BMRB Entry 36378
Click here to enlarge.
PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR36378
MolProbity Validation Chart
NMR-STAR file interactive viewer.
NMR-STAR v3 text file.
XML gzip file.
RDF gzip file.
All files associated with the entry
Title: NMR solution structures of the DNA minidumbbell formed by 5'-mCTTGXmCTTG-3' PubMed: 33501691
Deposition date: 2020-09-12 Original release date: 2021-08-02
Authors: Wan, L.; Guo, P.; Lam, S.
Citation: Wan, Liqi; Yi, Jie; Lam, Sik; Lee, Hung; Guo, Pei. "5-Methylcytosine Substantially Enhances the Thermal Stability of DNA Minidumbbell" Chemistry 27, 6740-6747 (2021).
Assembly members:
DNA (5'-D(*(MCY)P*TP*TP*GP*(3DR)P*(5CM)P*TP*TP*G)-3'), polymer, 9 residues, 2536.759 Da.
SODIUM ION, non-polymer, 22.990 Da.
Natural source: Common Name: Human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens
Experimental source: Production method: chemical synthesis
Entity Sequences (FASTA):
DNA (5'-D(*(MCY)P*TP*TP*GP*(3DR)P*(5CM)P*TP*TP*G)-3'): XTTGXXTTG
- assigned_chemical_shifts
- spectral_peak_list
| Data type | Count |
| 1H chemical shifts | 102 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | unit_1 | 1 |
| 2 | unit_2 | 2 |
| 3 | unit_3 | 2 |
| 4 | unit_4 | 2 |
| 5 | unit_5 | 2 |
| 6 | unit_6 | 2 |
| 7 | unit_7 | 2 |
| 8 | unit_8 | 2 |
| 9 | unit_9 | 2 |
Entities:
Entity 1, unit_1 9 residues - 2536.759 Da.
| 1 | MCY | DT | DT | DG | 3DR | 5CM | DT | DT | DG |
Entity 2, unit_2 - Na - 22.990 Da.
| 1 | NA |
Samples:
sample_1: DNA (5'-D(*(MC1)P*TP*TP*GP*(DX)P*(DMC)P*TP*TP*G)-3') 0.5 ± 0.05 mM; DSS 0.02 ± 0.005 mM; sodium phosphate 10 ± 1 mM; D2O, [U-2H], 99.96%
sample_conditions_1: ionic strength: 25 mM; pH: 7.0; pressure: 1 atm; temperature: 273 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-1H NOESY | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-1H COSY | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-1H TOCSY | sample_1 | isotropic | sample_conditions_1 |
Software:
Amber, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman - structure calculation
TopSpin, Bruker Biospin - chemical shift assignment
NMR spectrometers:
- Bruker AVANCE 500 MHz