BMRB Entry 18639
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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/BMR18639
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Title: Solution Structure of Duplex DNA Containing a b-Carba-Fapy-dG Lesion PubMed: 22897814
Deposition date: 2012-08-03 Original release date: 2013-02-18
Authors: Zalianyak, Tatiana; de los Santos, Carlos; Lukin, Mark; Attaluri, Sivaprasad; Johnson, Francis
Citation: Lukin, Mark; Zalianyak, Tatiana; Attaluri, Sivaprasad; Johnson, Francis; de los Santos, Carlos. "Solution Structure of Duplex DNA Containing a b-Carba-Fapy-dG Lesion" Chem. Res. Toxicol. 25, 2423-2431 (2012).
Assembly members:
11_mer_oligonucleotide-B, polymer, 11 residues, Formula weight is not available
11_mer_oligonucleotide-D, polymer, 11 residues, Formula weight is not available
Natural source: Common Name: not available Taxonomy ID: not available Superkingdom: not available Kingdom: not available Genus/species: not available not available
Experimental source: Production method: chemical synthesis
Entity Sequences (FASTA):
11_mer_oligonucleotide-B: CGTACXCATGC
11_mer_oligonucleotide-D: GCATGCGTACG
- assigned_chemical_shifts
| Data type | Count |
| 1H chemical shifts | 150 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | 11_mer_oligonucleotide-B | 1 |
| 2 | 11_mer_oligonucleotide-D | 2 |
Entities:
Entity 1, 11_mer_oligonucleotide-B 11 residues - Formula weight is not available
| 1 | DC | DG | DT | DA | DC | LWM | DC | DA | DT | DG | ||||
| 2 | DC |
Entity 2, 11_mer_oligonucleotide-D 11 residues - Formula weight is not available
| 1 | DG | DC | DA | DT | DG | DC | DG | DT | DA | DC | ||||
| 2 | DG |
Samples:
sample_1: 11_mer_oligonucleotide-B 1.57 mM; 11_mer_oligonucleotide-D 1.57 mM; phosphate buffer 25 mM; NaCl 50 mM; EDTA 0.5 mM; D2O 100%
sample_2: 11_mer_oligonucleotide-B 1.57 mM; 11_mer_oligonucleotide-D 1.57 mM; phosphate buffer 25 mM; NaCl 50 mM; EDTA 0.5 mM; D2O 10%; H2O 90%
sample_conditions_1: pH: 6.8; pressure: 1 atm; temperature: 273 K
sample_conditions_2: pH: 6.8; pressure: 1 atm; temperature: 273 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-1H NOESY | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-1H COSY | 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-13C HSQC | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-1H NOESY | sample_2 | isotropic | sample_conditions_2 |
Software:
TOPSPIN, Bruker Biospin - collection
NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing
SPARKY, Goddard - chemical shift assignment, data analysis, peak picking, peak volume calc.
X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - geometry optimization, refinement, structure solution
NMR spectrometers:
- Bruker Avance 800 MHz