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- PDB-2lgm: Structure of DNA Containing an Aristolactam II-dA Lesion -

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Basic information

Entry
Database: PDB / ID: 2lgm
TitleStructure of DNA Containing an Aristolactam II-dA Lesion
Components
  • DNA (5'-D(*CP*GP*TP*AP*CP*AP*CP*AP*TP*GP*C)-3')
  • DNA (5'-D(*GP*CP*AP*TP*GP*TP*GP*TP*AP*CP*G)-3')
KeywordsDNA / Duplex Stability / NER Recognition
Function / homologyChem-A4A / DNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / molecular dynamics
Model detailsminimized average structure, model 1
Model type detailsminimized average
AuthorsLukin, M. / Zaliznyak, T. / Johnson, F. / de los Santos, C.
CitationJournal: Nucleic Acids Res. / Year: 2012
Title: Structure and stability of DNA containing an aristolactam II-dA lesion: implications for the NER recognition of bulky adducts.
Authors: Lukin, M. / Zaliznyak, T. / Johnson, F. / de Los Santos, C.
History
DepositionJul 28, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 30, 2011Provider: repository / Type: Initial release
Revision 1.1Apr 11, 2012Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_conn / struct_site
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 / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3May 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
1: DNA (5'-D(*CP*GP*TP*AP*CP*AP*CP*AP*TP*GP*C)-3')
2: DNA (5'-D(*GP*CP*AP*TP*GP*TP*GP*TP*AP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,9713
Polymers6,7072
Non-polymers2631
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*AP*CP*AP*TP*GP*C)-3')


Mass: 3318.187 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*GP*CP*AP*TP*GP*TP*GP*TP*AP*CP*G)-3')


Mass: 3389.221 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical ChemComp-A4A / [1,3]benzodioxolo[6,5,4-cd]benzo[f]indol-5(6H)-one / Aristolactam II


Mass: 263.248 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H9NO3

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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 1H-1H COSY
1412D DQF-COSY
2522D 1H-1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.25 mM DNA 11m dupl ALII, 25 mM sodium phosphate, 50 mM sodium chloride, 100% D2O100% D2O
20.25 mM DNA 11m dupl ALII, 25 mM sodium phosphate, 50 mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
0.25 mMDNA 11m dupl ALII-11
25 mMsodium phosphate-21
50 mMsodium chloride-31
0.25 mMDNA 11m dupl ALII-42
25 mMsodium phosphate-52
50 mMsodium chloride-62
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
16.5 ambient 300 K
26.5 ambient 278 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
HYPERTejero, Monleon, Celda, Powers and Montelionegeometry optimization
VNMRVariancollection
TopSpinBruker Biospincollection
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
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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