BMRB Entry 30224
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PDB ID:
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Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR30224
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Title: Structure Effects of the Four-Adenine Loop of the Coliphage GA Replicase RNA Operator PubMed: 28488852
Deposition date: 2017-01-03 Original release date: 2017-05-25
Authors: Chang, A.; Tran, M.; DeJong, E.; Nikonowicz, E.
Citation: Chang, A.; Tran, M.; Nikonowicz, E.. "Structure and Dynamics of the Tetra-A Loop and (A-A)-U Sequence Motif within the Coliphage GA Replicase RNA Operator" Biochemistry 56, 2690-2700 (2017).
Assembly members:
phage GA operator RNA hairpin, polymer, 23 residues, 7394.496 Da.
Natural source: Common Name: Enterobacteria phage GA Taxonomy ID: 12018 Superkingdom: Viruses Kingdom: not available Genus/species: Levivirus Escherichia virus BZ13
Experimental source: Production method: chemical synthesis
Entity Sequences (FASTA):
phage GA operator RNA hairpin: GGACAUAAGGAAAACCUAUG
UCC
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 158 |
| 15N chemical shifts | 49 |
| 1H chemical shifts | 196 |
| 31P chemical shifts | 21 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | entity_1 | 1 |
Entities:
Entity 1, entity_1 23 residues - 7394.496 Da.
| 1 | G | G | A | C | A | U | A | A | G | G | ||||
| 2 | A | A | A | A | C | C | U | A | U | G | ||||
| 3 | U | C | C |
Samples:
sample_4: Pf1 phage 15 mg/mL; phage GA operator RNA hairpin, [U-13C; U-15N], 0.3 ± 0.01 mM; potassium chloride 10 mM; potassium phosphate 10 mM; D2O 100%
sample_5: EDTA 0.02 mM; phage GA operator RNA hairpin, 2H, 40%-85%, 1.2 mM; potassium chloride 10 mM; potassium phosphate 10 mM; D2O 100%
sample_6: EDTA 0.02 mM; phage GA operator RNA hairpin, 13C, 4%-20%, 1.1 mM; potassium chloride 10 mM; potassium phosphate 10 mM; D2O 100%
sample_1: EDTA 0.02 mM; phage GA operator RNA hairpin, [U-13C; U-15N], 1 ± 0.1 mM; potassium chloride 10 mM; potassium phosphate 10 mM; D2O 100%
sample_2: EDTA 0.02 mM; phage GA operator RNA hairpin 1.5 ± 0.1 mM; potassium chloride 10 mM; potassium phosphate 10 mM; D2O 100%
sample_3: EDTA 0.02 mM; phage GA operator RNA hairpin, [U-13C; U-15N], 1 ± 0.1 mM; potassium chloride 10 mM; potassium phosphate 10 mM; H2O 90%; D2O 10%
sample_conditions_1: ionic strength: 20 mM; pH: 6.8; pressure: 1 atm; temperature: 298 K
sample_conditions_2: ionic strength: 20 mM; pH: 6.8; pressure: 1 atm; temperature: 285 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-1H NOESY | sample_2 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC | sample_1 | isotropic | sample_conditions_1 |
| 3D HCCH-TOCSY | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-15N HSQC | sample_3 | isotropic | sample_conditions_2 |
| 2D 1H-31P HetCor | sample_5 | isotropic | sample_conditions_1 |
| 2D 1H-13C CTEP | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC | sample_6 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC | sample_4 | anisotropic | sample_conditions_1 |
| 3D 1H-15N NOESY | sample_3 | isotropic | sample_conditions_2 |
| 2D 1H-13C H(N)CO | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-15N HSQC | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-13C H(CN)CO | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-13C C(C)H-COSY | sample_1 | isotropic | sample_conditions_1 |
Software:
Felix, Accelrys Software Inc. - processing
X-PLOR NIH v2.43, Schwieters, Kuszewski, Tjandra and Clore - structure calculation
NMR spectrometers:
- Varian INOVA 600 MHz
- Varian INOVA 500 MHz