HEADER DNA-RNA HYBRID 03-MAR-03 1OO7 TITLE DNA.RNA HYBRID DUPLEX CONTAINING A 5-PROPYNE DNA STRAND AND PURINE- TITLE 2 RICH RNA STRAND, NMR, 4 STRUCTURES COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-R(*GP*AP*AP*GP*AP*GP*AP*AP*GP*C)-3'; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-D(*GP*(5PC)P*(PDU)P*(PDU)P*(5PC)P*(PDU)P*(5PC)P*(PDU) COMPND 7 P*(PDU)P*C)-3'; COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES KEYWDS DNA.RNA HYBRID, PURINE/PYRIMIDINE-RICH STRANDS, ANTISENSE, DNA-RNA KEYWDS 2 COMPLEX, DNA-RNA HYBRID EXPDTA SOLUTION NMR NUMMDL 4 MDLTYP MINIMIZED AVERAGE AUTHOR J.I.GYI,D.GAO,G.L.CONN,J.O.TRENT,T.BROWN,A.N.LANE REVDAT 4 28-JUL-21 1OO7 1 COMPND REMARK SEQRES FORMUL REVDAT 4 2 1 LINK ATOM REVDAT 3 24-FEB-09 1OO7 1 VERSN REVDAT 2 25-NOV-03 1OO7 3 ATOM REVDAT 1 11-NOV-03 1OO7 0 JRNL AUTH J.I.GYI,D.GAO,G.L.CONN,J.O.TRENT,T.BROWN,A.N.LANE JRNL TITL THE SOLUTION STRUCTURE OF A DNA*RNA DUPLEX CONTAINING JRNL TITL 2 5-PROPYNYL U AND C; COMPARISON WITH 5-ME MODIFICATIONS JRNL REF NUCLEIC ACIDS RES. V. 31 2683 2003 JRNL REFN ISSN 0305-1048 JRNL PMID 12736318 JRNL DOI 10.1093/NAR/GKG356 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH J.I.GYI,A.N.LANE,G.L.CONN,T.BROWN REMARK 1 TITL SOLUTION STRUCTURES OF DNA.RNA HYBRIDS WITH PURINE-RICH AND REMARK 1 TITL 2 PYRIMIDINE-RICH STRANDS: COMPARISON WITH THE HOMOLOGOUS DNA REMARK 1 TITL 3 AND RNA DUPLEXES REMARK 1 REF BIOCHEMISTRY V. 37 73 1998 REMARK 1 REFN ISSN 0006-2960 REMARK 1 DOI 10.1021/BI9719713 REMARK 1 REFERENCE 2 REMARK 1 AUTH J.I.GYI,G.L.CONN,A.N.LANE,T.BROWN REMARK 1 TITL COMPARISON OF THE THERMODYNAMIC STABILITIES AND SOLUTION REMARK 1 TITL 2 CONFORMATIONS OF DNA.RNA HYBRIDS CONTAINING PURINE-RICH AND REMARK 1 TITL 3 PYRIMIDINE-RICH STRANDS WITH DNA AND RNA DUPLEXES REMARK 1 REF BIOCHEMISTRY V. 35 12538 1996 REMARK 1 REFN ISSN 0006-2960 REMARK 1 DOI 10.1021/BI960948Z REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 7.0 REMARK 3 AUTHORS : CORNELL, W.D., ET AL. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: DISTANCE CONSTRAINTS FOR GLYCOSIDIC REMARK 3 TORSION ANGLES, PENTOSE PSEUDOROTATIONAL PHASE ANGLES/AMPLITUDES REMARK 3 AND FRACTION OF SOUTH STATE SUGARS CALCULATED FROM NOE BUILD-UP REMARK 3 CURVES AND COUPLING CONSTANTS BY A LEAST-SQUARES/GRID SEARCH REMARK 3 METHOD IMPLEMENTED IN NUCFIT AND PFIT (A.N. LANE, NIMR, UK). TEN REMARK 3 DIFFERENT SETS OF UNIQUE RESTRAINTS GENERATED 10 STRUCTURES, THE REMARK 3 AVERAGE OF WHICH SATISFIED THE EXPERIMENTALLY DERIVED FRACTION REMARK 3 OF SOUTH STATE SUGARS BETTER THAN STRUCTURES GENERATED FROM A REMARK 3 SINGLE SET OF RESTRAINTS. INTERNUCLEOTIDE DISTANCE CONSTRAINTS REMARK 3 CALCULATED FROM NOE-BUILD-UP CURVES. STRUCTURES CALCULATED BY REMARK 3 SIMULATED ANNEALING/RMD PROTOCOL WITHIN DISCOVER 95.0 USING AN REMARK 3 AMBER FORCE FIELD AND A DISTANCE DIELECTRIC CONSTANT. REMARK 4 REMARK 4 1OO7 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-MAR-03. REMARK 100 THE DEPOSITION ID IS D_1000018494. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 100 MM KCL REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY; COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : UNITY; UNITYPLUS REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : FELIX 95.0, NUCFIT, PFIT REMARK 210 METHOD USED : MULTIPLE STARTING CONFORMATIONS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 4 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 4 REMARK 210 CONFORMERS, SELECTION CRITERIA : ALL CALCULATED STRUCTURES REMARK 210 SUBMITTED REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED FROM 2D HOMONUCLEAR NMR REMARK 210 EXPERIMENTS USING UNLABELLED SAMPLE 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 G A 1 N3 - C2 - N2 ANGL. DEV. = -5.2 DEGREES REMARK 500 1 A A 2 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 A A 3 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 G A 4 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 G A 4 N3 - C2 - N2 ANGL. DEV. = -4.5 DEGREES REMARK 500 1 G A 4 N1 - C6 - O6 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 A A 5 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 A A 5 N1 - C6 - N6 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 G A 6 O4' - C1' - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 G A 6 N3 - C2 - N2 ANGL. DEV. = -4.6 DEGREES REMARK 500 1 A A 7 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 A A 8 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 A A 8 N1 - C6 - N6 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 G A 9 O4' - C1' - N9 ANGL. DEV. = 5.7 DEGREES REMARK 500 1 C A 10 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES REMARK 500 1 C A 10 N3 - C2 - O2 ANGL. DEV. = -4.3 DEGREES REMARK 500 1 DG B 1 N3 - C2 - N2 ANGL. DEV. = -4.3 DEGREES REMARK 500 2 G A 1 N3 - C2 - N2 ANGL. DEV. = -5.2 DEGREES REMARK 500 2 A A 2 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 2 A A 3 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 G A 4 O4' - C1' - N9 ANGL. DEV. = 6.0 DEGREES REMARK 500 2 G A 4 N3 - C2 - N2 ANGL. DEV. = -4.5 DEGREES REMARK 500 2 G A 4 N1 - C6 - O6 ANGL. DEV. = -3.6 DEGREES REMARK 500 2 A A 5 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 2 A A 5 N1 - C6 - N6 ANGL. DEV. = -3.9 DEGREES REMARK 500 2 G A 6 O4' - C1' - N9 ANGL. DEV. = 5.1 DEGREES REMARK 500 2 G A 6 N3 - C2 - N2 ANGL. DEV. = -5.0 DEGREES REMARK 500 2 G A 6 N1 - C6 - O6 ANGL. DEV. = -3.8 DEGREES REMARK 500 2 A A 7 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 2 A A 7 N1 - C6 - N6 ANGL. DEV. = -4.1 DEGREES REMARK 500 2 A A 8 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 2 A A 8 N1 - C6 - N6 ANGL. DEV. = -3.9 DEGREES REMARK 500 2 G A 9 O4' - C1' - N9 ANGL. DEV. = 5.0 DEGREES REMARK 500 2 G A 9 N3 - C2 - N2 ANGL. DEV. = -4.5 DEGREES REMARK 500 2 G A 9 N1 - C6 - O6 ANGL. DEV. = -3.6 DEGREES REMARK 500 2 C A 10 O4' - C1' - N1 ANGL. DEV. = 5.5 DEGREES REMARK 500 2 C A 10 N3 - C2 - O2 ANGL. DEV. = -4.3 DEGREES REMARK 500 2 DG B 1 N3 - C2 - N2 ANGL. DEV. = -5.0 DEGREES REMARK 500 2 DC B 10 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 3 G A 1 N3 - C2 - N2 ANGL. DEV. = -5.0 DEGREES REMARK 500 3 A A 2 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 3 A A 3 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 3 A A 3 N1 - C6 - N6 ANGL. DEV. = -3.6 DEGREES REMARK 500 3 G A 4 O4' - C1' - N9 ANGL. DEV. = 5.6 DEGREES REMARK 500 3 A A 5 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 3 G A 6 O4' - C1' - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 3 G A 6 N3 - C2 - N2 ANGL. DEV. = -4.8 DEGREES REMARK 500 3 G A 6 N1 - C6 - O6 ANGL. DEV. = -3.8 DEGREES REMARK 500 3 A A 7 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 3 A A 7 N1 - C6 - N6 ANGL. DEV. = -3.8 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 77 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 G A 1 0.06 SIDE CHAIN REMARK 500 2 DG B 1 0.06 SIDE CHAIN REMARK 500 4 DG B 1 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1DRR RELATED DB: PDB REMARK 900 DNA/RNA HYBRID DUPLEX CONTAINING A PURINE-RICH DNA STRAND, NMR, 10 REMARK 900 STRUCTURES REMARK 900 RELATED ID: 1RRD RELATED DB: PDB REMARK 900 DNA/RNA HYBRID DUPLEX CONTAINING A PURINE-RICH RNA STRAND, NMR, 10 REMARK 900 STRUCTURES DBREF 1OO7 A 1 10 PDB 1OO7 1OO7 1 10 DBREF 1OO7 B 1 10 PDB 1OO7 1OO7 1 10 SEQRES 1 A 10 G A A G A G A A G C SEQRES 1 B 10 DG 5PC PDU PDU 5PC PDU 5PC PDU PDU DC MODRES 1OO7 5PC B 2 DC MODRES 1OO7 PDU B 3 DU MODRES 1OO7 PDU B 4 DU MODRES 1OO7 5PC B 5 DC MODRES 1OO7 PDU B 6 DU MODRES 1OO7 5PC B 7 DC MODRES 1OO7 PDU B 8 DU MODRES 1OO7 PDU B 9 DU HET 5PC B 2 35 HET PDU B 3 34 HET PDU B 4 34 HET 5PC B 5 35 HET PDU B 6 34 HET 5PC B 7 35 HET PDU B 8 34 HET PDU B 9 34 HETNAM 5PC 5(1-PROPYNYL)-2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE HETNAM PDU 5(1-PROPYNYL)-2'-DEOXYURIDINE-5-MONOPHOSPHATE FORMUL 2 5PC 3(C12 H16 N3 O7 P) FORMUL 2 PDU 5(C12 H15 N2 O8 P) LINK O3' DG B 1 P 5PC B 2 1555 1555 1.61 LINK O3' 5PC B 2 P PDU B 3 1555 1555 1.60 LINK O3' PDU B 3 P PDU B 4 1555 1555 1.61 LINK O3' PDU B 4 P 5PC B 5 1555 1555 1.61 LINK O3' 5PC B 5 P PDU B 6 1555 1555 1.60 LINK O3' PDU B 6 P 5PC B 7 1555 1555 1.61 LINK O3' 5PC B 7 P PDU B 8 1555 1555 1.60 LINK O3' PDU B 8 P PDU B 9 1555 1555 1.61 LINK O3' PDU B 9 P DC B 10 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