HEADER DNA-RNA HYBRID 26-JUL-99 1C2Q TITLE SOLUTION STRUCTURE OF A DNA.RNA HYBRID CONTAINING AN ALPHAT-ANOMERIC TITLE 2 THYMIDINE AND POLARITY REVERSALS COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(ATGG-3'-3'-(T3P)-5'-5'-GCTC)-3'; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: T5 IS ALPHAT ANOMERIC; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: 5'-R(GAGCACCAU)-3'; COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: SYNTHETIC; SOURCE 4 MOL_ID: 2; SOURCE 5 SYNTHETIC: YES; SOURCE 6 OTHER_DETAILS: SYNTHETIC KEYWDS DNA/RNA HYBRID, ALPHAT-ANOMERIC THYMIDINE, 3'-3'/5'-5' PHOSPHODIESTER KEYWDS 2 LINKAGES, DNA-RNA HYBRID EXPDTA SOLUTION NMR MDLTYP MINIMIZED AVERAGE AUTHOR M.W.GERMANN,J.M.ARAMINI REVDAT 4 16-FEB-22 1C2Q 1 REMARK LINK REVDAT 3 24-FEB-09 1C2Q 1 VERSN REVDAT 2 01-APR-03 1C2Q 1 JRNL REVDAT 1 29-NOV-99 1C2Q 0 JRNL AUTH J.M.ARAMINI,M.W.GERMANN JRNL TITL SOLUTION STRUCTURE OF A DNA.RNA HYBRID CONTAINING AN JRNL TITL 2 ALPHA-ANOMERIC THYMIDINE AND POLARITY REVERSALS: JRNL TITL 3 D(ATGG-3'-3'-ALPHAT-5'-5'-GCTC). R(GAGCACCAU). JRNL REF BIOCHEMISTRY V. 38 15448 1999 JRNL REFN ISSN 0006-2960 JRNL PMID 10569927 JRNL DOI 10.1021/BI9915418 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH J.M.ARAMINI,A.MUJEEB,M.W.GERMANN REMARK 1 TITL NMR SOLUTION STRUCTURES OF REMARK 1 TITL 2 [D(GCGAAT-3'-3'-(ALPHA-T)-5'-5'-CGC)2] AND ITS UNMODIFIED REMARK 1 TITL 3 CONTROL REMARK 1 REF NUCLEIC ACIDS RES. V. 26 5644 1998 REMARK 1 REFN ISSN 0305-1048 REMARK 1 DOI 10.1093/NAR/26.24.5644 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : UXNMR 2.1, AMBER 4.1 REMARK 3 AUTHORS : BRUKER (UXNMR), PEARLMAN ET AL., 1995 (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURE IS BASED ON A TOTAL OF REMARK 3 405 RESTRAINTS: 268 RANDMARDI DERIVED INTERPROTON DISTANCE REMARK 3 RESTRAINTS (NON-EXCHANGEABLE: 246; EXCHANGEABLE: 22); 45 REMARK 3 DEOXYRIBOSE ENDOCYCLIC TORSION ANGLE RESTRAINTS DERIVED FROM REMARK 3 PSEUDOROTATION ANALYSIS; 45 RIBOSE ENDOCYCLIC TORSION ANGLE REMARK 3 RESTRAINTS (BROAD, N-TYPE); 46 WATSON-CRICK DISTANCE AND ANGLE REMARK 3 RESTRAINTS. THE FINAL AVERAGE STRUCTURE WAS OBTAINED BY REMARK 3 COORDINATE AVERAGING OF THE FINAL ENSEMBLE OF RMD/REM STRUCTURES, REMARK 3 FOLLOWED BY RESTRAINED ENERGY MINIMIZATION. ALL STRUCTURE REMARK 3 CALCULATIONS WERE PERFORMED USING THE SANDER PROGRAM WITHIN REMARK 3 AMBER 4.1, AND THE 1994 ALL ATOM NUCLEIC ACID PARAMETERIZATION. REMARK 3 ALL CALCULATIONS WERE CONDUCTED IN VACUO, USING A DISTANCE REMARK 3 DEPENDENT DIELECTRIC CONSTANT AND 30 A CUT-OFF FOR NON-BONDED REMARK 3 INTERACTIONS. REMARK 4 REMARK 4 1C2Q COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-JUL-99. REMARK 100 THE DEPOSITION ID IS D_1000009406. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298; 298 REMARK 210 PH : 6.6; 6.7 REMARK 210 IONIC STRENGTH : NULL; NULL REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 0.89 MM HYBRID, 50 MM NACL, 10 REMARK 210 MM PHOSPHATE BUFFER, 0.5 MM EDTA, REMARK 210 PH* 6.6, D2O; 0.89 MM HYBRID, REMARK 210 50 MM NACL, 10 MM PHOSPHATE REMARK 210 BUFFER, 0.5 MM EDTA, PH 6.7, 90% REMARK 210 H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; DQF-COSY; 31P-1H REMARK 210 CORRELATION SPECTROSCOPY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : MARDIGRAS 3.2, CORMA 5.2, SPARKY REMARK 210 3.33, SPHINX/LINSHA, CURVES 5.1, REMARK 210 AMBER 4.1 REMARK 210 METHOD USED : SIMULATED ANNEALING/MOLECULAR REMARK 210 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 : 1 REMARK 210 REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D REMARK 210 HOMONUCLEAR NMR TECHNIQUES 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 DA A 1 O4' - C4' - C3' ANGL. DEV. = 3.7 DEGREES REMARK 500 DA A 1 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 DT A 2 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 DG A 3 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 DG A 4 O4' - C4' - C3' ANGL. DEV. = 3.7 DEGREES REMARK 500 DG A 4 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 T3P A 5 O3' - P - O5' ANGL. DEV. = 53.2 DEGREES REMARK 500 DG A 6 O4' - C4' - C3' ANGL. DEV. = 5.3 DEGREES REMARK 500 DG A 6 C3' - C2' - C1' ANGL. DEV. = 8.2 DEGREES REMARK 500 DG A 6 O4' - C1' - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 DC A 7 O4' - C4' - C3' ANGL. DEV. = 4.2 DEGREES REMARK 500 DC A 7 C5' - C4' - O4' ANGL. DEV. = 7.1 DEGREES REMARK 500 DT A 8 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 DT A 8 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 DC A 9 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 G B 10 O4' - C1' - N9 ANGL. DEV. = 5.9 DEGREES REMARK 500 A B 11 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 A B 11 N1 - C6 - N6 ANGL. DEV. = -3.8 DEGREES REMARK 500 G B 12 O4' - C1' - N9 ANGL. DEV. = 6.6 DEGREES REMARK 500 C B 13 O4' - C1' - N1 ANGL. DEV. = 6.2 DEGREES REMARK 500 C B 15 O4' - C1' - N1 ANGL. DEV. = 6.4 DEGREES REMARK 500 C B 16 O4' - C1' - N1 ANGL. DEV. = 6.9 DEGREES REMARK 500 U B 18 O4' - C1' - N1 ANGL. DEV. = 4.8 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 6 0.07 SIDE CHAIN REMARK 500 A B 11 0.06 SIDE CHAIN REMARK 500 A B 14 0.10 SIDE CHAIN REMARK 500 A B 17 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1BX5 RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF A SELF-COMPLEMENTARY DNA DUPLEX CONTAINING REMARK 900 THE SAME MODIFICATIONS (1 ALPHA-ANOMERIC THYMIDINE AND FLANKING 3'- REMARK 900 3' AND 5'-5' PHOSPHODIESTER LINKAGES PER STRAND) DBREF 1C2Q A 1 9 PDB 1C2Q 1C2Q 1 9 DBREF 1C2Q B 10 18 PDB 1C2Q 1C2Q 10 18 SEQRES 1 A 9 DA DT DG DG T3P DG DC DT DC SEQRES 1 B 9 G A G C A C C A U MODRES 1C2Q T3P A 5 DT THYMIDINE-3'-PHOSPHATE HET T3P A 5 32 HETNAM T3P THYMIDINE-3'-PHOSPHATE HETSYN T3P ALPHA-ANOMERIC THYMIDINE-3'-PHOSPHATE FORMUL 1 T3P C10 H15 N2 O8 P LINK O3' DG A 4 P T3P A 5 1555 1555 1.61 LINK O5' T3P A 5 P DG 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