BMRB Entry 18430
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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/BMR18430
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Title: Structure and Stability of Duplex DNA Containing (5 S) 5 ,8-Cyclo-2 -Deoxyadenosine: An Oxidative Lesion Repair by NER. PubMed: 22928555
Deposition date: 2012-04-30 Original release date: 2012-09-10
Authors: Zaliznyak, Tatiana; de los Santos, Carlos; Lukin, Mark
Citation: Zaliznyak, Tatiana; Lukin, Mark; de los Santos, Carlos. "Structure and stability of duplex DNA containing (5'S)-5',8-cyclo-2'-deoxyadenosine: an oxidatively generated lesion repaired by NER." Chem. Res. Toxicol. 25, 2103-2111 (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: GCATGTGTACG
- assigned_chemical_shifts
| Data type | Count |
| 1H chemical shifts | 151 |
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
X represents (5 S) 5 ,8-Cyclo-2 -Deoxyadenosine
| 1 | DC | DG | DT | DA | DC | 02I | 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 | DT | DG | DT | DA | DC | ||||
| 2 | DG |
Samples:
sample_1: 11 mer DNA duplex 0.7 mM; 11 mer DNA duplex 0.7 mM; D2O 100%
sample_2: 11 mer DNA duplex 0.7 mM; 11 mer DNA duplex 0.7 mM; H2O 90%; D2O 10%
sample_conditions_1: pH: 6.7; pressure: 1 atm; temperature: 298 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-15N HSQC | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-1H NOESY | sample_2 | isotropic | sample_conditions_1 |
Software:
VNMR, Varian - collection
TOPSPIN, Bruker Biospin - collection
NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing
FELIX, Accelrys Software Inc. - processing
SPARKY, Goddard - chemical shift assignment, data analysis, peak picking
X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - geometry optimization, refinement, structure solution
HYPER, Tejero, Monleon, Celda, Powers and Montelione - data analysis, geometry optimization
InsightII, Accelrys Software Inc. - data analysis
NMR spectrometers:
- Varian INOVA 600 MHz
- Bruker Avance 400 MHz
- Bruker Avance 700 MHz