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NMR Solution Structure of the RNA Hairpin Binding Site for the Histone Stem-loop Binding Protein
SOLUTION NMR
NMR Experiment
Experiment
Type
Sample Contents
Solvent
Ionic Strength
pH
Pressure
Temperature (K)
Spectrometer
1
NOESY
2.8 mM unlabeled 20 mM KPi, 20 mM KCl, 0.02 mM EDTA, pH 6.8
100% D2O
100 mM
6.8
ambient
301
2
3D_13C-separated_NOESY
2.3 mM U-13C; 20 mM KPi, 20 mM KCl, 0.02 mM EDTA, pH 6.8
100% D2O
100 mM
6.8
ambient
301
3
3D_15N-separated_NOESY
2.5 mM U-15N; 20 mM KPi, 20 mM KCl, 0.02 mM EDTA, pH 6.8
10% D2O, 90% H2O
100 mM
6.8
ambient
280
4
3D_13C-separated_NOESY
2.0 mM U-13C,C5-2H; 20 mM KPi, 20 mM KCl, 0.02 mM EDTA, pH 6.8
100% D2O
100 mM
6.8
ambient
301
5
DQF-COSY
2.5 mM U-15N; 20 mM KPi, 20 mM KCl, 0.02 mM EDTA, pH 6.8
10% D2O, 90% H2O
100 mM
6.8
ambient
301
6
HetCor
2.8 mM unlabeled 20 mM KPi, 20 mM KCl, 0.02 mM EDTA, pH 6.8
100% D2O
100 mM
6.8
ambient
301
NMR Spectrometer Information
Spectrometer
Manufacturer
Model
Field Strength
1
Bruker
AMX
500
NMR Refinement
Method
Details
Software
simulated annealing and molecular dynamics
Calculations were performed using 232 conformationally restrictive NOE derived distance constraints and 55 backbone and 15 ribose torsion angle constraints. Base pair constraints were introduced for six base pairs using heavy atom-heavy atom constraints. Coordinates are for the hairpin domain only. 5' flanking (ggccaaa) and 3' flanking (accca) coordinates are not included with this deposition. Few constraints were obtained for these very dynamic regions and although they were included as part of the structure calculation, their conformations appear to be randomly distributed.
Felix
NMR Ensemble Information
Conformer Selection Criteria
structures with acceptable covalent geometry, structures with the least restraint violations, structures with the lowest energy
Conformers Calculated Total Number
60
Conformers Submitted Total Number
10
Representative Model
5 (closest to the average)
Additional NMR Experimental Information
Details
This structure was determined using a variety of 2D and 3D homo- and hetero-nuclear NMR methods.