1C2Q - Header Asymmetric Unit

HEADER DNA-RNA HYBRID 26-JUL-99 1C2Q

TITLE SOLUTION STRUCTURE OF A DNA.RNA HYBRID CONTAINING AN ALPHAT- TITLE 2 ANOMERIC 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' KEYWDS 2 PHOSPHODIESTER LINKAGES, DNA-RNA HYBRID

EXPDTA SOLUTION NMR

MDLTYP MINIMIZED AVERAGE

AUTHOR M.W.GERMANN,J.M.ARAMINI

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 JRNL TITL 2 AN ALPHA-ANOMERIC THYMIDINE AND POLARITY JRNL TITL 3 REVERSALS: D(ATGG-3'-3'-ALPHAT-5'-5'-GCTC). JRNL TITL 4 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 REMARK 1 TITL 3 UNMODIFIED 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 : AMBER 4.1 REMARK 3 AUTHORS : PEARLMAN ET AL., 1995 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 REMARK 3 STRUCTURES, FOLLOWED BY RESTRAINED ENERGY MINIMIZATION. ALL REMARK 3 STRUCTURE CALCULATIONS WERE PERFORMED USING THE SANDER PROGRAM REMARK 3 WITHIN AMBER 4.1, AND THE 1994 ALL ATOM NUCLEIC ACID REMARK 3 PARAMETERIZATION. ALL CALCULATIONS WERE CONDUCTED IN VACUO, REMARK 3 USING A DISTANCE DEPENDENT DIELECTRIC CONSTANT AND 30 A CUT- REMARK 3 OFF FOR NON-BONDED INTERACTIONS.

REMARK 4 REMARK 4 1C2Q COMPLIES WITH FORMAT V. 3.15, 01-DEC-08

REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-JUL-99. REMARK 100 THE RCSB ID CODE IS RCSB009406.

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, REMARK 210 10 MM PHOSPHATE BUFFER, 0.5 MM REMARK 210 EDTA, PH* 6.6, D2O; 0.89 MM REMARK 210 HYBRID, 50 MM NACL, 10 MM REMARK 210 PHOSPHATE BUFFER, 0.5 MM EDTA, REMARK 210 PH 6.7, 90% 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 : UXNMR 2.1, MARDIGRAS 3.2, REMARK 210 CORMA 5.2, SPARKY 3.33, REMARK 210 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 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 DG A 6 O4' - C4' - C3' ANGL. DEV. = 5.3 DEGREES REMARK 500 DG A 6 C3' - C2' - C1' ANGL. DEV. = 8.3 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. = 3.1 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. = 6.3 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 REMARK 900 CONTAINING THE SAME MODIFICATIONS (1 ALPHA-ANOMERIC REMARK 900 THYMIDINE AND FLANKING 3'-3' AND 5'-5' PHOSPHODIESTER REMARK 900 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