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- PDB-2jyk: NMR Structure of a 21 bp DNA duplex preferentially cleaved by Hum... -

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Basic information

Entry
Database: PDB / ID: 2jyk
TitleNMR Structure of a 21 bp DNA duplex preferentially cleaved by Human Topoisomerase II
Components
  • DNA (5'-D(*DAP*DCP*DAP*DGP*DCP*DTP*DTP*DAP*DTP*DCP*DAP*DTP*DCP*DGP*DAP*DTP*DCP*DAP*DCP*DGP*DT)-3')
  • DNA (5'-D(*DAP*DCP*DGP*DTP*DGP*DAP*DTP*DCP*DGP*DAP*DTP*DGP*DAP*DTP*DAP*DAP*DGP*DCP*DTP*DGP*DT)-3')
KeywordsDNA / B-DNA / DOUBLE HELIX / Topoisomerase II
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / SIMULATED ANNEALING, MOLECULAR DYNAMICS
AuthorsMasliah, G. / Mauffret, O.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Identification of intrinsic dynamics in a DNA sequence preferentially cleaved by topoisomerase II enzyme
Authors: Masliah, G. / Rene, B. / Zargarian, L. / Fermandjian, S. / Mauffret, O.
History
DepositionDec 14, 2007Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jul 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (5'-D(*DAP*DCP*DAP*DGP*DCP*DTP*DTP*DAP*DTP*DCP*DAP*DTP*DCP*DGP*DAP*DTP*DCP*DAP*DCP*DGP*DT)-3')
B: DNA (5'-D(*DAP*DCP*DGP*DTP*DGP*DAP*DTP*DCP*DGP*DAP*DTP*DGP*DAP*DTP*DAP*DAP*DGP*DCP*DTP*DGP*DT)-3')


Theoretical massNumber of molelcules
Total (without water)12,8842
Polymers12,8842
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: DNA chain DNA (5'-D(*DAP*DCP*DAP*DGP*DCP*DTP*DTP*DAP*DTP*DCP*DAP*DTP*DCP*DGP*DAP*DTP*DCP*DAP*DCP*DGP*DT)-3')


Mass: 6382.148 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*DAP*DCP*DGP*DTP*DGP*DAP*DTP*DCP*DGP*DAP*DTP*DGP*DAP*DTP*DAP*DAP*DGP*DCP*DTP*DGP*DT)-3')


Mass: 6502.221 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
1222D 1H-1H NOESY
1322D DQF-COSY
1422D 1H-1H TOCSY
1522D 1H-13C HSQC
1622D 1H-31P HETCOR

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Sample preparation

Details
Solution-IDContentsSolvent system
146mM sodium phosphate; 1mM EDTA; 1.5mM Strand1; 1.5mM Strand2; 90% H2O/10% D2O90% H2O/10% D2O
246mM sodium phosphate; 1mM EDTA; 1.5mM Strand1; 1.5mM Strand2; 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
46 mMsodium phosphate1
1 mMEDTA1
1.5 mMStrand11
1.5 mMStrand21
46 mMsodium phosphate2
1 mMEDTA2
1.5 mMStrand12
1.5 mMStrand22
Sample conditionsIonic strength: 0.1 / pH: 7 / Pressure: 1 atm / Temperature: 303 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIH2.16Schwieters, Kuszewski, Tjandra and Clorerefinement
MORASS2.51Luxondata analysis
RefinementMethod: SIMULATED ANNEALING, MOLECULAR DYNAMICS / Software ordinal: 1
Details: THE STRUCTURE IS BASED ON A TOTAL OF 670 NOE, 102 HYDROGEN BOND, AND 286 DIHEDRAL RESTRAINTS
NMR constraintsNA alpha-angle constraints total count: 40 / NA beta-angle constraints total count: 40 / NA chi-angle constraints total count: 42 / NA delta-angle constraints total count: 42 / NA epsilon-angle constraints total count: 40 / NA gamma-angle constraints total count: 42 / NA other-angle constraints total count: 40 / NA sugar pucker constraints total count: 0 / NOE constraints total: 670 / NOE intraresidue total count: 230 / NOE long range total count: 480 / NOE medium range total count: 190 / NOE sequential total count: 383 / Hydrogen bond constraints total count: 102
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 10
NMR ensemble rmsDistance rms dev: 0.011384338 Å

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