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- PDB-2k1y: Solution Structure of Duplex DNA Containing the Mutagenic Lesion:... -

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Basic information

Entry
Database: PDB / ID: 2k1y
TitleSolution Structure of Duplex DNA Containing the Mutagenic Lesion: 1,N2-Etheno-2'-deoxyguanine
Components
  • 5'-D(*DCP*DGP*DTP*DAP*DCP*(GNE)P*DCP*DAP*DTP*DGP*DC)-3'
  • 5'-D(*DGP*DCP*DAP*DTP*DGP*DCP*DGP*DTP*DAP*DCP*DG)-3'
KeywordsDNA / Damaged DNA structure / exocyclic DNA lesions / extrahelical base / BER recognition
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / molecular dynamics
Model type detailsminimized average
AuthorsZaliznyak, T. / Lukin, M. / Johnson, F. / de los Santos, C.
CitationJournal: Biochemistry / Year: 2008
Title: Solution structure of duplex DNA containing the mutagenic lesion 1,N(2)-etheno-2'-deoxyguanine.
Authors: Zaliznyak, T. / Lukin, M. / Johnson, F. / de los Santos, C.
History
DepositionMar 18, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
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: 5'-D(*DCP*DGP*DTP*DAP*DCP*(GNE)P*DCP*DAP*DTP*DGP*DC)-3'
B: 5'-D(*DGP*DCP*DAP*DTP*DGP*DCP*DGP*DTP*DAP*DCP*DG)-3'


Theoretical massNumber of molelcules
Total (without water)6,7322
Polymers6,7322
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)9 / 12structures with the lowest energy
RepresentativeModel #1minimized average structure

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Components

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


Mass: 3358.208 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*DGP*DCP*DAP*DTP*DGP*DCP*DGP*DTP*DAP*DCP*DG)-3'


Mass: 3374.210 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 TOCSY
1312D DQF-COSY
1412D 1H-1H COSY
2522D 1H-1H NOESY H2O
1611H-32P PHCorr

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Sample preparation

Details
Solution-IDContentsSolvent system
14.2mM duplex DNA, 1,N2-etheno-2 -deoxyguanosine, 100% D2O100% D2O
24.2mM duplex DNA, 1,N2-etheno-2 -deoxyguanosine, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
4.2 mM4.2mM duplex DNA, 1,N2-etheno-2 -deoxyguanosine1
4.2 mM4.2mM duplex DNA, 1,N2-etheno-2 -deoxyguanosine2
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
150mM NaCl 6.8 ambient atm300 K
250mM NaCl 6.8 ambient mbar278 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.85Brungerstructure solution
FelixAccelrys Software Inc.processing
FelixAccelrys Software Inc.chemical shift assignment
VNMR5.2Variancollection
X-PLOR3.85Brungerrefinement
RefinementMethod: molecular dynamics / Software ordinal: 1 / Details: Restrained MD simulation
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 12 / Conformers submitted total number: 9

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