BMRB Entry 16138
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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/BMR16138
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Title: NMR solution structure of metal-modified DNA PubMed: 21124482
Deposition date: 2009-01-27 Original release date: 2012-08-07
Authors: Johannsen, Silke; Duepre, Nicole; Boehme, Dominik; Mueller, Jens; Sigel, Roland
Citation: Johannsen, Silke; Megger, N.; Boehme, Dominik; Sigel, Roland; Mueller, Jens. "Solution structure of a DNA double helix with consecutive metal-mediated base pairs" Nat. Chem. 2, 229-234 (2010).
Assembly members:
DNA_(34-MER), polymer, 34 residues, 8484.617 Da.
AG, non-polymer, 107.868 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_(34-MER): TTAATTTXXXAAATTAATTA
ATTTXXXAAATTAA
- assigned_chemical_shifts
| Data type | Count |
| 1H chemical shifts | 332 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | DNA (34-MER) | 1 |
| 2 | SILVER ION_1 | 2 |
| 3 | SILVER ION_2 | 2 |
| 4 | SILVER ION_3 | 2 |
Entities:
Entity 1, DNA (34-MER) 34 residues - 8484.617 Da.
| 1 | DT | DT | DA | DA | DT | DT | DT | D33 | D33 | D33 | ||||
| 2 | DA | DA | DA | DT | DT | DA | DA | DT | DT | DA | ||||
| 3 | DA | DT | DT | DT | D33 | D33 | D33 | DA | DA | DA | ||||
| 4 | DT | DT | DA | DA |
Entity 2, SILVER ION_1 - Ag - 107.868 Da.
| 1 | AG |
Samples:
sample_1: DNA (34-MER)0.3 – 0.5 mM; sodium perchlorate 120 mM; SILVER ION0.9 – 1.5 mM
sample_2: DNA (34-MER)0.3 – 0.5 mM; sodium perchlorate 120 mM; SILVER ION0.9 – 1.5 mM
sample_conditions_1: ionic strength: 0.12 M; pD: 7.2; pressure: 1 atm; temperature: 298 K
sample_conditions_2: ionic strength: 0.12 M; pH: 7.2; pressure: 1 atm; temperature: 278 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-1H NOESY | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-1H TOCSY | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-15N HSQC | sample_1 | isotropic | sample_conditions_1 |
| 1D 31P | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-1H NOESY | sample_2 | isotropic | sample_conditions_2 |
Software:
TOPSPIN v1.3, 2.0, 2.1, Bruker Biospin - processing
SPARKY v3.1, Goddard - chemical shift assignment, data analysis, peak picking
DYANA v1.5, Guntert, Braun and Wuthrich - structure solution
X-PLOR NIH v2.15, Schwieters, Kuszewski, Tjandra and Clore - refinement, structure solution
NMR spectrometers:
- Bruker Avance 700 MHz
- Bruker AV-2 400 MHz