BMRB Entry 17814

Name: Structure of DNA Containing an Aristolactam II-dA Lesion.
Published: 2011-12-01

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PDB ID: 2lgm
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR17814
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Nicholas Rego and David Koes
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Structure of DNA Containing an Aristolactam II-dA Lesion.

Deposition date:

2011-07-28

Original release date:

2011-12-01

Authors:

Lukin, Mark; Zaliznyak, Tanya; Johnson, Francis; de los Santos, Carlos

Citation:

Citation: Lukin, Mark; Zaliznyak, Tanya; Johnson, Francis; de Los Santos, Carlos. "Structure and stability of DNA containing an aristolactam II-dA lesion: implications for the NER recognition of bulky adducts." Nucleic Acids Res. 40, 2759-2770 (2012).
PubMed: 22121223

Assembly members:

Assembly members:
DNA_11m_dupl_ALII, polymer, 11 residues, 111.103 Da.

Natural source:

Natural source: Common Name: not available Taxonomy ID: not available Superkingdom: not available Kingdom: not available Genus/species: not available not available

Experimental source:

Experimental source: Production method: chemical synthesis Vector: no

Entity Sequences (FASTA):

Entity Sequences (FASTA):
DNA_11m_dupl_ALII: GCATGTGTACG

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
1H chemical shifts	82

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	DNA_11m_dupl_ALII	1

Entities:

Entity 1, DNA_11m_dupl_ALII 11 residues - 111.103 Da.

1

DG

DC

DA

DT

DG

DT

DG

DT

DA

DC

2

DG

Samples:

sample_1: DNA 11m dupl ALII 0.25 mM; sodium phosphate 25 mM; sodium chloride 50 mM; D2O 100%

sample_2: DNA 11m dupl ALII 0.25 mM; sodium phosphate 25 mM; sodium chloride 50 mM; D2O 10%; H2O 90%

sample_1_conditions: pH: 6.5; pressure: 1 atm; temperature: 273 K

sample_2_conditions: pH: 6.5; pressure: 1 atm; temperature: 273 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_1	isotropic	sample_1_conditions
2D 1H-1H TOCSY	sample_1	isotropic	sample_1_conditions
2D 1H-1H COSY	sample_1	isotropic	sample_1_conditions
2D DQF-COSY	sample_1	isotropic	sample_1_conditions
2D 1H-1H NOESY	sample_2	isotropic	sample_2_conditions

Software:

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - structure solution

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

SPARKY, Goddard - chemical shift assignment, peak picking

HYPER, Tejero, Monleon, Celda, Powers and Montelione - geometry optimization

VNMR, Varian - collection

TOPSPIN, Bruker Biospin - collection

NMR spectrometers:

Bruker Avance 800 MHz
Varian INOVA 600 MHz