HEADER DNA 17-JAN-00 1DUF TITLE THE NMR STRUCTURE OF DNA DODECAMER DETERMINED IN AQUEOUS DILUTE LIQUID TITLE 2 CRYSTALLINE PHASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3'); COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS B-DNA, DOUBLE HELIX, DIPOLAR COUPLING, DNA EXPDTA SOLUTION NMR NUMMDL 5 AUTHOR N.TJANDRA,S.TATE,A.ONO,M.KAINOSHO,A.BAX REVDAT 4 22-MAY-24 1DUF 1 REMARK REVDAT 3 16-FEB-22 1DUF 1 REMARK 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 DILUTE JRNL TITL 2 LIQUID CRYSTALLINE PHASE JRNL REF J.AM.CHEM.SOC. V. 122 6190 2000 JRNL REFN ISSN 0002-7863 JRNL DOI 10.1021/JA000324N 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: REMARK 3 THE STRUCTURE IS BASED ON A TOTAL OF 162 NOE, 32 HYDROGEN BOND, AND REMARK 3 156 DIHEDRAL RESTRAINTS; AS WELL AS 198 CH AND 10 NH ONE-BOND REMARK 3 DIPOLAR REMARK 3 COUPLING RESTRAINTS IN ADDITION TO 200 APPROXIMATE PROTON -PROTON REMARK 3 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 DEPOSITION ID IS D_1000010377. 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 SODIUM REMARK 210 PHOSPHATE, PH 7.0 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 13C-HSQC-J-MODULATED; COSY; 13C REMARK 210 -HSQC-F1- COUPLED; 15N-HSQC-F1- REMARK 210 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 1999.039.11.31, REMARK 210 XWINNMR VERSION 2.4, PIPP/CAPP REMARK 210 VERSION 4.2.8 REMARK 210 METHOD USED : SIMULATED ANNEALING, MOLECULAR REMARK 210 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: REMARK 210 THIS STRUCTURE WAS DETERMINED USING A COMPLETE SET OF HOMONUCLEAR REMARK 210 AND REMARK 210 HETERONUCLEAR DIPOLAR COUPLINGS IN LIQUID 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 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: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O2 DC A 11 H21 DG B 14 1.55 REMARK 500 H21 DG A 2 O2 DC B 23 1.55 REMARK 500 REMARK 500 REMARK: NULL 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. = 6.8 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. = 6.7 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. = 6.0 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. = 5.8 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. = 6.7 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. = 6.7 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 MODEL 1