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- PDB-2m3y: DNA containing a cluster of 8-oxo-guanine and abasic site lesion:... -

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Basic information

Entry
Database: PDB / ID: 2m3y
TitleDNA containing a cluster of 8-oxo-guanine and abasic site lesion: beta anomer
Components
  • DNA (5'-D(*CP*GP*CP*TP*CP*(AAB)P*CP*AP*CP*GP*C)-3')
  • DNA (5'-D(*GP*CP*GP*TP*GP*GP*GP*AP*(8OG)P*CP*G)-3')
KeywordsDNA / DNA lesion cluster / 8-oxo-guanine / abasic site
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing, molecular dynamics
AuthorsZalesak, J. / Jourdan, M. / Constant, J. / Lourdin, M.
CitationJournal: J.Mol.Biol. / Year: 2014
Title: Structure and dynamics of DNA duplexes containing a cluster of mutagenic 8-oxoguanine and abasic site lesions.
Authors: Zalesak, J. / Lourdin, M. / Krejc, L. / Constant, J.F. / Jourdan, M.
History
DepositionJan 28, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 8, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2014Group: Database references
Revision 1.2Jul 30, 2014Group: Non-polymer description
Revision 1.3Jun 14, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_validate_polymer_linkage / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (5'-D(*CP*GP*CP*TP*CP*(AAB)P*CP*AP*CP*GP*C)-3')
B: DNA (5'-D(*GP*CP*GP*TP*GP*GP*GP*AP*(8OG)P*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)6,6332
Polymers6,6332
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 / 500structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: DNA chain DNA (5'-D(*CP*GP*CP*TP*CP*(AAB)P*CP*AP*CP*GP*C)-3')


Mass: 3162.039 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*GP*CP*GP*TP*GP*GP*GP*AP*(8OG)P*CP*G)-3')


Mass: 3471.246 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 TOCSY
1212D 1H-1H NOESY
1312D DQF-COSY

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Sample preparation

DetailsContents: 0.55 mM DNA (5'-D(*CP*GP*CP*TP*CP*AAB*CP*AP*CP*GP*C)-3'), 0.55 mM DNA (5'-D(*GP*CP*GP*TP*GP*GP*GP*AP*(8OG)P*CP*G)-3'), 100% D2O
Solvent system: 100% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
0.55 mMDNA (5'-D(*CP*GP*CP*TP*CP*AAB*CP*AP*CP*GP*C)-3')-11
0.55 mMDNA (5'-D(*GP*CP*GP*TP*GP*GP*GP*AP*(8OG)P*CP*G)-3')-21
Sample conditionsIonic strength: 120 / pH: 6 / Pressure: ambient / Temperature: 283 K

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NMR measurement

NMR spectrometerType: Varian UnityPlus / Manufacturer: Varian / Model: UNITYPLUS / Field strength: 500 MHz

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Processing

NMR software
NameDeveloperClassification
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollmanstructure solution
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollmanrefinement
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 500 / Conformers submitted total number: 10

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