BMRB Entry 30252
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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/BMR30252
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Title: Solution Structure of a DNA Dodecamer with 5-methylcytosine at the 9th position and 8-oxoguanine at the 10th position PubMed: 30289469
Deposition date: 2017-02-24 Original release date: 2017-05-25
Authors: Gruber, D.; Hoppins, J.; Miears, H.; Endutkin, A.; Zharkov, D.; Smirnov, S.
Citation: Gruber, David; Toner, Joanna; Miears, Heather; Shernyukov, Andrey; Kiryutin, Alexey; Lomzov, Alexander; Endutkin, Anton; Grin, Inga; Petrova, Darya; Kupryushkin, Maxim; Yurkovskaya, Alexandra; Johnson, Eric; Okon, Mark; Bagryanskaya, Elena; Zharkov, Dmitry; Smirnov, Serge. "Oxidative damage to epigenetically methylated sites affects DNA stability, dynamics and enzymatic demethylation" Nucleic Acids Res. 46, 10827-10839 (2018).
Assembly members:
entity_1, polymer, 12 residues, 3693.419 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):
entity_1: CGCGAATTXXCG
- assigned_chemical_shifts
Data type | Count |
1H chemical shifts | 172 |
Additional metadata:
Assembly:
Entity Assembly ID | Entity Name | Entity ID |
---|---|---|
1 | entity_1 | 1 |
2 | entity_1 | 1 |
Entities:
Entity 1, entity_1 12 residues - 3693.419 Da.
1 | DC | DG | DC | DG | DA | DA | DT | DT | 5CM | 8OG | ||||
2 | DC | DG |
Samples:
sample_1: DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(DMC)P*(8OG)P*CP*G)-3') 1 mM; EDTA 0.1 mM; potassium chloride 10 mM; sodium chloride 50 mM
sample_conditions_1: ionic strength: 120 mM; pH: 6.8; pressure: 1 .; temperature: 298 K
sample_conditions_2: ionic strength: 120 mM; pH: 6.8; pressure: 1 .; 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 |
Software:
AMBER, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement
NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing
NMRView, Johnson, One Moon Scientific - chemical shift assignment, peak picking
NMR spectrometers:
- Bruker AvanceIII 500 MHz
- Bruker AvanceIII 700 MHz