.077 -4.588 -1.423 1.00 0.00 H HETATM 23 H2'2 DCZ A 1 3.733 -3.942 -1.505 1.00 0.00 H HETATM 24 H3' DCZ A 1 2.754 -6.438 -2.549 1.00 0.00 H HETATM 25 H4' DCZ A 1 3.696 -4.945 -4.934 1.00 0.00 H HETATM 26 H5'1 DCZ A 1 1.816 -6.019 -6.055 1.00 0.00 H HETATM 27 H5'2 DCZ A 1 2.741 -7.201 -5.125 1.00 0.00 H HETATM 28 HO5' DCZ A 1 0.274 -5.973 -4.304 1.00 0.00 H