BMRB Entry 34596
Click here to enlarge.
PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34596
MolProbity Validation Chart
NMR-STAR file interactive viewer.
NMR-STAR v3 text file.
XML gzip file.
RDF gzip file.
All files associated with the entry
Title: Solution structure of DNA duplex containing a 7,8-dihydro-8-oxo-1,N6-ethenoadenine base modification that induces exclusively A->T transversions in Escherichia coli PubMed: 35234900
Deposition date: 2021-01-27 Original release date: 2022-02-25
Authors: Aralov, A.; Gubina, N.; Cabrero, C.; Tsvetkov, V.; Turaev, A.; Fedeles, B.; Croy, R.; Isaakova, E.; Melnik, D.; Dukova, S.; Khrulev, A.; Varizhuk, A.; Gonzalez, C.; Zatsepin, T.; Essigmann, J.
Citation: Aralov, Andrey; Gubina, Nina; Cabrero, Cristina; Tsvetkov, Vladimir; Turaev, Anton; Fedeles, Bogdan; Croy, Robert; Isaakova, Ekaterina; Melnik, Denis; Dukova, Svetlana; Ryazantsev, Dmitriy; Khrulev, Alexei; Varizhuk, Anna; Gonzalez, Carlos; Zatsepin, Timofei; Essigmann, John. "7,8-Dihydro-8-oxo-1,N6-ethenoadenine: an exclusively Hoogsteen-paired thymine mimic in DNA that induces A\u2192T transversions in Escherichia coli" Nucleic Acids Res. 50, 3056-3069 (2022).
Assembly members:
entity_1, polymer, 9 residues, 2763.845 Da.
entity_2, polymer, 9 residues, 2739.824 Da.
Natural source: Common Name: not available Taxonomy ID: 32630 Superkingdom: not available Kingdom: not available Genus/species: synthetic construct
Experimental source: Production method: chemical synthesis
Entity Sequences (FASTA):
entity_1: GTACXCATG
entity_2: CATGAGTAC
- assigned_chemical_shifts
| Data type | Count |
| 1H chemical shifts | 146 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | unit_1 | 1 |
| 2 | unit_2 | 2 |
Entities:
Entity 1, unit_1 9 residues - 2763.845 Da.
| 1 | DG | DT | DA | DC | U7T | DC | DA | DT | DG |
Entity 2, unit_2 9 residues - 2739.824 Da.
| 1 | DC | DA | DT | DG | DA | DG | DT | DA | DC |
Samples:
sample_1: DNA (5'-D(*GP*TP*AP*CP*(EDA)P*CP*AP*TP*G)-3') 0.5 M; DNA (5'-D(*CP*AP*TP*GP*AP*GP*TP*AP*C)-3') 0.5 M; sodium phosphate 25 mM; sodium chloride 100 mM; DSS 0.5 % v/v
sample_conditions_1: ionic strength: 125 mM; pH: 7; pressure: 1 atm; temperature: 276 K
sample_conditions_2: ionic strength: 125 mM; pH: 7; 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 TOCSY | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-1H NOESY | sample_1 | isotropic | sample_conditions_2 |
Software:
TopSpin, Bruker Biospin - collection, processing
NMRFAM-SPARKY, Goddard & Kneller - chemical shift assignment
Amber v18, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement, structure calculation
MOLMOL, Koradi, Billeter and Wuthrich - data analysis
3DNA, Lu & Olson - data analysis
NMR spectrometers:
- Bruker AVANCE 600 MHz