BMRB Entry 25378
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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/BMR25378
MolProbity Validation Chart
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NMR-STAR v3 text file.
XML gzip file.
RDF gzip file.
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Citation: Cheong, Vee Vee; Heddi, Brahim; Lech, Christopher; Phan, Anh Tuan. "Xanthine and 8-oxoguanine in G-quadruplexes: formation of a GGXO tetrad" Nucleic Acids Res. 43, 10506-10514 (2015).
PubMed: 26400177
Assembly members:
DNA_(5'-D(*TP*TP*GP*GP*GP*TP*TP*AP*(8OG)P*GP*GP*TP*TP*AP*GP*GP*(3ZO)P*TP*TP*AP*GP*GP*GP*A)-3'), polymer, 24 residues, 7259.721 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_(5'-D(*TP*TP*GP*GP*GP*TP*TP*AP*(8OG)P*GP*GP*TP*TP*AP*GP*GP*(3ZO)P*TP*TP*AP*GP*GP*GP*A)-3'): TTGGGTTAXGGTTAGGXTTA
GGGA
- assigned_chemical_shifts
| Data type | Count |
| 1H chemical shifts | 232 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | DNA (5'-D(*TP*TP*GP*GP*GP*TP*TP*AP*(8OG)P*GP*GP*TP*TP*AP*GP*GP*(3ZO)P*TP*TP*AP*GP*GP*GP*A)-3') | 1 |
Entities:
Entity 1, DNA (5'-D(*TP*TP*GP*GP*GP*TP*TP*AP*(8OG)P*GP*GP*TP*TP*AP*GP*GP*(3ZO)P*TP*TP*AP*GP*GP*GP*A)-3') 24 residues - 7259.721 Da.
| 1 | DT | DT | DG | DG | DG | DT | DT | DA | 8OG | DG | ||||
| 2 | DG | DT | DT | DA | DG | DG | 3ZO | DT | DT | DA | ||||
| 3 | DG | DG | DG | DA |
Samples:
sample_1: DNA (5'-D(*TP*TP*GP*GP*GP*TP*TP*AP*(8OG)P*GP*GP*TP*TP*AP*GP*GP*(3ZO)P*TP*TP*AP*GP*GP*GP*A)-3') 0.7 mM; potassium phosphate 20 mM; potassium chloride 70 mM
sample_conditions_1: ionic strength: 90 mM; pH: 8.0; 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-13C HSQC aromatic | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC aliphatic | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-15N HSQC | sample_1 | isotropic | sample_conditions_1 |
Software:
X-PLOR_NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement, structure solution
AMBER, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement
SPARKY, Goddard - chemical shift assignment, data analysis, peak picking
TOPSPIN, Bruker Biospin - collection
NMR spectrometers:
- Bruker Avance 600 MHz
- Bruker Avance 700 MHz