BMRB Entry 30054
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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/BMR30054
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Title: NMR solution structure of [Sp, Sp]-PT dsDNA PubMed: 27169778
Deposition date: 2016-03-30 Original release date: 2016-11-14
Authors: Lan, Wenxian; Hu, Zhongpei; Cao, Chunyang
Citation: Lan, Wenxian; Hu, Zhongpei; Cao, Chunyang. "Structural investigation into physiological DNA phosphorothioate modification" Sci. Rep. 6, 25737-25737 (2016).
Assembly members:
DNA (5'-D(*CP*GP*(SSG)P*CP*CP*GP*CP*CP*GP*A)-3'), polymer, 10 residues, 3047.047 Da.
DNA (5'-D(*TP*CP*GP*GP*CP*GP*(SSG)P*CP*CP*G)-3'), polymer, 10 residues, 3078.058 Da.
Natural source: Common Name: high GC Gram+ Taxonomy ID: 1916 Superkingdom: Bacteria Kingdom: not available Genus/species: Streptomyces lividans
Experimental source: Production method: recombinant technology Host organism: Streptomyces lividans
Entity Sequences (FASTA):
DNA (5'-D(*CP*GP*(SSG)P*CP*CP*GP*CP*CP*GP*A)-3'): CGXCCGCCGA
DNA (5'-D(*TP*CP*GP*GP*CP*GP*(SSG)P*CP*CP*G)-3'): TCGGCGXCCG
- assigned_chemical_shifts
| Data type | Count |
| 1H chemical shifts | 112 |
| 31P chemical shifts | 18 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | entity_1 | 1 |
| 2 | entity_2 | 2 |
Entities:
Entity 1, entity_1 10 residues - 3047.047 Da.
| 1 | DC | DG | GS | DC | DC | DG | DC | DC | DG | DA |
Entity 2, entity_2 10 residues - 3078.058 Da.
| 1 | DT | DC | DG | DG | DC | DG | GS | DC | DC | DG |
Samples:
sample_1: Sp dsDNA 1.0 mM; H2O 90%; D2O 10%
sample_conditions_1: ionic strength: 360 mM; pH: 7.0; pressure: 1.0 atm; temperature: 298 K
sample_conditions_2: ionic strength: 360 mM; pH: 7.0; pressure: 1.0 atm; temperature: 298 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-1H NOESY | sample_1 | anisotropic | sample_conditions_1 |
| 2D 1H-1H TOCSY | sample_1 | anisotropic | sample_conditions_2 |
| 2D 1H-1H DQCOSY | sample_1 | anisotropic | sample_conditions_2 |
| 2D 1H-1H NOESY | sample_1 | anisotropic | sample_conditions_2 |
| 2D 1H-31P HETCOR | sample_1 | anisotropic | sample_conditions_2 |
Software:
SPARKY, Goddard - chemical shift assignment, peak picking
X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement, structure calculation
NMR spectrometers:
- Agilent DD2 600 MHz
- Agilent DD2 500 MHz