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- PDB-2k0v: High Resolution Solution NMR Structures of Undamaged DNA Dodecame... -

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Basic information

Entry
Database: PDB / ID: 2k0v
TitleHigh Resolution Solution NMR Structures of Undamaged DNA Dodecamer Duplex
Components
  • DNA (5'-D(*DCP*DCP*DTP*DCP*DTP*DGP*DGP*DTP*DCP*DTP*DCP*DC)-3')
  • DNA (5'-D(*DGP*DGP*DAP*DGP*DAP*DCP*DCP*DAP*DGP*DAP*DGP*DG)-3')
KeywordsDNA / Undamaged DNA Duplex
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing
AuthorsBhattacharyya, D. / King, C.L. / Chaney, S.G. / Campbell, S.L.
CitationJournal: Plos One / Year: 2011
Title: Flanking Bases Influence the Nature of DNA Distortion by Platinum 1,2-Intrastrand (GG) Cross-Links.
Authors: Bhattacharyya, D. / Ramachandran, S. / Sharma, S. / Pathmasiri, W. / King, C.L. / Baskerville-Abraham, I. / Boysen, G. / Swenberg, J.A. / Campbell, S.L. / Dokholyan, N.V. / Chaney, S.G.
History
DepositionFeb 15, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 31, 2011Group: Database references
Revision 1.3May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)7,3272
Polymers7,3272
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)1 / 20structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 3565.316 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*DGP*DGP*DAP*DGP*DAP*DCP*DCP*DAP*DGP*DAP*DGP*DG)-3')


Mass: 3761.468 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
1212D DQF-COSY
1312D 1H-13C HSQC

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Sample preparation

DetailsContents: 1 mM Undamaged DNA Duplex, 90% H2O, 10% D2O / Solvent system: 90% H2O/10% D2O
SampleConc.: 1 mM / Component: Undamaged DNA Duplex
Sample conditionsIonic strength: 50 mM NaCl / pH: 6.8 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian Unity / Manufacturer: Varian / Model: UNITY / Field strength: 700 MHz

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Processing

NMR softwareName: CNS / Developer: Brunger A. T. et.al. / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: energy based refinement with NOE distance constraints
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 1
NMR ensemble rmsBond angle rms dev: 0.461 ° / Covalent bond rms dev: 0.0024 Å / Dihedral angles rms dev: 0 ° / Improper torsion angle rms dev: 0.296 °

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