BMRB Entry 30038
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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/BMR30038
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Title: Solution Structure of DNA Dodecamer with 8-oxoguanine at 4th Position
Deposition date: 2016-03-18 Original release date: 2016-07-20
Authors: Miears, H.; Gruber, D.; Hoppins, J.; Kiryutin, A.; Kasymov, R.; Yurkovskaya, A.; Zharkov, D.; Smirnov, S.
Citation: Miears, H.; Gruber, D.; Hoppins, J.; Kiryutin, A.; Kasymov, R.; Yurkovskaya, A.; Zharkov, D.; Smirnov, S.. "Structure of 8-oxoguanine in the EcoRI recognition site and loss of EcoRI function/recognition." . ., .-..
Assembly members:
DNA (5'-D(*CP*GP*CP*(8OG)P*AP*AP*TP*TP*CP*GP*CP*G)-3'), polymer, 12 residues, 3679.392 Da.
Natural source: Common Name: not available Taxonomy ID: 32630 Superkingdom: not available Kingdom: not available Genus/species: not available not available
Experimental source: Production method: chemical synthesis
Entity Sequences (FASTA):
DNA (5'-D(*CP*GP*CP*(8OG)P*AP*AP*TP*TP*CP*GP*CP*G)-3'): CGCXAATTCGCG
- assigned_chemical_shifts
Data type | Count |
1H chemical shifts | 186 |
31P chemical shifts | 14 |
Additional metadata:
Assembly:
Entity Assembly ID | Entity Name | Entity ID |
---|---|---|
1 | entity_1, chain 1 | 1 |
2 | entity_1, chain 2 | 1 |
Entities:
Entity 1, entity_1, chain 1 12 residues - 3679.392 Da.
1 | DC | DG | DC | 8OG | DA | DA | DT | DT | DC | DG | ||||
2 | DC | DG |
Samples:
sample_1: DNA (5'-D(*CP*GP*CP*(8OG)P*AP*AP*TP*TP*CP*GP*CP*G)-3') 0.2 mM; EDTA 1 mM; potassium phosphate 10 mM; sodium chloride 50 mM; D2O 100%
sample_conditions_1: ionic strength: 120 mM; pH: 6.8; pressure: 1 atm; temperature: 298 K
sample_conditions_2: ionic strength: 120 mM; pH: 6.8; pressure: 1 atm; temperature: 278 K
Experiments:
Name | Sample | Sample state | Sample conditions |
---|---|---|---|
2D 1H-1H NOESY | sample_1 | isotropic | sample_conditions_1 |
2D 1H-1H NOESY | sample_1 | isotropic | sample_conditions_2 |
2D DQF-COSY | sample_1 | isotropic | sample_conditions_1 |
31P HETCOR | sample_1 | isotropic | sample_conditions_1 |
2D 1H-1H TOCSY | sample_1 | isotropic | sample_conditions_1 |
Software:
AMBER v12, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollman - refinement, structure calculation
CYANA v2.1, Guntert, Mumenthaler and Wuthrich - data analysis
NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing
NMRView v9.0, Johnson, One Moon Scientific - chemical shift assignment, data analysis, peak picking
NMR spectrometers:
- Bruker Avance 700 MHz