HEADER DNA 14-DEC-07 2JYK TITLE NMR STRUCTURE OF A 21 BP DNA DUPLEX PREFERENTIALLY CLEAVED BY HUMAN TITLE 2 TOPOISOMERASE II COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'- COMPND 3 D(*DAP*DCP*DAP*DGP*DCP*DTP*DTP*DAP*DTP*DCP*DAP*DTP*DCP*DGP*DAP*DTP*DC COMPND 4 P*DAP*DCP*DGP*DT)-3'); COMPND 5 CHAIN: A; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA (5'- COMPND 9 D(*DAP*DCP*DGP*DTP*DGP*DAP*DTP*DCP*DGP*DAP*DTP*DGP*DAP*DTP*DAP*DAP*DG COMPND 10 P*DCP*DTP*DGP*DT)-3'); COMPND 11 CHAIN: B; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES KEYWDS B-DNA, DOUBLE HELIX, TOPOISOMERASE II, DNA EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR G.MASLIAH,O.MAUFFRET REVDAT 5 29-MAY-24 2JYK 1 REMARK REVDAT 4 16-MAR-22 2JYK 1 REMARK DBREF REVDAT 3 24-FEB-09 2JYK 1 VERSN REVDAT 2 12-AUG-08 2JYK 1 JRNL REVDAT 1 15-JUL-08 2JYK 0 JRNL AUTH G.MASLIAH,B.RENE,L.ZARGARIAN,S.FERMANDJIAN,O.MAUFFRET JRNL TITL IDENTIFICATION OF INTRINSIC DYNAMICS IN A DNA SEQUENCE JRNL TITL 2 PREFERENTIALLY CLEAVED BY TOPOISOMERASE II ENZYME JRNL REF J.MOL.BIOL. V. 381 692 2008 JRNL REFN ISSN 0022-2836 JRNL PMID 18585388 JRNL DOI 10.1016/J.JMB.2008.06.024 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH 2.16 REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 THE STRUCTURE IS BASED ON A TOTAL OF 670 NOE, 102 HYDROGEN REMARK 3 BOND, AND 286 DIHEDRAL RESTRAINTS REMARK 4 REMARK 4 2JYK COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 18-DEC-07. REMARK 100 THE DEPOSITION ID IS D_1000100451. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 7.00 REMARK 210 IONIC STRENGTH : 0.1 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 46MM SODIUM PHOSPHATE; 1MM EDTA; REMARK 210 1.5MM STRAND1; 1.5MM STRAND2; 90% REMARK 210 H2O/10% D2O; 46MM SODIUM REMARK 210 PHOSPHATE; 1MM EDTA; 1.5MM REMARK 210 STRAND1; 1.5MM STRAND2; 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D DQF-COSY; 2D REMARK 210 1H-1H TOCSY; 2D 1H-13C HSQC; 2D REMARK 210 1H-31P HETCOR REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : MORASS 2.51 REMARK 210 METHOD USED : SIMULATED ANNEALING, MOLECULAR REMARK 210 DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 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: NULL 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 N1 DA A 8 H3 DT B 35 1.59 REMARK 500 H3 DT A 6 N1 DA B 37 1.59 REMARK 500 H3 DT A 16 N1 DA B 27 1.59 REMARK 500 H3 DT A 9 N1 DA B 34 1.59 REMARK 500 O2 DC A 13 H22 DG B 30 1.59 REMARK 500 N1 DA A 3 H3 DT B 40 1.60 REMARK 500 REMARK 500 REMARK: NULL DBREF 2JYK A 1 21 PDB 2JYK 2JYK 1 21 DBREF 2JYK B 22 42 PDB 2JYK 2JYK 22 42 SEQRES 1 A 21 DA DC DA DG DC DT DT DA DT DC DA DT DC SEQRES 2 A 21 DG DA DT DC DA DC DG DT SEQRES 1 B 21 DA DC DG DT DG DA DT DC DG DA DT DG DA SEQRES 2 B 21 DT DA DA DG DC DT DG DT 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