HEADER DNA 11-MAY-21 7OHJ TITLE A SELF-COMPLEMENTARY DNA DODECAMER DUPLEX CONTANING 5- TITLE 2 HYDROXYMETHYLCITOSINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*CP*GP*AP*CP*GP*TP*CP*G)-3'); COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 3 ORGANISM_TAXID: 32630; SOURCE 4 EXPRESSION_SYSTEM: SYNTHETIC CONSTRUCT; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 32630 KEYWDS 5-HYDROXYMETHYLCITOSINE, CHEMICALLY MODIFIED DNA, DNA DUPLEX, KEYWDS 2 EPIGENETICS, DNA EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR F.BATTISTINI,P.D.DANS,M.TERRAZAS,C.L.CASTELLAZZI,G.PORTELLA, AUTHOR 2 M.LABRADOR,N.VILLEGAS,I.BRUN-HEATH,C.GONZALEZ,M.OROZCO REVDAT 4 19-JUN-24 7OHJ 1 REMARK REVDAT 3 14-JUN-23 7OHJ 1 REMARK REVDAT 2 17-NOV-21 7OHJ 1 JRNL REVDAT 1 03-NOV-21 7OHJ 0 JRNL AUTH F.BATTISTINI,P.D.DANS,M.TERRAZAS,C.L.CASTELLAZZI,G.PORTELLA, JRNL AUTH 2 M.LABRADOR,N.VILLEGAS,I.BRUN-HEATH,C.GONZALEZ,M.OROZCO JRNL TITL THE IMPACT OF THE HYDROXYMETHYLCYTOSINE EPIGENETIC SIGNATURE JRNL TITL 2 ON DNA STRUCTURE AND FUNCTION. JRNL REF PLOS COMPUT.BIOL. V. 17 09547 2021 JRNL REFN ESSN 1553-7358 JRNL PMID 34748533 JRNL DOI 10.1371/JOURNAL.PCBI.1009547 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 7OHJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 11-MAY-21. REMARK 100 THE DEPOSITION ID IS D_1292115778. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 278 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 125 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 1 MM DNA (5' REMARK 210 -D(*CP*GP*AP*CP*GP*TP*CP*G)-3'), REMARK 210 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D DQF-COSY; 2D REMARK 210 1H-1H TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : AMBER, SPARKY REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 10 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : NONE 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 780 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 3140 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -3.0 KCAL/MOL 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 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 1 DA A 3 C5' DA A 3 C4' 0.043 REMARK 500 1 DA A 3 C5 DA A 3 N7 0.044 REMARK 500 1 DC A 4 C5' DC A 4 C4' 0.055 REMARK 500 1 DG A 5 O3' DG A 5 C3' -0.041 REMARK 500 1 DG A 5 C8 DG A 5 N9 -0.058 REMARK 500 1 DG A 8 N3 DG A 8 C4 0.044 REMARK 500 1 DC B 9 C5' DC B 9 C4' 0.061 REMARK 500 1 DG B 16 C8 DG B 16 N9 -0.060 REMARK 500 2 DG A 2 C2 DG A 2 N2 -0.075 REMARK 500 2 DG A 5 P DG A 5 O5' 0.060 REMARK 500 2 DG A 5 C5' DG A 5 C4' 0.050 REMARK 500 2 DT A 6 C5' DT A 6 C4' 0.050 REMARK 500 2 DG A 8 C5 DG A 8 N7 0.039 REMARK 500 2 DA B 11 N9 DA B 11 C4 -0.043 REMARK 500 2 DG B 13 O4' DG B 13 C4' -0.071 REMARK 500 2 DG B 13 N3 DG B 13 C4 0.045 REMARK 500 2 DG B 16 C5' DG B 16 C4' 0.074 REMARK 500 3 DC A 1 C5' DC A 1 C4' 0.042 REMARK 500 3 DG A 2 O4' DG A 2 C4' -0.065 REMARK 500 3 DG A 2 N1 DG A 2 C2 -0.052 REMARK 500 3 DC A 4 P DC A 4 O5' 0.074 REMARK 500 3 DC A 4 C5' DC A 4 C4' 0.042 REMARK 500 3 DC A 7 C5' DC A 7 C4' 0.046 REMARK 500 3 DG A 8 O4' DG A 8 C4' -0.082 REMARK 500 3 DG A 8 N1 DG A 8 C2 -0.058 REMARK 500 3 DG A 8 C2 DG A 8 N2 -0.065 REMARK 500 3 DC B 9 N3 DC B 9 C4 -0.052 REMARK 500 3 DA B 11 N9 DA B 11 C4 -0.036 REMARK 500 3 DG B 13 C8 DG B 13 N9 -0.045 REMARK 500 4 DG A 2 C5' DG A 2 C4' 0.044 REMARK 500 4 DA A 3 C5 DA A 3 N7 0.043 REMARK 500 4 DG A 5 C5' DG A 5 C4' 0.047 REMARK 500 4 DG A 5 N1 DG A 5 C2 -0.062 REMARK 500 4 DT A 6 O4' DT A 6 C4' -0.084 REMARK 500 4 DG A 8 C5' DG A 8 C4' 0.079 REMARK 500 4 DG A 8 C8 DG A 8 N9 -0.058 REMARK 500 4 DG B 10 N3 DG B 10 C4 0.051 REMARK 500 4 DA B 11 C5 DA B 11 N7 0.047 REMARK 500 4 DA B 11 C6 DA B 11 N6 -0.052 REMARK 500 4 DG B 13 C5' DG B 13 C4' 0.066 REMARK 500 4 DT B 14 C6 DT B 14 N1 -0.050 REMARK 500 4 DG B 16 N3 DG B 16 C4 0.048 REMARK 500 4 DG B 16 C8 DG B 16 N9 -0.046 REMARK 500 5 DG A 2 C2 DG A 2 N2 -0.067 REMARK 500 5 DG A 5 C2 DG A 5 N2 -0.068 REMARK 500 5 DC A 7 C5' DC A 7 C4' 0.064 REMARK 500 5 DG A 8 C5' DG A 8 C4' 0.063 REMARK 500 5 DA B 11 C5' DA B 11 C4' 0.048 REMARK 500 5 DG B 13 C2 DG B 13 N2 -0.060 REMARK 500 5 DT B 14 C5 DT B 14 C7 0.039 REMARK 500 REMARK 500 THIS ENTRY HAS 100 BOND DEVIATIONS. 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 1 DC A 1 C2 - N3 - C4 ANGL. DEV. = -4.0 DEGREES REMARK 500 1 DC A 1 N3 - C4 - C5 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 DG A 2 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DA A 3 O4' - C4' - C3' ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DA A 3 C4 - C5 - C6 ANGL. DEV. = -4.9 DEGREES REMARK 500 1 DA A 3 C5 - C6 - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 1 DA A 3 C6 - C5 - N7 ANGL. DEV. = 5.8 DEGREES REMARK 500 1 DA A 3 N1 - C6 - N6 ANGL. DEV. = -6.1 DEGREES REMARK 500 1 DC A 4 O4' - C4' - C3' ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DG A 5 O4' - C4' - C3' ANGL. DEV. = 4.2 DEGREES REMARK 500 1 DG A 5 N1 - C6 - O6 ANGL. DEV. = -4.1 DEGREES REMARK 500 1 DT A 6 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 1 DC A 7 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 1 DC A 7 N1 - C2 - O2 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DG A 8 C5 - N7 - C8 ANGL. DEV. = -3.2 DEGREES REMARK 500 1 DG A 8 N9 - C4 - C5 ANGL. DEV. = -2.7 DEGREES REMARK 500 1 DG A 8 C5 - C6 - O6 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DC B 9 C3' - C2' - C1' ANGL. DEV. = -5.3 DEGREES REMARK 500 1 DC B 9 O4' - C1' - C2' ANGL. DEV. = 4.7 DEGREES REMARK 500 1 DC B 9 N1 - C2 - N3 ANGL. DEV. = 5.1 DEGREES REMARK 500 1 DC B 9 C2 - N3 - C4 ANGL. DEV. = -5.4 DEGREES REMARK 500 1 DC B 9 N3 - C4 - C5 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DC B 9 N1 - C2 - O2 ANGL. DEV. = 4.9 DEGREES REMARK 500 1 DC B 9 N3 - C2 - O2 ANGL. DEV. = -10.0 DEGREES REMARK 500 1 DG B 10 O4' - C4' - C3' ANGL. DEV. = 4.7 DEGREES REMARK 500 1 DG B 10 O4' - C1' - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DG B 10 C5 - N7 - C8 ANGL. DEV. = -3.3 DEGREES REMARK 500 1 DG B 10 N7 - C8 - N9 ANGL. DEV. = 5.2 DEGREES REMARK 500 1 DG B 10 C8 - N9 - C4 ANGL. DEV. = -4.0 DEGREES REMARK 500 1 DG B 10 N9 - C4 - C5 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DG B 10 N1 - C6 - O6 ANGL. DEV. = -4.3 DEGREES REMARK 500 1 DG B 10 C5 - C6 - O6 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DA B 11 O4' - C4' - C3' ANGL. DEV. = 6.4 DEGREES REMARK 500 1 DA B 11 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 DA B 11 N1 - C2 - N3 ANGL. DEV. = -4.6 DEGREES REMARK 500 1 DA B 11 C2 - N3 - C4 ANGL. DEV. = 4.0 DEGREES REMARK 500 1 DA B 11 C4 - C5 - C6 ANGL. DEV. = -5.1 DEGREES REMARK 500 1 DA B 11 C5 - C6 - N1 ANGL. DEV. = 5.6 DEGREES REMARK 500 1 DA B 11 C6 - C5 - N7 ANGL. DEV. = 5.3 DEGREES REMARK 500 1 DA B 11 N1 - C6 - N6 ANGL. DEV. = -6.5 DEGREES REMARK 500 1 DA B 11 C3' - O3' - P ANGL. DEV. = 9.0 DEGREES REMARK 500 1 DC B 12 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 DC B 12 N3 - C2 - O2 ANGL. DEV. = -5.5 DEGREES REMARK 500 1 DC B 12 N3 - C4 - N4 ANGL. DEV. = -7.4 DEGREES REMARK 500 1 DC B 12 C5 - C4 - N4 ANGL. DEV. = 5.5 DEGREES REMARK 500 1 DG B 13 O4' - C4' - C3' ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DG B 13 C6 - N1 - C2 ANGL. DEV. = -3.6 DEGREES REMARK 500 1 DG B 13 C5 - C6 - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 1 DG B 13 C5 - N7 - C8 ANGL. DEV. = -3.8 DEGREES REMARK 500 1 DG B 13 N1 - C6 - O6 ANGL. DEV. = -5.3 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 602 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 1 DC A 1 0.08 SIDE CHAIN REMARK 500 1 DG A 2 0.16 SIDE CHAIN REMARK 500 1 DA A 3 0.08 SIDE CHAIN REMARK 500 1 DG A 5 0.07 SIDE CHAIN REMARK 500 1 DC A 7 0.09 SIDE CHAIN REMARK 500 1 DG A 8 0.10 SIDE CHAIN REMARK 500 1 DA B 11 0.12 SIDE CHAIN REMARK 500 1 DC B 12 0.06 SIDE CHAIN REMARK 500 1 DG B 13 0.07 SIDE CHAIN REMARK 500 1 DC B 15 0.08 SIDE CHAIN REMARK 500 2 DG A 2 0.07 SIDE CHAIN REMARK 500 2 DA A 3 0.07 SIDE CHAIN REMARK 500 2 DG A 5 0.07 SIDE CHAIN REMARK 500 2 DC A 7 0.09 SIDE CHAIN REMARK 500 2 DG A 8 0.10 SIDE CHAIN REMARK 500 2 DG B 10 0.08 SIDE CHAIN REMARK 500 2 DA B 11 0.13 SIDE CHAIN REMARK 500 2 DG B 13 0.09 SIDE CHAIN REMARK 500 2 DT B 14 0.10 SIDE CHAIN REMARK 500 2 DC B 15 0.07 SIDE CHAIN REMARK 500 3 DC A 1 0.10 SIDE CHAIN REMARK 500 3 DG A 2 0.11 SIDE CHAIN REMARK 500 3 DC A 4 0.09 SIDE CHAIN REMARK 500 3 DG A 5 0.08 SIDE CHAIN REMARK 500 3 DT A 6 0.09 SIDE CHAIN REMARK 500 3 DC A 7 0.07 SIDE CHAIN REMARK 500 3 DG A 8 0.12 SIDE CHAIN REMARK 500 3 DC B 9 0.12 SIDE CHAIN REMARK 500 3 DG B 10 0.08 SIDE CHAIN REMARK 500 3 DA B 11 0.15 SIDE CHAIN REMARK 500 3 DC B 12 0.07 SIDE CHAIN REMARK 500 3 DG B 13 0.08 SIDE CHAIN REMARK 500 3 DC B 15 0.10 SIDE CHAIN REMARK 500 4 DC A 1 0.08 SIDE CHAIN REMARK 500 4 DG A 2 0.10 SIDE CHAIN REMARK 500 4 DA A 3 0.06 SIDE CHAIN REMARK 500 4 DG A 5 0.10 SIDE CHAIN REMARK 500 4 DC A 7 0.10 SIDE CHAIN REMARK 500 4 DC B 9 0.10 SIDE CHAIN REMARK 500 4 DG B 10 0.10 SIDE CHAIN REMARK 500 4 DA B 11 0.08 SIDE CHAIN REMARK 500 4 DC B 12 0.06 SIDE CHAIN REMARK 500 4 DT B 14 0.06 SIDE CHAIN REMARK 500 4 DC B 15 0.10 SIDE CHAIN REMARK 500 5 DC A 1 0.12 SIDE CHAIN REMARK 500 5 DG A 2 0.11 SIDE CHAIN REMARK 500 5 DC A 4 0.11 SIDE CHAIN REMARK 500 5 DG A 5 0.07 SIDE CHAIN REMARK 500 5 DT A 6 0.08 SIDE CHAIN REMARK 500 5 DC A 7 0.07 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 111 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7OGV RELATED DB: PDB REMARK 900 RELATED STRUCTURE REMARK 900 RELATED ID: 7OHE RELATED DB: PDB REMARK 900 RELATED STRUCTURE REMARK 900 RELATED ID: 34625 RELATED DB: BMRB REMARK 900 A SELF-COMPLEMENTARY DNA DODECAMER DUPLEX CONTANING 5- REMARK 900 HYDROXYMETHYLCITOSINE DBREF 7OHJ A 1 8 PDB 7OHJ 7OHJ 1 8 DBREF 7OHJ B 9 16 PDB 7OHJ 7OHJ 9 16 SEQRES 1 A 8 DC DG DA DC DG DT DC DG SEQRES 1 B 8 DC DG DA DC DG DT DC DG 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