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- PDB-2lt0: NMR structure of duplex DNA containing the beta-OH-PdG dA base pa... -

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Basic information

Entry
Database: PDB / ID: 2lt0
TitleNMR structure of duplex DNA containing the beta-OH-PdG dA base pair: A mutagenic intermediate of acrolein
Components
  • DNA (5'-D(*CP*GP*TP*AP*CP*(63G)P*CP*AP*TP*GP*C)-3')
  • DNA (5'-D(*GP*CP*AP*TP*GP*AP*GP*TP*AP*CP*G)-3')
KeywordsDNA / acrolein adducts / DNA lesions / damaged DNA structure
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / molecular dynamics
Model type detailsminimized average
AuthorsZaliznyak, T. / de los Santos, C. / Lukin, M. / El-khateeb, M. / Bonala, R. / Johnson, F.
CitationJournal: Biopolymers / Year: 2010
Title: NMR structure of duplex DNA containing the alpha-OH-PdG.dA base pair: a mutagenic intermediate of acrolein.
Authors: Zaliznyak, T. / Lukin, M. / El-khateeb, M. / Bonala, R. / Johnson, F. / de los Santos, C.
History
DepositionMay 9, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 13, 2012Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: DNA (5'-D(*CP*GP*TP*AP*CP*(63G)P*CP*AP*TP*GP*C)-3')
D: DNA (5'-D(*GP*CP*AP*TP*GP*AP*GP*TP*AP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)6,7882
Polymers6,7882
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)26 / 26all calculated structures submitted
RepresentativeModel #1minimized average structure

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Components

#1: DNA chain DNA (5'-D(*CP*GP*TP*AP*CP*(63G)P*CP*AP*TP*GP*C)-3')


Mass: 3390.249 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*GP*CP*AP*TP*GP*AP*GP*TP*AP*CP*G)-3')


Mass: 3398.235 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 1H-1H COSY
1312D 1H-1H TOCSY
1412D 1H-1H COSY45
1512D DQF-COSY
2622D 1H-1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM 11 mer duplex oligo, 100% D2O100% D2O
20.5 mM 11 mer duplex oligo, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
0.5 mM11 mer duplex oligo-11
0.5 mM11 mer duplex oligo-22
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
16.6ambient 298 K
26.6ambient 278 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
VNMRVariancollection
FelixAccelrys Software Inc.data analysis
FelixAccelrys Software Inc.chemical shift assignment
FelixAccelrys Software Inc.peak picking
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Cloregeometry optimization
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 26 / Conformers submitted total number: 26

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