1DUF - Header Asymmetric Unit

HEADER DNA 17-JAN-00 1DUF

TITLE THE NMR STRUCTURE OF DNA DODECAMER DETERMINED IN AQUEOUS TITLE 2 DILUTE LIQUID CRYSTALLINE PHASE

COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)- COMPND 3 3'); COMPND 4 CHAIN: A, B; COMPND 5 ENGINEERED: YES

SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES

KEYWDS B-DNA, DOUBLE HELIX, DIPOLAR COUPLING

EXPDTA SOLUTION NMR

NUMMDL 5

AUTHOR N.TJANDRA,S.TATE,A.ONO,M.KAINOSHO,A.BAX

REVDAT 2 24-FEB-09 1DUF 1 VERSN REVDAT 1 14-JUL-00 1DUF 0

JRNL AUTH N.TJANDRA,S.TATE,A.ONO,M.KAINOSHO,A.BAX JRNL TITL THE NMR STRUCTURE OF A DNA DODECAMER IN AN AQUEOUS JRNL TITL 2 DILUTE LIQUID CRYSTALLINE PHASE JRNL REF J.AM.CHEM.SOC. V. 122 6190 2000 JRNL REFN ISSN 0002-7863 JRNL DOI 10.1021/JA000324N

REMARK 1

REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.

REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.841 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURE IS BASED ON A TOTAL OF REMARK 3 162 NOE, 32 HYDROGEN BOND, AND 156 DIHEDRAL RESTRAINTS; AS REMARK 3 WELL AS 198 CH AND 10 NH ONE-BOND DIPOLAR COUPLING RESTRAINTS REMARK 3 IN ADDITION TO 200 APPROXIMATE PROTON -PROTON DIPOLAR COUPLINGS

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

REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-JAN-00. REMARK 100 THE RCSB ID CODE IS RCSB010377.

REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 308.00 REMARK 210 PH : 7.00 REMARK 210 IONIC STRENGTH : 40 MM REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.5 MM DUPLEX DNA, 40MM REMARK 210 SODIUM PHOSPHATE, PH 7.0 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 13C-HSQC-J-MODULATED, COSY, REMARK 210 13C-HSQC-F1- COUPLED, 15N-HSQC REMARK 210 -F1- COUPLED, 2D NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ, 750 MHZ REMARK 210 SPECTROMETER MODEL : DMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 1.7 REV REMARK 210 1999.039.11.31, XWINNMR REMARK 210 VERSION 2.4, PIPP/CAPP VERSION REMARK 210 4.2.8 REMARK 210 METHOD USED : SIMULATED ANNEALING, REMARK 210 MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 20 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 5 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING A COMPLETE SET OF REMARK 210 HOMONUCLEAR AND HETERONUCLEAR DIPOLAR COUPLINGS IN LIQUID REMARK 210 CRYSTAL

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 1 DC A 1 C4' - C3' - C2' ANGL. DEV. = 6.8 DEGREES REMARK 500 1 DG A 2 C4' - C3' - C2' ANGL. DEV. = 6.0 DEGREES REMARK 500 1 DC A 3 C4' - C3' - C2' ANGL. DEV. = 6.9 DEGREES REMARK 500 1 DA A 5 C4' - C3' - C2' ANGL. DEV. = 5.9 DEGREES REMARK 500 1 DA A 6 C4' - C3' - C2' ANGL. DEV. = 6.2 DEGREES REMARK 500 1 DT A 7 C4' - C3' - C2' ANGL. DEV. = 6.6 DEGREES REMARK 500 1 DT A 8 C4' - C3' - C2' ANGL. DEV. = 6.7 DEGREES REMARK 500 1 DC A 9 C4' - C3' - C2' ANGL. DEV. = 6.8 DEGREES REMARK 500 1 DG A 10 C4' - C3' - C2' ANGL. DEV. = 6.3 DEGREES REMARK 500 1 DC A 11 C4' - C3' - C2' ANGL. DEV. = 6.5 DEGREES REMARK 500 1 DG A 12 C4' - C3' - C2' ANGL. DEV. = 6.6 DEGREES REMARK 500 1 DC B 13 C4' - C3' - C2' ANGL. DEV. = 6.8 DEGREES REMARK 500 1 DG B 14 C4' - C3' - C2' ANGL. DEV. = 6.0 DEGREES REMARK 500 1 DC B 15 C4' - C3' - C2' ANGL. DEV. = 6.9 DEGREES REMARK 500 1 DA B 17 C4' - C3' - C2' ANGL. DEV. = 5.9 DEGREES REMARK 500 1 DA B 18 C4' - C3' - C2' ANGL. DEV. = 6.2 DEGREES REMARK 500 1 DT B 19 C4' - C3' - C2' ANGL. DEV. = 6.6 DEGREES REMARK 500 1 DT B 20 C4' - C3' - C2' ANGL. DEV. = 6.6 DEGREES REMARK 500 1 DC B 21 C4' - C3' - C2' ANGL. DEV. = 6.7 DEGREES REMARK 500 1 DG B 22 C4' - C3' - C2' ANGL. DEV. = 6.4 DEGREES REMARK 500 1 DC B 23 C4' - C3' - C2' ANGL. DEV. = 6.4 DEGREES REMARK 500 1 DG B 24 C4' - C3' - C2' ANGL. DEV. = 6.6 DEGREES REMARK 500 2 DC A 1 C4' - C3' - C2' ANGL. DEV. = 6.8 DEGREES REMARK 500 2 DG A 2 C4' - C3' - C2' ANGL. DEV. = 5.9 DEGREES REMARK 500 2 DC A 3 C4' - C3' - C2' ANGL. DEV. = 6.8 DEGREES REMARK 500 2 DA A 5 C4' - C3' - C2' ANGL. DEV. = 5.9 DEGREES REMARK 500 2 DA A 6 C4' - C3' - C2' ANGL. DEV. = 6.3 DEGREES REMARK 500 2 DT A 7 C4' - C3' - C2' ANGL. DEV. = 6.5 DEGREES REMARK 500 2 DT A 8 C4' - C3' - C2' ANGL. DEV. = 6.6 DEGREES REMARK 500 2 DC A 9 C4' - C3' - C2' ANGL. DEV. = 6.8 DEGREES REMARK 500 2 DG A 10 C4' - C3' - C2' ANGL. DEV. = 6.4 DEGREES REMARK 500 2 DC A 11 C4' - C3' - C2' ANGL. DEV. = 6.6 DEGREES REMARK 500 2 DG A 12 C4' - C3' - C2' ANGL. DEV. = 6.7 DEGREES REMARK 500 2 DC B 13 C4' - C3' - C2' ANGL. DEV. = 6.9 DEGREES REMARK 500 2 DG B 14 C4' - C3' - C2' ANGL. DEV. = 5.8 DEGREES REMARK 500 2 DC B 15 C4' - C3' - C2' ANGL. DEV. = 6.8 DEGREES REMARK 500 2 DA B 17 C4' - C3' - C2' ANGL. DEV. = 5.9 DEGREES REMARK 500 2 DA B 18 C4' - C3' - C2' ANGL. DEV. = 6.2 DEGREES REMARK 500 2 DT B 19 C4' - C3' - C2' ANGL. DEV. = 6.5 DEGREES REMARK 500 2 DT B 20 C4' - C3' - C2' ANGL. DEV. = 6.6 DEGREES REMARK 500 2 DC B 21 C4' - C3' - C2' ANGL. DEV. = 6.7 DEGREES REMARK 500 2 DG B 22 C4' - C3' - C2' ANGL. DEV. = 6.5 DEGREES REMARK 500 2 DC B 23 C4' - C3' - C2' ANGL. DEV. = 6.5 DEGREES REMARK 500 2 DG B 24 C4' - C3' - C2' ANGL. DEV. = 6.7 DEGREES REMARK 500 3 DC A 1 C4' - C3' - C2' ANGL. DEV. = 6.8 DEGREES REMARK 500 3 DG A 2 C4' - C3' - C2' ANGL. DEV. = 6.0 DEGREES REMARK 500 3 DC A 3 C4' - C3' - C2' ANGL. DEV. = 6.9 DEGREES REMARK 500 3 DA A 5 C4' - C3' - C2' ANGL. DEV. = 5.7 DEGREES REMARK 500 3 DA A 6 C4' - C3' - C2' ANGL. DEV. = 6.1 DEGREES REMARK 500 3 DT A 7 C4' - C3' - C2' ANGL. DEV. = 6.7 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 110 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL

REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1BNA RELATED DB: PDB REMARK 900 DREW AND DICKERSON DODECAMER REMARK 900 RELATED ID: 355D RELATED DB: PDB REMARK 900 HIGH RESOLUTION DREW AND DICKERSON DODECAMER

DBREF 1DUF A 1 12 PDB 1DUF 1DUF 1 12 DBREF 1DUF B 13 24 PDB 1DUF 1DUF 13 24

SEQRES 1 A 12 DC DG DC DG DA DA DT DT DC DG DC DG SEQRES 1 B 12 DC DG DC DG DA DA DT DT DC DG DC DG

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