BMRB Entry 19571
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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/BMR19571
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Title: Solution NMR structure of the d(GGGTTTTGGGTGGGTTTTGGG) quadruplex in sodium conditions. PubMed: 30182059
Deposition date: 2013-10-22 Original release date: 2014-10-20
Authors: Karsisiotis, Andreas Ioannis; Webba da Silva, Mateus; Karsisiotis, Andreas Ioannis
Citation: Dvorkin, Scarlett; Karsisiotis, Andreas; Webba da Silva, Mateus. "Encoding canonical DNA quadruplex structure." Sci. Adv. 4, eaat3007-eaat3007 (2018).
Assembly members:
DNA, polymer, 21 residues, 6643.305 Da.
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):
DNA: GGGTTTTGGGTGGGTTTTGG
G
- assigned_chemical_shifts
| Data type | Count |
| 1H chemical shifts | 345 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | DNA (5'-D(*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*TP*GP*GP*GP*TP*TP*TP*TP*GP*GP*G)-3') | 1 |
Entities:
Entity 1, DNA (5'-D(*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*TP*GP*GP*GP*TP*TP*TP*TP*GP*GP*G)-3') 21 residues - 6643.305 Da.
| 1 | DG | DG | DG | DT | DT | DT | DT | DG | DG | DG | ||||
| 2 | DT | DG | DG | DG | DT | DT | DT | DT | DG | DG | ||||
| 3 | DG |
Samples:
Exchangeable_Protons_(278K): DNA (5'-D(*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*TP*GP*GP*GP*TP*TP*TP*TP*GP*GP*G)-3') 2 mM; sodium phosphate 20 mM; H2O 93%; D2O, [U-100% 2H], 7%
Non_exchangeable_Protons_(293K): DNA (5'-D(*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*TP*GP*GP*GP*TP*TP*TP*TP*GP*GP*G)-3') 2 mM; sodium phosphate 20 mM; D2O, [U-100% 2H], 100%
Exchangeable_Protons_(278K)_conditions: ionic strength: 20 mM; pH: 7.8; pressure: 1 atm; temperature: 278 K
Non_exchangeable_Protons_(293K)_conditions: ionic strength: 20 mM; pH: 7.8; pressure: 1 atm; temperature: 293 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-1H TOCSY | Non_exchangeable_Protons_(293K) | isotropic | Non_exchangeable_Protons_(293K)_conditions |
| 2D 1H-1H COSY | Non_exchangeable_Protons_(293K) | isotropic | Non_exchangeable_Protons_(293K)_conditions |
| 2D 1H-1H NOESY | Non_exchangeable_Protons_(293K) | isotropic | Non_exchangeable_Protons_(293K)_conditions |
| 2D 1H-1H NOESY | Exchangeable_Protons_(278K) | isotropic | Exchangeable_Protons_(278K)_conditions |
| 2D 1H-31P HSQC | Non_exchangeable_Protons_(293K) | isotropic | Non_exchangeable_Protons_(293K)_conditions |
Software:
FELIX, Accelrys Software Inc. - processing
VNMRJ, Varian - collection
SPARKY, Goddard - chemical shift assignment, data analysis
X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement, structure solution
Molmol, Koradi, Billeter and Wuthrich - data analysis
NMR spectrometers:
- Varian VNMRS 500 500 MHz