HEADER DNA 09-NOV-12 2M11 TITLE STRUCTURE OF PERIMIDINONE-DERIVED SYNTHETIC NUCLEOSIDE PAIRED WITH TITLE 2 GUANINE IN DNA DUPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(D3N)P*GP*CP*G)-3'); COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS B-FORM DNA, DPER, PERIMIDINONE-DERIVED NUCLEOSIDE, DICKERSON-DREW KEYWDS 2 DODECAMER, DNA EXPDTA SOLUTION NMR NUMMDL 10 MDLTYP MINIMIZED AVERAGE AUTHOR E.A.KOWAL,R.LAD,P.S.PALLAN,E.MUFFLY,Z.WAWRZAK,M.EGLI,S.J.STURLA, AUTHOR 2 M.P.STONE REVDAT 3 11-SEP-13 2M11 1 JRNL REVDAT 2 03-JUL-13 2M11 1 JRNL REVDAT 1 12-JUN-13 2M11 0 JRNL AUTH E.A.KOWAL,R.R.LAD,P.S.PALLAN,E.DHUMMAKUPT,Z.WAWRZAK,M.EGLI, JRNL AUTH 2 S.J.STURLA,M.P.STONE JRNL TITL RECOGNITION OF O6-BENZYL-2'-DEOXYGUANOSINE BY A JRNL TITL 2 PERIMIDINONE-DERIVED SYNTHETIC NUCLEOSIDE: A DNA INTERSTRAND JRNL TITL 3 STACKING INTERACTION. JRNL REF NUCLEIC ACIDS RES. V. 41 7566 2013 JRNL REFN ISSN 0305-1048 JRNL PMID 23748954 JRNL DOI 10.1093/NAR/GKT488 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 2M11 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-NOV-12. REMARK 100 THE RCSB ID CODE IS RCSB103073. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 283; 278 REMARK 210 PH : 7.0; 7.0 REMARK 210 IONIC STRENGTH : 100; 100 REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 0.53 MM 5'-D(*CP*GP*CP*GP*AP*AP* REMARK 210 TP*TP)[D3N]P-D(*GP*CP*GP)-3', 100 MM SODIUM CHLORIDE, 50 UM EDTA, REMARK 210 10 MM SODIUM PHOSPHATE, 100% D2O; 0.53 MM 5'-D(*CP*GP*CP*GP*AP* REMARK 210 AP*TP*TP)[D3N]P-D(*GP*CP*GP)-3', 10 MM SODIUM PHOSPHATE, 50 UM REMARK 210 EDTA, 100 MM SODIUM CHLORIDE, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-1H COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN, CORMA, CURVES 5.3, REMARK 210 MARDIGRAS, SPARKY REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 10 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : BACK CALCULATED DATA AGREE WITH REMARK 210 EXPERIMENTAL NOESY SPECTRUM 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 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 DC A 1 O5' DC A 1 C5' -0.417 REMARK 500 1 DC A 1 C5' DC A 1 C4' -0.135 REMARK 500 1 DC A 1 C4' DC A 1 C3' -0.167 REMARK 500 1 DC A 1 C2' DC A 1 C1' -0.063 REMARK 500 1 DC A 1 O4' DC A 1 C1' -0.095 REMARK 500 1 DC A 1 O3' DC A 1 C3' -0.092 REMARK 500 1 DC A 1 N1 DC A 1 C6 -0.039 REMARK 500 1 DC A 1 N3 DC A 1 C4 -0.048 REMARK 500 1 DG A 2 P DG A 2 OP1 -0.157 REMARK 500 1 DG A 2 P DG A 2 OP2 -0.139 REMARK 500 1 DG A 2 O5' DG A 2 C5' -0.528 REMARK 500 1 DC A 1 O3' DG A 2 P -0.127 REMARK 500 1 DC B 13 O5' DC B 13 C5' -0.556 REMARK 500 2 DC B 13 C5' DC B 13 C4' 0.046 REMARK 500 3 DG B 22 C5 DG B 22 N7 0.036 REMARK 500 4 DT B 19 C5 DT B 19 C7 0.042 REMARK 500 5 DG B 16 C5' DG B 16 C4' 0.047 REMARK 500 7 DG A 12 C5' DG A 12 C4' 0.042 REMARK 500 7 DT B 19 C5 DT B 19 C7 0.040 REMARK 500 8 DG A 4 C5 DG A 4 N7 0.036 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 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES REMARK 500 1 DC A 1 N3 - C2 - O2 ANGL. DEV. = -5.2 DEGREES REMARK 500 1 DG A 2 O5' - C5' - C4' ANGL. DEV. = 26.2 DEGREES REMARK 500 1 DG A 2 P - O5' - C5' ANGL. DEV. = 22.5 DEGREES REMARK 500 1 DC A 3 O4' - C1' - N1 ANGL. DEV. = 5.1 DEGREES REMARK 500 1 DC A 3 N3 - C2 - O2 ANGL. DEV. = -5.2 DEGREES REMARK 500 1 DG A 4 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DA A 5 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DA A 5 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 1 DA A 5 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DA A 5 N1 - C6 - N6 ANGL. DEV. = -4.7 DEGREES REMARK 500 1 DA A 6 C5 - C6 - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DA A 6 N1 - C6 - N6 ANGL. DEV. = -4.9 DEGREES REMARK 500 1 DT A 7 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 1 DT A 7 N3 - C2 - O2 ANGL. DEV. = -3.9 DEGREES REMARK 500 1 DT A 8 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 1 DT A 8 N3 - C2 - O2 ANGL. DEV. = -4.0 DEGREES REMARK 500 1 DT A 8 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 1 DG A 10 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 1 DC A 11 N1 - C2 - O2 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DC A 11 N3 - C2 - O2 ANGL. DEV. = -5.4 DEGREES REMARK 500 1 DG A 12 O4' - C1' - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DC B 13 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 1 DC B 13 N3 - C2 - O2 ANGL. DEV. = -5.1 DEGREES REMARK 500 1 DC B 15 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 1 DC B 15 N1 - C2 - O2 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 DC B 15 N3 - C2 - O2 ANGL. DEV. = -5.2 DEGREES REMARK 500 1 DG B 16 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DA B 17 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 1 DA B 17 C4 - C5 - C6 ANGL. DEV. = -3.3 DEGREES REMARK 500 1 DA B 17 C5 - C6 - N1 ANGL. DEV. = 3.3 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. = 3.5 DEGREES REMARK 500 1 DA B 18 N1 - C6 - N6 ANGL. DEV. = -4.6 DEGREES REMARK 500 1 DT B 19 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 1 DT B 19 N3 - C2 - O2 ANGL. DEV. = -4.1 DEGREES REMARK 500 1 DT B 20 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 1 DT B 20 N3 - C2 - O2 ANGL. DEV. = -4.2 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. = -5.1 DEGREES REMARK 500 1 DG B 24 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 2 DC A 1 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 2 DC A 1 N3 - C2 - O2 ANGL. DEV. = -5.1 DEGREES REMARK 500 2 DG A 2 N1 - C6 - O6 ANGL. DEV. = -4.0 DEGREES REMARK 500 2 DC A 3 O4' - C1' - N1 ANGL. DEV. = 5.9 DEGREES REMARK 500 2 DC A 3 N1 - C2 - O2 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 DC A 3 N3 - C2 - O2 ANGL. DEV. = -5.6 DEGREES REMARK 500 2 DG A 4 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 2 DG A 4 N1 - C6 - O6 ANGL. DEV. = -3.7 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 394 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 6 DG A 2 0.06 SIDE CHAIN REMARK 500 7 DG B 14 0.07 SIDE CHAIN REMARK 500 8 DG A 2 0.08 SIDE CHAIN REMARK 500 9 DG A 2 0.05 SIDE CHAIN REMARK 500 10 DG A 2 0.07 SIDE CHAIN REMARK 500 10 DG B 14 0.06 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 18835 RELATED DB: BMRB REMARK 900 RELATED ID: 4HQI RELATED DB: PDB DBREF 2M11 A 1 12 PDB 2M11 2M11 1 12 DBREF 2M11 B 13 24 PDB 2M11 2M11 13 24 SEQRES 1 A 12 DC DG DC DG DA DA DT DT D3N DG DC DG SEQRES 1 B 12 DC DG DC DG DA DA DT DT D3N DG DC DG HET D3N A 9 39 HET D3N B 21 39 HETNAM D3N 1-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO- HETNAM 2 D3N PENTOFURANOSYL)-1H-PERIMIDIN-2(3H)-ONE FORMUL 1 D3N 2(C16 H17 N2 O7 P) LINK O3' DT A 8 P D3N A 9 1555 1555 1.62 LINK O3' DT B 20 P D3N B 21 1555 1555 1.62 LINK O3' D3N A 9 P DG A 10 1555 1555 1.60 LINK O3' D3N B 21 P DG B 22 1555 1555 1.60 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