BMRB Entry 18656
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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/BMR18656
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Title: Major Conformation of the Internal Loop 5'GAGU/3'UGAG PubMed: 23134175
Deposition date: 2012-08-12 Original release date: 2011-05-05
Authors: Kennedy, Scott; Turner, Douglas
Citation: Kennedy, Scott; Kierzek, Ryszard; Turner, Douglas. "Novel conformation of an RNA structural switch." Biochemistry 51, 9257-9259 (2012).
Assembly members:
RNA_loop, polymer, 11 residues, 3546.203 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):
RNA_loop: GACGAGUGUCA
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 13 |
| 15N chemical shifts | 5 |
| 1H chemical shifts | 164 |
| 31P chemical shifts | 10 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | RNA (5'-R(*GP*AP*CP*GP*AP*GP*UP*GP*UP*CP*A)-3'), strand 1 | 1 |
| 2 | RNA (5'-R(*GP*AP*CP*GP*AP*GP*UP*GP*UP*CP*A)-3'), strand 2 | 1 |
Entities:
Entity 1, RNA (5'-R(*GP*AP*CP*GP*AP*GP*UP*GP*UP*CP*A)-3'), strand 1 11 residues - 3546.203 Da.
| 1 | G | A | C | G | A | G | U | G | U | C | ||||
| 2 | A |
Samples:
sample_1: RNA_loop 1.5 mM; sodium chloride 80 mM; sodium phosphate 10 mM; EDTA 0.05 mM; H2O 95%; D2O 5%
sample_2: RNA_loop 1.5 mM; sodium chloride 80 mM; sodium phosphate 10 mM; EDTA 0.05 mM; D2O 100%
sample_conditions_1: ionic strength: 0.1 M; pH: 6.1; pressure: 1 atm; temperature: 274 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-13C HSQC | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-15N HSQC | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-1H TOCSY 30 ms | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-1H NOESY 75 ms | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-1H NOESY 150 ms | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC | sample_2 | isotropic | sample_conditions_1 |
| 2D 1H-1H TOCSY 14ms | sample_2 | isotropic | sample_conditions_1 |
| 2D 1H-1H TOCSY 36 ms | sample_2 | isotropic | sample_conditions_1 |
| 2D 1H-1H NOESY 75 ms | sample_2 | isotropic | sample_conditions_1 |
| 2D 1H-1H NOESY 175 ms | sample_2 | isotropic | sample_conditions_1 |
| 2D 1H-1H NOESY 400 ms | sample_2 | isotropic | sample_conditions_1 |
| 2D 1H-31P HETCOR | sample_2 | isotropic | sample_conditions_1 |
Software:
SPARKY v3.12, Goddard - chemical shift assignment, data analysis
NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing
AMBER v10, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman - structure solution
NMR spectrometers:
- Varian INOVA 600 MHz