2G1W
NMR structure of the Aquifex aeolicus tmRNA pseudoknot PK1
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D NOESY | 1mM unlabeled PK1, 50mM NaCl, 0.5 mM EDTA | 95%H2O-5%D2O and 100% D2O | 50mM NaCl | 6.3 | ambient | 278 | |
| 2 | HCN, 1H 13C HSQC, 1H 13C constant time HSQC, 1H 13C long-range HSQC, HCCH-TOCSY, HCCH E.COSY, HCC-TOCSY-CCH-E.COSY, 3D NOESY-HSQC | 0.7mM 13C,15N PK1, 50mM NaCl, 0.5 mM EDTA | 95%H2O-5%D2O and 100% D2O | 50mM NaCl | 6.3 | ambient | 293 | |
| 3 | HMBC, 1H 15N TROSY, 2JNN HNN-COSY, 2JNH HNN-COSY, 3D NOESY-HMBC | 0.7mM 13C,15N PK1, 50mM NaCl, 0.5 mM EDTA | 95%H2O-5%D2O and 100% D2O | 50mM NaCl | 6.3 | ambient | 278 | |
| 4 | 2D NOESY, TOCSY | 1mM unlabeled PK1, 50mM NaCl, 0.5 mM EDTA | 95%H2O-5%D2O and 100% D2O | 50mM NaCl | 6.3 | ambient | 293 | |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Bruker | AVANCE | 600 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| CNS dynamical annealing protocol for nucleic acids | A- dynamical annealing protocol: 1. TAMD 30 ps at 20000K 2. first cooling stage TAMD 40ps 3. second slow cooling annealing stage, restrained molecular dynamics 35ps. 4. 10 cycles of energy minimization of 300 steps each. B- Energy minimization: 1-TAMD 10ps at 300K, 2- cooling over 9 ps and 10 Powell cycles of 800 steps each. | UXNMR |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | structures with acceptable covalent geometry, structures with favorable non-bond energy, structures with the least restraint violations, structures with the lowest energy |
| Conformers Calculated Total Number | 100 |
| Conformers Submitted Total Number | 15 |
| Representative Model | 1 (lowest energy) |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | collection | UXNMR | 3.1 | Bruker |
| 2 | data analysis | Felix | 2000.1 | MSI Inc. |
| 3 | refinement | CNS | 1.1 | Brunger, Adams,Clore, DeLano,Gross, Grosse-Kunstleve, Jiang, Kuzewski, Nilges, Pannu, Read, Rice, Simmonson, Warren |
| 4 | data analysis | MOLMOL | 2K.1 | Reto Koradi |
