HEADER DNA 20-MAR-03 1OSR TITLE STRUCTURAL STUDY OF DNA DUPLEX CONTAINAING A N-(2-DEOXY-BETA-ERYTHO- TITLE 2 PENTOFURANOSYL) FORMAMIDE FRAMESHIFT BY NMR AND RESTRAINED MOLECULAR TITLE 3 DYNAMICS COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*AP*GP*GP*AP*CP*CP*AP*CP*G)-3'; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-D(*CP*GP*TP*GP*GP*(2DF)P*TP*CP*CP*T)-3'; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES KEYWDS MODIFIED BASE, MUTAGENESIS, DEOXYRIBONUCLEIC ACID, DNA EXPDTA SOLUTION NMR NUMMDL 2 AUTHOR C.MAUFRAIS,G.V.FAZAKERLEY,J.CADET,Y.BOULARD REVDAT 4 23-FEB-22 1OSR 1 REMARK LINK REVDAT 3 24-FEB-09 1OSR 1 VERSN REVDAT 2 13-JAN-04 1OSR 1 JRNL REVDAT 1 14-OCT-03 1OSR 0 JRNL AUTH C.MAUFRAIS,G.V.FAZAKERLEY,J.CADET,Y.BOULARD JRNL TITL STRUCTURAL STUDY OF DNA DUPLEX CONTAINING AN JRNL TITL 2 N-(2-DEOXY-BETA-D-ERYTHRO-PENTOFURANOSYL) FORMAMIDE JRNL TITL 3 FRAMESHIFT BY NMR AND RESTRAINED MOLECULAR DYNAMICS. JRNL REF NUCLEIC ACIDS RES. V. 31 5930 2003 JRNL REFN ISSN 0305-1048 JRNL PMID 14530441 JRNL DOI 10.1093/NAR/GKG803 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER, MORCAD, MOLMOL 2.6 REMARK 3 AUTHORS : KOLLMAN (AMBER), LEBRET (MORCAD), KORADI, WUTHRICH REMARK 3 (MOLMOL) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1OSR COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-MAR-03. REMARK 100 THE DEPOSITION ID IS D_1000018631. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 290; 278 REMARK 210 PH : 6.5; 5.5 REMARK 210 IONIC STRENGTH : 10 MM PHOSPHATE BUFFER, 150 MM REMARK 210 NACL, 0.2 MM EDTA; 10 MM REMARK 210 PHOSPHATE BUFFER, 150 MM NACL, REMARK 210 0.2 MM EDTA REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 2 MM DNA, 10 MM PHOSPHATE REMARK 210 BUFFER, 50 MM NACL, 0.2 MM EDTA; REMARK 210 2 MM DNA, 10 MM PHOSPHATE BUFFER, REMARK 210 50 MM NACL, 0.2 MM EDTA REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY; COSY; DQFCOSY; TOCSY; REMARK 210 HSQC 1H-31P REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XWINNMR 2.5 REMARK 210 METHOD USED : MOLECULAR MODELING; SIMULATED REMARK 210 ANNEALING; RESTRAINED MOLECULAR REMARK 210 DYNAMICS SIMULATIONS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL REMARK 210 CONFORMERS, NUMBER SUBMITTED : 2 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 2 REMARK 210 REMARK 210 REMARK: REMARK 210 THE STRUCTURES WERE DETERMINED USING PROTON NMR FOLLOWED BY REMARK 210 DISTANCE REMARK 210 RESTRAINED MOLECULAR DYNAMICS SIMULATIONS. TWO REPRESENTATIVE REMARK 210 STRUCTURES OF THE TWO ISOMER CIS AND TRANS FOR THE FORMAMIDE REMARK 210 RESIDUE REMARK 210 ARE PRESENTED. 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 DA A 1 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DG A 2 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DA A 4 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DC A 6 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 1 DC B 10 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 1 DT B 12 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 1 DT B 12 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 DT B 16 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 1 DC B 18 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 1 DT B 19 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 2 DA A 1 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 2 DG A 2 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 2 DA A 4 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 2 DC A 6 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 2 DC B 10 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 2 DT B 12 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 2 DT B 16 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 2 DC B 18 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 2 DT B 19 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES 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 DA A 1 0.06 SIDE CHAIN REMARK 500 1 DG A 9 0.06 SIDE CHAIN REMARK 500 1 DC B 18 0.06 SIDE CHAIN REMARK 500 2 DA A 1 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 1OSR A 1 9 PDB 1OSR 1OSR 1 9 DBREF 1OSR B 10 19 PDB 1OSR 1OSR 10 19 SEQRES 1 A 9 DA DG DG DA DC DC DA DC DG SEQRES 1 B 10 DC DG DT DG DG 2DF DT DC DC DT HET 2DF B 15 23 HETNAM 2DF N-(2-DEOXY-BETA-D-ERYTHO-PENTOFURANOSYL-5-PHOSPHATE) HETNAM 2 2DF FORMAMIDE FORMUL 2 2DF C6 H12 N O7 P LINK O3' DG B 14 P 2DF B 15 1555 1555 1.62 LINK O3' 2DF B 15 P DT B 16 1555 1555 1.61 CRYST1 P 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