BMRB Entry 34386
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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/BMR34386
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Title: SC14 G-hairpin PubMed: 33524154
Deposition date: 2019-04-01 Original release date: 2021-02-01
Authors: Lenarcic Zivkovic, M.; Trantirek, L.; Plavec, J.
Citation: Zdivkovic, Martina Lenarcic; Gajarsky, Martin; Bekova, Katerina; Stadlbauer, Petr; Vicherek, Lukas; Petrova, Magdalena; Fiala, Radovan; Rosenberg, Ivan; Sponer, Jiri; Plavec, Janez; Trantirek, Lukas. "Insight into formation propensity of pseudocircular DNA G-hairpins" Nucleic Acids Res. 49, 2317-2332 (2021).
Assembly members:
entity_1, polymer, 14 residues, 4413.846 Da.
Natural source: Common Name: baker's yeast Taxonomy ID: 4932 Superkingdom: Eukaryota Kingdom: Fungi Genus/species: Saccharomyces cerevisiae
Experimental source: Production method: chemical synthesis
Entity Sequences (FASTA):
entity_1: GTGTGTGGGTGTGT
- assigned_chemical_shifts
| Data type | Count |
| 1H chemical shifts | 135 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | entity_1 | 1 |
Entities:
Entity 1, entity_1 14 residues - 4413.846 Da.
| 1 | DG | DT | DG | DT | DG | DT | DG | DG | DG | DT | ||||
| 2 | DG | DT | DG | DT |
Samples:
sample_1: DNA (5'-D(*GP*TP*GP*TP*GP*TP*GP*GP*GP*TP*GP*TP*GP*T)-3') 0.6 mM
sample_2: DNA (5'-D(*GP*TP*GP*TP*GP*TP*GP*GP*GP*TP*GP*TP*GP*T)-3') 0.6 mM
sample_conditions_1: ionic strength: 120 mM; pH: 7.0; pressure: 1 atm; temperature: 283 K
sample_conditions_2: ionic strength: 120 mM; pH: 7.0 pD; pressure: 1 atm; temperature: 283 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D NOESY | sample_1 | isotropic | sample_conditions_1 |
| 2D NOESY | sample_2 | isotropic | sample_conditions_2 |
| 2D TOCSY | sample_2 | isotropic | sample_conditions_2 |
| 2D DQF COSY | sample_2 | isotropic | sample_conditions_2 |
| 1D 15N-edited HSQC | sample_1 | isotropic | sample_conditions_1 |
| 2D NOESY | sample_1 | isotropic | sample_conditions_1 |
| 2D NOESY | sample_2 | isotropic | sample_conditions_2 |
Software:
SPARKY, Goddard - chemical shift assignment
AMBER14, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman - structure calculation
VNMR, Varian - processing
TOPSPIN, Bruker Biospin - processing
NMR spectrometers:
- Bruker AvanceIII 700 MHz
- Bruker AvanceIII 850 MHz
- Agilent DD2 600 MHz
- Bruker AvanceIII 950 MHz
- Bruker AvanceIII 600 MHz