1K5I
NMR Structure of a Ribosomal RNA Hairpin Containing a Conserved CUCAA Pentaloop
SOLUTION NMR
NMR Experiment | ||||||||
---|---|---|---|---|---|---|---|---|
Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D NOESY | 0.8 mM RNA; 10 mM Sodium Phosphate; 0.1 mM EDTA; pH 6.5 | 90% H2O/10% D2O | 10 mM Sodium Phosphate | 6.5 | ambient | 298 | |
2 | DQF-COSY | 0.8 mM RNA; 10 mM Sodium Phosphate; 0.1 mM EDTA; pH 6.5 | 90% H2O/10% D2O | 10 mM Sodium Phosphate | 6.5 | ambient | 298 | |
3 | 1H-31P HETCOR | 0.8 mM RNA; 10 mM Sodium Phosphate; 0.1 mM EDTA; pH 6.5 | 90% H2O/10% D2O | 10 mM Sodium Phosphate | 6.5 | ambient | 298 | |
4 | COSY-35 | 0.8 mM RNA; 10 mM Sodium Phosphate; 0.1 mM EDTA; pH 6.5 | 90% H2O/10% D2O | 10 mM Sodium Phosphate | 6.5 | ambient | 298 | |
5 | TOCSY | 0.8 mM RNA; 10 mM Sodium Phosphate; 0.1 mM EDTA; pH 6.5 | 90% H2O/10% D2O | 10 mM Sodium Phosphate | 6.5 | ambient | 298 | |
6 | 0.8 mM RNA; 10 mM Sodium Phosphate; 0.1 mM EDTA; pH 6.5 | 90% H2O/10% D2O | 10 mM Sodium Phosphate | 6.5 | ambient | 298 |
NMR Spectrometer Information | |||
---|---|---|---|
Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | AMX | 600 |
NMR Refinement | ||
---|---|---|
Method | Details | Software |
Distance Geometry, Simulated Annealing, Restrained Molecular Dynamics | A total of 300 structures were calculated using distance geometry utilizing 123 experimentally derived distance restraints for the loop and 918 (258-experimental distances, 660-A form distances) distance restraints for the stem region and 143 dihedral angle restraints. Additionally, 50 distance restraints were used to maintain the Watson-Crick geometry of the base pairs in the stem region. Final refinement resulted in 10 lowest energy structures. | X-PLOR |
NMR Ensemble Information | |
---|---|
Conformer Selection Criteria | structures with the lowest energy |
Conformers Calculated Total Number | 33 |
Conformers Submitted Total Number | 10 |
Computation: NMR Software | ||||
---|---|---|---|---|
# | Classification | Version | Software Name | Author |
1 | refinement | X-PLOR | 3.1 | Brunger |