BMRB Entry 25369

Name: Solution Structure of DNA Dodecamer with 8-oxoguanine at 10th Position.
Published: 2017-03-22

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR25369

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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Solution Structure of DNA Dodecamer with 8-oxoguanine at 10th Position.

Deposition date:

2014-11-26

Original release date:

2017-03-22

Authors:

Gruber, David; Miears, Heather; Hoppins, Joanna; Kiryutin, Aleksey; Kasymov, Rustem; Smirnov, Serge

Citation:

Citation: Hoppins, Joanna; Gruber, David; Miears, Heather; Kiryutin, Alexey; Kasymov, Rustem; Petrova, Darya; Endutkin, Anton; Popov, Alexander; Yurkovskaya, Alexandra; Fedechkin, Stanislav; Brockerman, Jacob; Zharkov, Dmitry; Smirnov, Serge. "8-Oxoguanine Affects DNA Backbone Conformation in the EcoRI Recognition Site and Inhibits Its Cleavage by the Enzyme" PLoS ONE 11, e0164424-e0164424 (2016).
PubMed: 27749894

Assembly members:

Assembly members:
DNA_(5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*(8OG)P*CP*G)-3'), polymer, 12 residues, 3679.421 Da.

Natural source:

Natural source: Common Name: E. coli Taxonomy ID: 562 Superkingdom: Bacteria Kingdom: not available Genus/species: Escherichia coli

Experimental source:

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
DNA_(5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*(8OG)P*CP*G)-3'): CGCGAATTCXCG

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
1H chemical shifts	160

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	DNA (5'-D(CPGPCPGPAPAPTPTPCP(8OG)PCPG)-3')_1	1
2	DNA (5'-D(CPGPCPGPAPAPTPTPCP(8OG)PCPG)-3')_2	1

Entities:

Entity 1, DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*(8OG)P*CP*G)-3')_1 12 residues - 3679.421 Da.

1

DC

DG

DC

DG

DA

DT

DC

8OG

2

DC

DG

Samples:

sample_1: sodium chloride 50 mM; potassium phosphate 10 mM; EDTA 1 mM; DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*(8OG)P*CP*G)-3') 1 mM

sample_2: sodium chloride 50 mM; potassium phosphate 10 mM; EDTA 1 mM; DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*(8OG)P*CP*G)-3') 1 mM

sample_conditions_1: ionic strength: 120 mM; pH: 6.8; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D DQF-COSY	sample_1	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_1

Software:

NMRView v9.0.0-b77, Johnson, One Moon Scientific - chemical shift assignment, data analysis, peak picking

X-PLOR_NIH v2.37, Schwieters, Kuszewski, Tjandra and Clore - refinement, structure solution

CYANA v2.1, Guntert, Mumenthaler and Wuthrich - data analysis, structure solution

NMRPipe v7.9 Rev 2013.021.23.09, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

AMBER, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman - Structural Modeling, structure solution

NMR spectrometers:

Bruker Avance 700 MHz