BMRB Entry 11608
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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/BMR11608
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Title: SOLUTION STRUCTURE OF DNA CONTAINING METALLO-BASE-PAIR PubMed: 27505707
Deposition date: 2016-03-22 Original release date: 2016-08-22
Authors: Dairaku, Takenori; Furuita, Kyoko; Sato, Hajime; Sebera, Jakub; Nakashima, Katsuyuki; Kondo, Jiro; Yamanaka, Daichi; Kondo, Yoshinori; Okamoto, Itaru; Ono, Akira; Sychrovsky, Vladimir; Kojima, Chojiro; Tanaka, Yoshiyuki
Citation: Dairaku, Takenori; Furuita, Kyoko; Sato, Hajime; Sebera, Jakub; Nakashima, Katsuyuki; Kondo, Jiro; Yamanaka, Daichi; Kondo, Yoshinori; Okamoto, Itaru; Ono, Akira; Sychrovsky, Vladimir; Kojima, Chojiro; Tanaka, Yoshiyuki. "Structure Determination of an AgI-Mediated Cytosine-Cytosine Base Pair within DNA Duplex in Solution with 1H/15N/109Ag NMR Spectroscopy" Chem. Eur. J. ., .-. (2016).
Assembly members:
DNA_(5'-D(*TP*AP*AP*TP*AP*TP*AP*CP*TP*TP*AP*AP*TP*TP*A)-3'), polymer, 15 residues, 4566.059 Da.
DNA_(5'-D(*TP*AP*AP*TP*TP*AP*AP*CP*TP*AP*TP*AP*TP*TP*A)-3'), polymer, 15 residues, 4566.059 Da.
SILVER ION, 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_(5'-D(*TP*AP*AP*TP*AP*TP*AP*CP*TP*TP*AP*AP*TP*TP*A)-3'): TAATATACTTAATTA
DNA_(5'-D(*TP*AP*AP*TP*TP*AP*AP*CP*TP*AP*TP*AP*TP*TP*A)-3'): TAATTAACTATATTA
- assigned_chemical_shifts
| Data type | Count |
| 1H chemical shifts | 244 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | DNA (5'-D(*TP*AP*AP*TP*AP*TP*AP*CP*TP*TP*AP*AP*TP*TP*A)-3') | 1 |
| 2 | DNA (5'-D(*TP*AP*AP*TP*TP*AP*AP*CP*TP*AP*TP*AP*TP*TP*A)-3') | 2 |
| 3 | SILVER ION | 3 |
Entities:
Entity 1, DNA (5'-D(*TP*AP*AP*TP*AP*TP*AP*CP*TP*TP*AP*AP*TP*TP*A)-3') 15 residues - 4566.059 Da.
| 1 | DT | DA | DA | DT | DA | DT | DA | DC | DT | DT | ||||
| 2 | DA | DA | DT | DT | DA |
Entity 2, DNA (5'-D(*TP*AP*AP*TP*TP*AP*AP*CP*TP*AP*TP*AP*TP*TP*A)-3') 15 residues - 4566.059 Da.
| 1 | DT | DA | DA | DT | DT | DA | DA | DC | DT | DA | ||||
| 2 | DT | DA | DT | DT | DA |
Entity 3, SILVER ION - Ag - 107.868 Da.
| 1 | AG |
Samples:
sample_1: DNA (5'-D(*TP*AP*AP*TP*AP*TP*AP*CP*TP*TP*AP*AP*TP*TP*A)-3') 2 mM; DNA (5'-D(*TP*AP*AP*TP*TP*AP*AP*CP*TP*AP*TP*AP*TP*TP*A)-3') 2 mM; AgNO3 2.1 mM; NaNO3 100 mM; H2O 90%; D2O, [U-2H], 10%
sample_2: DNA (5'-D(*TP*AP*AP*TP*AP*TP*AP*CP*TP*TP*AP*AP*TP*TP*A)-3') 2 mM; DNA (5'-D(*TP*AP*AP*TP*TP*AP*AP*CP*TP*AP*TP*AP*TP*TP*A)-3') 2 mM; AgNO3 2.1 mM; NaNO3 100 mM; D2O, [U-2H], 100%
sample_conditions_1: ionic strength: 0.1 M; pH: 6.9; pressure: 1 atm; temperature: 298 K
sample_conditions_2: ionic strength: 0.1 M; pH: 7.1; 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 NOESY | sample_2 | isotropic | sample_conditions_2 |
| 2D DQF-COSY | sample_2 | isotropic | sample_conditions_2 |
| 2D 1H-13C HSQC | sample_2 | isotropic | sample_conditions_2 |
Software:
SPARKY, Goddard - chemical shift assignment, peak picking
MARDIGRAS, Thomas L. James - data analysis, structure solution
CNS, Brunger, Adams, Clore, Gros, Nilges and Read - structure solution
NMR spectrometers:
- Bruker Avance 950 MHz