BMRB Entry 18454
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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/BMR18454
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Title: NMR structure of duplex DNA containing the -OH-PdG dA base pair: A mutagenic intermediate of acrolein PubMed: 20049919
Deposition date: 2012-05-09 Original release date: 2012-06-11
Authors: Zaliznyak, Tanya; de los Santos, Carlos; Lukin, Mark; El-khateeb, Mahmoud; Bonala, Rahda; Johnson, Francis
Citation: Zaliznyak, Tanya; de los Santos, Carlos; Lukin, Mark; El-khateeb, Mahmoud; Bonala, Rahda; Johnson, Francis. "NMR structure of duplex DNA containing the -OH-PdG dA base pair: A mutagenic intermediate of acrolein" Biopolymers 93, 391-401 (2010).
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 Host organism: n/a
Entity Sequences (FASTA):
11_mer_oligonucleotide-B: CGTACGCATGC
11_mer_oligonucleotide-D: GCATGAGTACG
- 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
(aG) : (S)1,N2-a-(OH)-PdG
| 1 | DC | DG | DT | DA | DC | DG | DC | DA | DT | DG | ||||
| 2 | DC |
Entity 2, 11_mer_oligonucleotide-D 11 residues - Formula weight is not available
A+: (N1H)+ adenine
| 1 | DG | DC | DA | DT | DG | DA | DG | DT | DA | DC | ||||
| 2 | DG |
Samples:
sample_1: 11_mer_oligonucleotide-B 0.5 mM; D2O 100%
sample_2: 11_mer_oligonucleotide-B 0.5 mM; D2O 10%; H2O 90%
sample_conditions_1: pH: 6.6; pressure: 1 atm; temperature: 273 K
sample_conditions_2: pH: 6.6; 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 1H-1H TOCSY | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-1H COSY45 | sample_1 | isotropic | sample_conditions_1 |
| 2D DQF-COSY | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-1H NOESY | sample_2 | isotropic | sample_conditions_2 |
Software:
VNMR, Varian - collection
FELIX, Accelrys Software Inc. - chemical shift assignment, data analysis, peak picking
X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - geometry optimization, refinement, structure solution
NMR spectrometers:
- Varian INOVA 600 MHz