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Solution Structure of pseudouridine-32 modified anticodon stem-loop of E. coli tRNAPhe
SOLUTION NMR
NMR Experiment
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
Spectrometer
Manufacturer
Model
Field Strength
1
Bruker
AMX
500
2
Varian
INOVA
600
NMR Refinement
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
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
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.