BMRB Entry 34805
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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/BMR34805
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Title: Solution structure of the 8-17 DNAzyme in presence of Zn2+ PubMed: 38760331
Deposition date: 2023-04-13 Original release date: 2023-04-19
Authors: Andralojc, W.; Gdaniec, Z.
Citation: Wieruszewska, Julia; Pawlowicz, Aleksandra; Polomska, Ewa; Pasternak, Karol; Gdaniec, Zofia; Andralojc, Witold. "The 8-17 DNAzyme can operate in a single active structure regardless of metal ion cofactor" Nat. Commun. 15, 4218-4218 (2024).
Assembly members:
entity_1, polymer, 35 residues, 10841.923 Da.
Natural source: Common Name: not available Taxonomy ID: 32630 Superkingdom: not available Kingdom: not available Genus/species: synthetic construct
Experimental source: Production method: chemical synthesis
Entity Sequences (FASTA):
entity_1: CGCCGGGGTCGAAGACTGCC
AGCGGCTCGACGGCG
- assigned_chemical_shifts
| Data type | Count |
| 1H chemical shifts | 302 |
| 31P chemical shifts | 32 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | unit_1 | 1 |
Entities:
Entity 1, unit_1 35 residues - 10841.923 Da.
| 1 | DC | DG | DC | DC | DG | DG | DG | DG | DT | DC | ||||
| 2 | DG | DA | DA | DG | DA | DC | DT | DG | DC | DC | ||||
| 3 | DA | DG | DC | DG | DG | DC | DT | DC | DG | DA | ||||
| 4 | DC | DG | DG | DC | DG |
Samples:
sample_1: 8-17 DNAzyme 2.2 mM; cacodylate 10 mM; zinc chloride 4 mM; sodium chloride 200 mM
sample_2: 8-17 DNAzyme 2.2 mM; cacodylate 10 mM; zinc chloride 4 mM; sodium chloride 200 mM
sample_conditions_1: ionic strength: 200 mM; pH: 6.0; pressure: 1 atm; temperature: 308 K
sample_conditions_2: ionic strength: 200 mM; pH: 6.0; pressure: 1 atm; temperature: 293 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-1H NOESY | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-31P COSY | 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-1H NOESY | sample_2 | isotropic | sample_conditions_2 |
Software:
Amber, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement, structure calculation
NMRFAM-SPARKY, NMRFAM - chemical shift assignment, peak picking
NMR spectrometers:
- Bruker AVANCE III 700 MHz