BMRB Entry 36699
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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/BMR36699
MolProbity Validation Chart
NMR-STAR file interactive viewer.
NMR-STAR v3 text file.
All files associated with the entry
Citation: Yamasaki, Kazuhiko; Inomata, Rika; Yamasaki, Tomoko; Kubota, Tomomi; Miyashita, Naoyuki; Takeuchi, Koh; Miyagishi, Makoto. "A minimal RNA-cleaving DNAzyme and its catalytic mechanism." Nucleic Acids Res. 54, gkaf1502-gkaf1502 (2026).
PubMed: 41538318
Assembly members:
DNAzyme minGAA, polymer, 26 residues, 8094.208 Da.
ZINC ION, non-polymer, 65.409 Da.
Natural source: Common Name: not available Taxonomy ID: 32630 Superkingdom: not available Kingdom: not available Genus/species: not available not available
Experimental source: Production method: chemical synthesis Host organism: unidentified
Entity Sequences (FASTA):
DNAzyme minGAA: GGATCACCCGCGAAGCGXAA
GGATCC
- assigned_chemical_shifts
| Data type | Count |
| 1H chemical shifts | 249 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | entity_1 | 1 |
| 2 | entity_ZN | 2 |
Entities:
Entity 1, entity_1 26 residues - 8094.208 Da.
| 1 | DG | DG | DA | DT | DC | DA | DC | DC | DC | DG | ||||
| 2 | DC | DG | DA | DA | DG | DC | DG | OMG | A | A | ||||
| 3 | DG | DG | DA | DT | DC | DC |
Entity 2, entity_ZN - Zn - 65.409 Da.
| 1 | ZN |
Samples:
sample_1: DNAzyme minGAA 0.44 mM; ZnCl2 1 mM; Tris-D11 10 mM; DSS 0.1 mM; H2O 95%; D2O, [U-2H], 5%
sample_conditions_1: ionic strength: 11 mM; pH: 7.0; 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 TOCSY | sample_1 | isotropic | sample_conditions_1 |
| 2D DQF-COSY | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC | sample_1 | isotropic | sample_conditions_1 |
Software:
CNS v1.3, Brunger, Adams, Clore, Gros, Nilges and Read - refinement
CNS v1.3, Brunger, Adams, Clore, Gros, Nilges and Read - structure calculation
Felix, Accelrys Software Inc. - chemical shift assignment
Felix, Accelrys Software Inc. - peak picking
NMR spectrometers:
- Bruker AVANCE III HD 900 MHz