BMRB Entry 16951
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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/BMR16951
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Title: The Structure of RNA Internal Loops with Tandem AG Pairs: 5'GAGC/3'CGAG PubMed: 20481618
Deposition date: 2010-05-25 Original release date: 2010-07-02
Authors: Hammond, Nicholas; Kennedy, Scott; Turner, Douglas
Citation: Hammond, Nicholas; Tolbert, Blanton; Kierzek, Ryszard; Turner, Douglas; Kennedy, Scott. "RNA internal loops with tandem AG pairs: the structure of the 5'GAGU/3'UGAG loop can be dramatically different from others, including 5'AAGU/3'UGAA." Biochemistry 49, 5817-5827 (2010).
Assembly members:
RNA_(5'-R(*GP*AP*CP*GP*AP*GP*CP*GP*UP*CP*A)-3'), polymer, 11 residues, 3530.203 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: obtained from a vendor
Entity Sequences (FASTA):
RNA_(5'-R(*GP*AP*CP*GP*AP*GP*CP*GP*UP*CP*A)-3'): GACGAGCGUCA
- assigned_chemical_shifts
Data type | Count |
13C chemical shifts | 50 |
1H chemical shifts | 107 |
31P chemical shifts | 10 |
Additional metadata:
Assembly:
Entity Assembly ID | Entity Name | Entity ID |
---|---|---|
1 | RNA (5'-R(*GP*AP*CP*GP*AP*GP*CP*GP*UP*CP*A)-3')_1 | 1 |
2 | RNA (5'-R(*GP*AP*CP*GP*AP*GP*CP*GP*UP*CP*A)-3')_2 | 1 |
Entities:
Entity 1, RNA (5'-R(*GP*AP*CP*GP*AP*GP*CP*GP*UP*CP*A)-3')_1 11 residues - 3530.203 Da.
1 | G | A | C | G | A | G | C | G | U | C | ||||
2 | A |
Samples:
sample_1: RNA (5'-R(*GP*AP*CP*GP*AP*GP*CP*GP*UP*CP*A)-3') 1 mM; sodium chloride 80 mM; sodium phosphate 10 mM; EDTA 0.5 mM; H2O 90%; D2O 10%
sample_2: RNA (5'-R(*GP*AP*CP*GP*AP*GP*CP*GP*UP*CP*A)-3') 1 mM; sodium chloride 80 mM; sodium phosphate 10 mM; EDTA 0.5 mM; D2O 100%
sample_conditions_1: ionic strength: 0.1 M; pH: 6.1; pressure: 1 atm; temperature: 273 K
sample_conditions_2: ionic strength: 0.1 M; pH: 6.1; pressure: 1 atm; temperature: 288 K
Experiments:
Name | Sample | Sample state | Sample conditions |
---|---|---|---|
2D 1H-1H NOESY | sample_1 | isotropic | sample_conditions_1 |
2D 1H-13C HSQC | sample_1 | isotropic | sample_conditions_1 |
2D 1H-1H TOCSY | sample_2 | isotropic | sample_conditions_2 |
2D DQF-COSY | sample_2 | isotropic | sample_conditions_2 |
2D 1H-31P HETCOR | sample_2 | isotropic | sample_conditions_2 |
2D 1H-1H NOESY | sample_2 | isotropic | sample_conditions_2 |
Software:
SPARKY v3.12, Goddard - chemical shift assignment, data analysis
VNMR v6.1C, Varian - collection
CNS v1.2, Brunger, Adams, Clore, Gros, Nilges and Read - structure solution
AMBER v9, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm - refinement
NMR spectrometers:
- Varian INOVA 600 MHz
- Varian INOVA 500 MHz