HEADER DNA 05-DEC-06 2O4Y TITLE SOLUTION STRUCTURE OF A DNA DUPLEX CONTAINING THE UNIVERSAL BASE 5- TITLE 2 NITROINDOLE-3-CARBOXAMIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*GP*TP*AP*CP*(NCX)P*AP*CP*G)-3'); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'-D(*CP*GP*TP*TP*GP*TP*AP*C)-3'); COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630; SOURCE 5 OTHER_DETAILS: SYNTHESIZED BY SOLID PHASE METHODS USING 5- SOURCE 6 NITROINDOLE-3-CARBOXAMIDE PHOSPHORAMIDITE; SOURCE 7 MOL_ID: 2; SOURCE 8 SYNTHETIC: YES; SOURCE 9 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 10 ORGANISM_TAXID: 32630 KEYWDS DNA UNIVERSAL BASE NITROINDOLE INTERCALATION DYNAMICS, DNA EXPDTA SOLUTION NMR NUMMDL 28 AUTHOR J.GALLEGO,D.LOAKES REVDAT 4 03-OCT-18 2O4Y 1 SOURCE REMARK REVDAT 3 24-FEB-09 2O4Y 1 VERSN REVDAT 2 29-MAY-07 2O4Y 1 JRNL REVDAT 1 24-APR-07 2O4Y 0 JRNL AUTH J.GALLEGO,D.LOAKES JRNL TITL SOLUTION STRUCTURE AND DYNAMICS OF DNA DUPLEXES CONTAINING JRNL TITL 2 THE UNIVERSAL BASE ANALOGUES 5-NITROINDOLE AND 5-NITROINDOLE JRNL TITL 3 3-CARBOXAMIDE. JRNL REF NUCLEIC ACIDS RES. V. 35 2904 2007 JRNL REFN ISSN 0305-1048 JRNL PMID 17438041 JRNL DOI 10.1093/NAR/GKM074 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 8.0 REMARK 3 AUTHORS : D.A. CASE ET AL. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES WERE DETERMINED USING REMARK 3 SIMULATED ANNEALING USING MOLECULAR DYNAMICS WITH 440 NOE REMARK 3 DISTANCE RESTRAINTS (144 INTRA-RESIDUE AND 296 INTER-RESIDUE), REMARK 3 16 HYDROGEN BONDING DISTANCE RESTRAINTS AND 167 DIHEDRAL REMARK 3 RESTRAINTS. REMARK 4 REMARK 4 2O4Y COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-JAN-07. REMARK 100 THE DEPOSITION ID IS D_1000040692. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 311; 287 REMARK 210 PH : 6.9; 6.9 REMARK 210 IONIC STRENGTH : 100 MM NACL, 20MM SODIUM REMARK 210 PHOSPHATE; 100 MM NACL, 20MM REMARK 210 SODIUM PHOSPHATE REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 1.9 MM DNA, 20 MM PHOSPHATE REMARK 210 BUFFER, 100 MM NACL, 0.2 MM EDTA, REMARK 210 100% D2O; 1.9 MM DNA, 20 MM REMARK 210 PHOSPHATE BUFFER, 100 MM NACL, REMARK 210 0.2 MM EDTA, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 2D DQF-COSY; 2D TOCSY; REMARK 210 2D 1H-31P HETCOR; 2D ROESY 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 : TOPSPIN 1.3, NMRPIPE 2004, REMARK 210 SPARKY 3.110 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 28 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS,STRUCTURES REMARK 210 WITH THE LOWEST ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: MODEL 1 IS THE BEST REPRESENTATIVE CONFORMER BASED ON REMARK 210 LOWEST TOTAL ENERGY. MODEL 2 IS THE BEST REPRESENTATIVE REMARK 210 CONFORMER BASED ON RESTRAINT ENERGY. MODELS 1 AND 2 REPRESENT REMARK 210 TWO DIFFERENT STACKING CONFIGURATIONS OF THE NITROINDOLE BASE. 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 400 REMARK 400 COMPOUND REMARK 400 THE STRUCTURE OF ONE SYMMETRICAL HALF OF THE REMARK 400 SELF-COMPLEMENTARY (5'-D(*GP*TP*AP*CP*(NCX)P* REMARK 400 AP*CP*GP*CP*GP*TP*TP*GP*TP*AP*C)-3')2 DUPLEX REMARK 400 IS PROVIDED. THUS IN THE EXPERIMENT, CHAINS REMARK 400 A AND B HAD THE SAME SEQUENCE 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 1 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DA A 3 C5 - C6 - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DC A 7 O4' - C1' - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DG A 8 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DC B 9 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DC B 9 N3 - C2 - O2 ANGL. DEV. = -4.2 DEGREES REMARK 500 1 DT B 11 O4' - C4' - C3' ANGL. DEV. = 5.1 DEGREES REMARK 500 1 DT B 11 O4' - C1' - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DT B 11 N3 - C2 - O2 ANGL. DEV. = -3.8 DEGREES REMARK 500 1 DT B 12 N3 - C2 - O2 ANGL. DEV. = -4.3 DEGREES REMARK 500 1 DG B 13 O4' - C1' - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 1 DA B 15 C5 - C6 - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 2 DG A 1 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 2 DA A 3 C5 - C6 - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 2 DA A 6 O4' - C1' - N9 ANGL. DEV. = 1.8 DEGREES REMARK 500 2 DC A 7 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 2 DG A 8 O4' - C1' - N9 ANGL. DEV. = 1.8 DEGREES REMARK 500 2 DT B 11 O4' - C4' - C3' ANGL. DEV. = 5.0 DEGREES REMARK 500 2 DT B 11 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 2 DT B 11 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 2 DT B 12 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 2 DT B 12 N3 - C2 - O2 ANGL. DEV. = -4.0 DEGREES REMARK 500 2 DG B 13 O4' - C1' - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 2 DA B 15 C5 - C6 - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 3 DG A 1 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 3 DA A 3 C5 - C6 - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 3 DA A 6 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 3 DC A 7 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 3 DG B 10 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 3 DT B 11 O4' - C4' - C3' ANGL. DEV. = 5.1 DEGREES REMARK 500 3 DT B 11 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 3 DT B 11 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 3 DT B 12 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 3 DT B 12 N3 - C2 - O2 ANGL. DEV. = -4.0 DEGREES REMARK 500 3 DG B 13 O4' - C1' - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 3 DA B 15 C5 - C6 - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 4 DG A 1 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 4 DT A 2 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 4 DA A 3 C5 - C6 - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 4 DA A 6 O4' - C1' - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 4 DA A 6 C5 - C6 - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 4 DA A 6 N1 - C6 - N6 ANGL. DEV. = -5.7 DEGREES REMARK 500 4 DC A 7 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 4 DC A 7 N3 - C2 - O2 ANGL. DEV. = -4.3 DEGREES REMARK 500 4 DC B 9 N3 - C2 - O2 ANGL. DEV. = -4.3 DEGREES REMARK 500 4 DT B 11 O4' - C4' - C3' ANGL. DEV. = 5.6 DEGREES REMARK 500 4 DT B 11 C3' - C2' - C1' ANGL. DEV. = 7.5 DEGREES REMARK 500 4 DT B 11 O4' - C1' - N1 ANGL. DEV. = 5.2 DEGREES REMARK 500 4 DT B 11 N3 - C2 - O2 ANGL. DEV. = -4.0 DEGREES REMARK 500 4 DT B 12 N3 - C2 - O2 ANGL. DEV. = -4.0 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 344 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 DT B 12 0.12 SIDE CHAIN REMARK 500 2 DT B 12 0.10 SIDE CHAIN REMARK 500 3 DT B 12 0.10 SIDE CHAIN REMARK 500 4 DA A 6 0.07 SIDE CHAIN REMARK 500 4 DG A 8 0.08 SIDE CHAIN REMARK 500 4 DC B 9 0.06 SIDE CHAIN REMARK 500 4 DT B 11 0.08 SIDE CHAIN REMARK 500 4 DT B 12 0.11 SIDE CHAIN REMARK 500 5 DT B 12 0.10 SIDE CHAIN REMARK 500 6 DT B 12 0.10 SIDE CHAIN REMARK 500 7 DT B 12 0.10 SIDE CHAIN REMARK 500 10 DC A 4 0.09 SIDE CHAIN REMARK 500 10 DT B 12 0.10 SIDE CHAIN REMARK 500 11 DT B 11 0.06 SIDE CHAIN REMARK 500 12 DT B 11 0.06 SIDE CHAIN REMARK 500 12 DT B 12 0.10 SIDE CHAIN REMARK 500 13 DC A 4 0.09 SIDE CHAIN REMARK 500 13 DT B 12 0.10 SIDE CHAIN REMARK 500 14 DT B 12 0.12 SIDE CHAIN REMARK 500 15 DC A 4 0.07 SIDE CHAIN REMARK 500 15 DT B 12 0.10 SIDE CHAIN REMARK 500 16 DT B 12 0.09 SIDE CHAIN REMARK 500 17 DT B 12 0.10 SIDE CHAIN REMARK 500 18 DT B 12 0.09 SIDE CHAIN REMARK 500 19 DT B 12 0.09 SIDE CHAIN REMARK 500 20 DT B 12 0.12 SIDE CHAIN REMARK 500 21 DT B 12 0.10 SIDE CHAIN REMARK 500 23 DC A 4 0.07 SIDE CHAIN REMARK 500 23 DT B 12 0.10 SIDE CHAIN REMARK 500 24 DT B 11 0.06 SIDE CHAIN REMARK 500 24 DT B 12 0.10 SIDE CHAIN REMARK 500 25 DC A 7 0.06 SIDE CHAIN REMARK 500 25 DT B 12 0.10 SIDE CHAIN REMARK 500 26 DT B 12 0.08 SIDE CHAIN REMARK 500 27 DT A 2 0.07 SIDE CHAIN REMARK 500 27 DA A 6 0.07 SIDE CHAIN REMARK 500 27 DG A 8 0.07 SIDE CHAIN REMARK 500 27 DG B 10 0.07 SIDE CHAIN REMARK 500 27 DT B 12 0.18 SIDE CHAIN REMARK 500 28 DT B 11 0.07 SIDE CHAIN REMARK 500 28 DT B 12 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 2O4Y A 1 8 PDB 2O4Y 2O4Y 1 8 DBREF 2O4Y B 9 16 PDB 2O4Y 2O4Y 9 16 SEQRES 1 A 8 DG DT DA DC NCX DA DC DG SEQRES 1 B 8 DC DG DT DT DG DT DA DC HET NCX A 5 39 HETNAM NCX 1-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO- HETNAM 2 NCX PENTOFURANOSYL)-5-NITRO-1H-INDOLE-3-CARBOXAMIDE FORMUL 1 NCX C14 H16 N3 O9 P LINK O3' DC A 4 P NCX A 5 1555 1555 1.61 LINK O3' NCX A 5 P DA A 6 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 ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL MASTER 213 0 1 0 0 0 0 6 0 0 0 2 END