HEADER DNA-RNA HYBRID 25-JUL-95 219D TITLE DNA/RNA HYBRID DUPLEX (5'-D(*GP*CP*TP*AP*TP*AP*APS*TP*GP*G)-3')(DOT) TITLE 2 (5'-R(*CP*CP*AP*UP*UP*AP*UP*AP*GP*C)-3') WITH A PHOSPHOROTHIOATE TITLE 3 MOIETY COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*GP*CP*TP*AP*TP*AP*AP*TP*GP*G)-3'); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: PHOSPHOROTHIOATE LINK BETWEEN A 7 AND T 8; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: RNA (5'-R(*CP*CP*AP*UP*UP*AP*UP*AP*GP*C)-3'); COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES; COMPND 10 OTHER_DETAILS: PHOSPHOROTHIOATE LINK BETWEEN A 7 AND T 8 SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: CHEMICALLY SYNTHESIZED; SOURCE 4 MOL_ID: 2; SOURCE 5 SYNTHETIC: YES; SOURCE 6 OTHER_DETAILS: CHEMICALLY SYNTHESIZED KEYWDS DNA, RNA, HYBRID, PHOSPHOROTHIOATE, DNA-RNA COMPLEX, DNA-RNA HYBRID EXPDTA SOLUTION NMR AUTHOR C.GONZALEZ,T.L.JAMES REVDAT 4 09-MAR-22 219D 1 REMARK LINK REVDAT 3 24-FEB-09 219D 1 VERSN REVDAT 2 01-APR-03 219D 1 JRNL REVDAT 1 15-OCT-95 219D 0 JRNL AUTH C.GONZALEZ,W.STEC,M.A.REYNOLDS,T.L.JAMES JRNL TITL STRUCTURE AND DYNAMICS OF A DNA.RNA HYBRID DUPLEX WITH A JRNL TITL 2 CHIRAL PHOSPHOROTHIOATE MOIETY: NMR AND MOLECULAR DYNAMICS JRNL TITL 3 WITH CONVENTIONAL AND TIME-AVERAGED RESTRAINTS. JRNL REF BIOCHEMISTRY V. 34 4969 1995 JRNL REFN ISSN 0006-2960 JRNL PMID 7711019 JRNL DOI 10.1021/BI00015A008 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH C.GONZALEZ,W.STEC,A.KOBYLANSKA,R.I.HOGREFE,M.A.REYNOLDS, REMARK 1 AUTH 2 T.L.JAMES REMARK 1 TITL STRUCTURAL STUDY OF A DNA(DOT)RNA HYBRID DUPLEX WITH A REMARK 1 TITL 2 CHIRAL PHOSPHOROTHIOATE MOIETY BY NMR: EXTRACTION OF REMARK 1 TITL 3 DISTANCE AND TORSION ANGLE CONSTRAINTS AND IMINO PROTON REMARK 1 TITL 4 EXCHANGE RATES REMARK 1 REF BIOCHEMISTRY V. 33 11062 1994 REMARK 1 REFN ISSN 0006-2960 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER REMARK 3 AUTHORS : PEARLMAN,KOLLMAN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NUMBER OF ATOMS USED IN REFINEMENT. REMARK 3 NUMBER OF PROTEIN ATOMS 0 NUMBER OF NUCLEIC ACID ATOMS 411 REMARK 3 NUMBER OF HETEROGEN ATOMS 0 NUMBER OF SOLVENT ATOMS 0 REMARK 4 REMARK 4 219D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000177585. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : NULL REMARK 210 PH : NULL REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NULL REMARK 210 SPECTROMETER FIELD STRENGTH : NULL REMARK 210 SPECTROMETER MODEL : NULL REMARK 210 SPECTROMETER MANUFACTURER : NULL REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: THE PHOSPHATE BETWEEN NUCLEOTIDES SEVEN AND EIGHT IS REMARK 210 MODIFIED BY SUBSTITUTING A SULFUR FOR ONE OF THE OXYGEN ATOMS. REMARK 210 TWO SAMPLES WITH PURE CHIRALITY (R OR S) HAVE BEEN STUDIED; ONLY REMARK 210 MINOR DIFFERENCES COULD BE DETECTED. THE COORDINATES REPRESENT REMARK 210 THE S STEREOISOMER OF THE MODIFIED PHOSPHATE. THE SIXTH ROOT R- REMARK 210 FACTOR, EXPRESSING THE FIT TO THE EXPERIMENTAL NOE DATA, REMARK 210 CALCULATED WITH THE PROGRAM CORMA (KEEPERS AND JAMES), HAS A REMARK 210 VALUE OF 0.074. THE ROOT MEAN SQUARE DEVIATION BETWEEN REMARK 210 EXPERIMENTAL AND THEORETICAL DEOXYRIBOSE J-COUPLING CONSTRAINTS REMARK 210 IS 2.01 HZ. THIS POOR FIT OF THE COUPLING CONSTANTS IS DUE TO REMARK 210 CONFORMATIONAL FLEXIBILITY IN THE SUGAR RING. 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 DG A 1 C4' - C3' - C2' ANGL. DEV. = -5.3 DEGREES REMARK 500 DG A 1 O4' - C1' - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 DC A 2 O4' - C1' - C2' ANGL. DEV. = 3.2 DEGREES REMARK 500 DC A 2 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 DT A 3 O4' - C1' - C2' ANGL. DEV. = -4.9 DEGREES REMARK 500 DT A 3 C6 - C5 - C7 ANGL. DEV. = -4.2 DEGREES REMARK 500 DA A 4 C3' - C2' - C1' ANGL. DEV. = 8.4 DEGREES REMARK 500 DA A 4 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 DT A 5 C6 - C5 - C7 ANGL. DEV. = -4.4 DEGREES REMARK 500 DA A 6 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 DA A 7 O4' - C4' - C3' ANGL. DEV. = 4.7 DEGREES REMARK 500 DA A 7 C4' - C3' - C2' ANGL. DEV. = -9.7 DEGREES REMARK 500 DA A 7 O4' - C1' - C2' ANGL. DEV. = -10.2 DEGREES REMARK 500 DA A 7 O4' - C1' - N9 ANGL. DEV. = 8.2 DEGREES REMARK 500 DG A 9 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 DG A 10 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 C B 12 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 A B 13 O4' - C1' - N9 ANGL. DEV. = 5.3 DEGREES REMARK 500 U B 14 O4' - C1' - N1 ANGL. DEV. = 6.4 DEGREES REMARK 500 U B 15 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 A B 16 C3' - C2' - C1' ANGL. DEV. = 4.8 DEGREES REMARK 500 A B 16 O4' - C1' - N9 ANGL. DEV. = 5.9 DEGREES REMARK 500 U B 17 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 A B 18 C5' - C4' - O4' ANGL. DEV. = 5.7 DEGREES REMARK 500 A B 18 C3' - C2' - C1' ANGL. DEV. = 6.1 DEGREES REMARK 500 C B 20 O4' - C1' - N1 ANGL. DEV. = 5.8 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 DG A 1 0.07 SIDE CHAIN REMARK 500 DA A 6 0.07 SIDE CHAIN REMARK 500 DA A 7 0.07 SIDE CHAIN REMARK 500 C B 11 0.09 SIDE CHAIN REMARK 500 C B 12 0.07 SIDE CHAIN REMARK 500 A B 13 0.11 SIDE CHAIN REMARK 500 A B 18 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 219D A 1 10 PDB 219D 219D 1 10 DBREF 219D B 11 20 PDB 219D 219D 11 20 SEQRES 1 A 10 DG DC DT DA DT DA DA PST DG DG SEQRES 1 B 10 C C A U U A U A G C MODRES 219D PST A 8 DT THYMIDINE-5'-THIOPHOSPHATE HET PST A 8 20 HETNAM PST THYMIDINE-5'-THIOPHOSPHATE FORMUL 1 PST C10 H15 N2 O7 P S LINK O3' DA A 7 P PST A 8 1555 1555 1.60 LINK O3' PST A 8 P DG A 9 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