HEADER DNA-RNA HYBRID 11-FEB-97 1AC3 TITLE SOLUTION STRUCTURE OF AN RNA-DNA HYBRID DUPLEX CONTAINING A 3'- TITLE 2 THIOFORMACETAL LINKER AND AN RNA A-TRACT, NMR, 8 STRUCTURES COMPND MOL_ID: 1; COMPND 2 MOLECULE: ANTISENSE HYBRID DUPLEX; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: T6-3'-THIOFORMACETAL IN THE DNA STRAND; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA (5'-D(*(TCP)P*TP*GP*CP*GP*C)-3'); COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES; COMPND 10 OTHER_DETAILS: T6-3'-THIOFORMACETAL IN THE DNA STRAND SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES KEYWDS RNA, DNA, ANTISENSE OLIGONUCLEOTIDES, THIOFORMACETAL BACKBONE KEYWDS 2 MODIFICATION, HYBRID DUPLEX, DNA-RNA HYBRID COMPLEX, DNA-RNA HYBRID EXPDTA SOLUTION NMR NUMMDL 8 AUTHOR C.W.CROSS,J.S.RICE,X.GAO REVDAT 5 10-APR-24 1AC3 1 LINK REVDAT 4 22-JUL-20 1AC3 1 REMARK SEQRES REVDAT 3 31-JUL-19 1AC3 1 KEYWDS REMARK LINK REVDAT 2 24-FEB-09 1AC3 1 VERSN REVDAT 1 16-JUN-97 1AC3 0 JRNL AUTH C.W.CROSS,J.S.RICE,X.GAO JRNL TITL SOLUTION STRUCTURE OF AN RNA X DNA HYBRID DUPLEX CONTAINING JRNL TITL 2 A 3'-THIOFORMACETAL LINKER AND AN RNA A-TRACT. JRNL REF BIOCHEMISTRY V. 36 4096 1997 JRNL REFN ISSN 0006-2960 JRNL PMID 9100003 JRNL DOI 10.1021/BI962382K REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: 1. GENERATE DISTANCE RESTRAINTS USING REMARK 3 MARDIGRAS PROGRAM FROM T. JAMES' LAB. 2. MODEL BUILDING T. JAMES' REMARK 3 LAB.USING QUANTA. 3. RANDOMIZE STRUCTURES BY DYNAMICS REMARK 3 SIMULATIONS. 4. ITERATIVE CALCULATIONS. 5. FINAL RELAXATION REMARK 3 MATRIX REFINEMENT. REMARK 4 REMARK 4 1AC3 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000170640. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298; 288 REMARK 210 PH : 7.0; 7.0 REMARK 210 IONIC STRENGTH : NULL; NULL REMARK 210 PRESSURE : NULL; NULL REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY; DQF-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AMX-II REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : X-PLOR REMARK 210 METHOD USED : SIMULATED ANNEALING, MOLECULAR REMARK 210 DYNAMICS SIMULATIONS AND REMARK 210 RELAXATION MATRIX REFINEMENT REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 10 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 8 REMARK 210 CONFORMERS, SELECTION CRITERIA : IDEAL GEOMETRY, NOE VIOLATIONS, REMARK 210 COORDINATE RMSD REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: IONIC_STRENGTH: 0.1 M NACL, 10 MM PO4 PRESSURE: 1 SOLVENT REMARK 210 SYSTEM: AQUEOUS THE STRUCTURE WAS DETERMINED USING PROTON-PROTON REMARK 210 AND PROTON-PHOSPHOROUS 1D AND 2D NMR SPECTROSCOPY. 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 DC A 1 O4' - C1' - N1 ANGL. DEV. = 5.3 DEGREES REMARK 500 1 DG A 2 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 DC A 3 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 DG A 4 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 1 DT A 5 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 1 DG A 9 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 DC A 10 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 DG A 11 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 1 DC A 12 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 C B 14 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 C B 16 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 1 A B 19 O4' - C1' - N9 ANGL. DEV. = 5.1 DEGREES REMARK 500 1 C B 21 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 C B 23 O4' - C1' - N1 ANGL. DEV. = 6.0 DEGREES REMARK 500 2 DC A 1 O4' - C1' - N1 ANGL. DEV. = 5.1 DEGREES REMARK 500 2 DG A 2 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 2 DC A 3 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 DG A 4 O4' - C1' - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 DT A 5 O4' - C1' - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 2 DG A 9 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 2 DC A 10 O4' - C1' - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 2 DG A 11 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 2 DC A 12 O4' - C1' - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 C B 14 O4' - C1' - N1 ANGL. DEV. = 5.2 DEGREES REMARK 500 2 C B 16 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 A B 19 O4' - C1' - N9 ANGL. DEV. = 5.1 DEGREES REMARK 500 2 C B 21 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 2 C B 23 O4' - C1' - N1 ANGL. DEV. = 5.9 DEGREES REMARK 500 3 DC A 1 O4' - C1' - N1 ANGL. DEV. = 5.4 DEGREES REMARK 500 3 DG A 2 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 3 DC A 3 O4' - C1' - N1 ANGL. DEV. = 5.2 DEGREES REMARK 500 3 DG A 4 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 3 DT A 5 O4' - C1' - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 3 DG A 9 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 3 DC A 10 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 3 DG A 11 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 3 DC A 12 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 3 C B 14 O4' - C1' - N1 ANGL. DEV. = 5.2 DEGREES REMARK 500 3 C B 16 O4' - C1' - N1 ANGL. DEV. = 5.5 DEGREES REMARK 500 3 A B 19 O4' - C1' - N9 ANGL. DEV. = 5.0 DEGREES REMARK 500 3 C B 21 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 3 C B 23 O4' - C1' - N1 ANGL. DEV. = 6.0 DEGREES REMARK 500 4 DC A 1 O4' - C1' - N1 ANGL. DEV. = 5.4 DEGREES REMARK 500 4 DG A 2 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 4 DC A 3 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 4 DG A 4 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 4 DT A 5 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 4 DG A 9 O4' - C1' - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 4 DC A 10 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 4 DG A 11 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 113 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 2 G B 15 0.07 SIDE CHAIN REMARK 500 3 C B 21 0.06 SIDE CHAIN REMARK 500 6 C B 21 0.07 SIDE CHAIN REMARK 500 7 C B 21 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 1AC3 A 1 12 PDB 1AC3 1AC3 1 12 DBREF 1AC3 B 13 24 PDB 1AC3 1AC3 13 24 SEQRES 1 A 12 DC DG DC DG DT TSP TCP DT DG DC DG DC SEQRES 1 B 12 G C G C A A A A C G C G MODRES 1AC3 TSP A 6 T 3'-THIO-THYMIDINE-5'-PHOSPHATE MODRES 1AC3 TCP A 7 DT 5'-METHYLTHYMIDINE HET TSP A 6 32 HET TCP A 7 32 HETNAM TSP 3'-THIO-THYMIDINE-5'-PHOSPHATE HETNAM TCP 5'-METHYLTHYMIDINE FORMUL 1 TSP C10 H15 N2 O7 P S FORMUL 1 TCP C11 H16 N2 O5 LINK O3' DT A 5 P TSP A 6 1555 1555 1.61 LINK S3' TSP A 6 CP TCP A 7 1555 1555 1.81 LINK O3' TCP A 7 P DT A 8 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