1Q8N
Solution Structure of the Malachite Green RNA Binding Aptamer
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D NOESY | 1.5mM RNA Aptamer, 10mM phosphate buffer | 100% D2O | 10mM KCl | 5.8 | ambient | 298 | |
| 2 | 2D TOCSY | 1.5mM RNA Aptamer, 10mM phosphate buffer | 100% D2O | 10mM KCl | 5.8 | ambient | 298 | |
| 3 | DQF-COSY | 1.5mM RNA Aptamer, 10mM phosphate buffer | 100% D2O | 10mM KCl | 5.8 | ambient | 298 | |
| 4 | 3D_13C-separated_NOESY | 1mM RNA Aptamer U-15N,13C, 10mM phosphate buffer | 100% D2O | 10mM KCl | 5.8 | ambient | 298 | |
| 5 | 2D HMQC | 1mM RNA Aptamer U-15N,13C, 10mM phosphate buffer, 90% H2O, 10% D2O | 90% H2O/10% D2O | 10mM KCl | 5.8 | ambient | 274 | |
| 6 | HCNCH | 1mM RNA Aptamer U-15N,13C, 10mM phosphate buffer | 100% D2O | 10mM KCl | 5.8 | ambient | 298 | |
| 7 | 2D NOESY | 1.5mM RNA Aptamer, 10mM phosphate buffer, 90% H2O, 10% D2O | 90% H2O/10% D2O | 10mM KCl | 5.8 | ambient | 274 | |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Bruker | DRX | 600 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| simulated annealing | The structure was based on 423 NOE constraints (148 intranucleotide, 119 sequential, 66 medium to long range, and 90 RNA to ligand NOEs) and 219 dihedral angle restraints. | XwinNMR |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | structures with the lowest energy |
| Conformers Calculated Total Number | 100 |
| Conformers Submitted Total Number | 25 |
| Representative Model | 1 (lowest energy) |
| Additional NMR Experimental Information | |
|---|---|
| Details | This structure was determined with the aid of the crystal structure of a similar RNA aptamer. |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | collection | XwinNMR | 2.6 | Bruker |
| 2 | structure solution | CNS | 1.1 | A.T. Brunger, P.D. Adams, G.M. Clore, W.L. Delano, P. Gros, R.W. Grosse-Kunstleve, J.S. Jiang, J. Kuszewski, M. Nilges, N.S. Pannu, R.J. Read, L.M.R ice, T. Simonson, G.L. Warren |
| 3 | data analysis | XEASY | 1.3.13 | C. Bartels, T.H. Xia, M. Billeter, P. Gntert and K. Wthrich |
| 4 | refinement | CNS | 1.1 | A.T. Brunger, P.D. Adams, G.M. Clore, W.L. Delano, P. Gros, R.W. Grosse-Kunstleve, J.S. Jiang, J. Kuszewski, M. Nilges, N.S. Pannu, R.J. Read, L.M.R ice, T. Simonson, G.L. Warren |
