BMRB Entry 25528

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR25528
MolProbity Validation Chart

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Title:
Solution Structure of DNA Dodecamer with 8-oxoguanine at 4th Position
Deposition date:
2015-03-09
Original release date:
2016-03-07
Authors:
Miears, Heather; Gruber, David; Hoppins, Joanna; Kiryutin, Aleksey; Kasymov, Rustem; Yurkovskaya, Alexandra; Zharkov, Dmitry; 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*(8OG)P*AP*AP*TP*TP*CP*GP*CP*G)-3'), polymer, 12 residues, 3679.421 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

Entity Sequences (FASTA):

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

Data sets:
Data typeCount
1H chemical shifts162

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
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Assembly:

Entity Assembly IDEntity NameEntity ID
1DNA (5'-D(*CP*GP*CP*(8OG)P*AP*AP*TP*TP*CP*GP*CP*G)-3')_11
2DNA (5'-D(*CP*GP*CP*(8OG)P*AP*AP*TP*TP*CP*GP*CP*G)-3')_21

Entities:

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

1   DCDGDC8OGDADADTDTDCDG
2   DCDG

Samples:

sample_1: DNA (5'-D(*CP*GP*CP*(8OG)P*AP*AP*TP*TP*CP*GP*CP*G)-3') 0.2 mM; sodium chloride 50 mM; potassium phosphate 10 mM; EDTA 1 mM; D2O, [U2-H], 100%

sample_2: DNA (5'-D(*CP*GP*CP*(8OG)P*AP*AP*TP*TP*CP*GP*CP*G)-3') 0.2 mM; sodium chloride 50 mM; potassium phosphate 10 mM; EDTA 1 mM; D2O, [U-2H], 10%; H2O 90%

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

Experiments:

NameSampleSample stateSample conditions
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
2D 1H-1H TOCSYsample_1isotropicsample_conditions_1
2D 1H-1H COSYsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_2isotropicsample_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