2AWQ
Solution Structure of pseudouridine-32 modified anticodon stem-loop of E. coli tRNAPhe
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 3D_13C-separated_NOESY | 2.3 mM C-13 labeled RNA hairpin, 10 mM NaCl, 10 mM potassium phosphate, pH 6.8 | 100% D2O | 10 mM NaCl, 10 mM potassium phosphate | 6.8 | ambient | 298 | |
2 | HCCH-TOCSY | 2.3 mM C-13 labeled RNA hairpin, 10 mM NaCl, 10 mM potassium phosphate, pH 6.8 | 100% D2O | 10 mM NaCl, 10 mM potassium phosphate | 6.8 | ambient | 298 | |
3 | CCH-RELAY | 2.3 mM C-13 labeled RNA hairpin, 10 mM NaCl, 10 mM potassium phosphate, pH 6.8 | 100% D2O | 10 mM NaCl, 10 mM potassium phosphate | 6.8 | ambient | 298 | |
4 | 3D_15N-separated_NOESY | 2.8 mM N-15 labeled RNA hairpin, 10 mM NaCl, 10 mM potassium phosphate, pH 6.8 | 90% H2O/10% D2O | 10 mM NaCl, 10 mM potassium phosphate | 6.8 | ambient | 285 | |
5 | DQF-COSY | 2.8 mM N-15 labeled RNA hairpin, 10 mM NaCl, 10 mM potassium phosphate, pH 6.8 | 90% H2O/10% D2O | 10 mM NaCl, 10 mM potassium phosphate | 6.8 | ambient | 298 | |
6 | HP-HetCor | 2.8 mM N-15 labeled RNA hairpin, 10 mM NaCl, 10 mM potassium phosphate, pH 6.8 | 90% H2O/10% D2O | 10 mM NaCl, 10 mM potassium phosphate | 6.8 | ambient | 298 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | AMX | 500 |
2 | Varian | INOVA | 600 |
NMR Refinement | ||
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Method | Details | Software |
torsion angle randomization simulated annealing and molecular dynamics | structure determined using NOE derived distance constraints, and torsional angle restraints derived from J-couplings. Hydrogen bonds derived from NOESY and NN-COSY data. | X-PLOR |
NMR Ensemble Information | |
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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 | 75 |
Conformers Submitted Total Number | 10 |
Representative Model | 1 (closest to the average,fewest violations) |
Additional NMR Experimental Information | |
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Details | pseudouridine assigned using CCH-RELAY type experiments. Base pairing determined from interresidue N-N scalar correlations. Distances derived from multiple mixing time NOESY experiments. |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | refinement | X-PLOR | 3.851 | Brunger |
2 | processing | Felix | 2000 | accelrys |