1F79
SOLUTION STRUCTURE OF RNASE P RNA (M1 RNA) P4 STEM C70U MUTANT OLIGORIBONUCLEOTIDE COMPLEXED WITH COBALT(III) HEXAMMINE, NMR, MINIMIZED AVERAGE STRUCTURE
SOLUTION NMR
NMR Experiment | ||||||||
---|---|---|---|---|---|---|---|---|
Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D NOESY | 2 mM P4m RNA; 100 mM sodium chloride; 10 mM phosphate buffer; 90% H2O, 10% D2O | 90% H2O/10% D2O | 100 mM Na | 6.5 | ambient | 288 | |
2 | 2D NOESY | 2 mM P4m RNA; 100 mM sodium chloride; 10 mM phosphate buffer; 99.96% D2O | 99.96% D2O | 100 mM Na | 6.5 | ambient | 288 | |
3 | 2D NOESY | 2 mM P4m RNA; 100 mM sodium chloride; 10 mM magnesium chloride; 10 mM phosphate buffer; 90% H2O, 10% D2O | 90% H2O/10% D2O | 100 mM Na, 10 mM Mg | 6.5 | ambient | 288 | |
4 | 2D NOESY | 2 mM P4m RNA; 100 mM sodium chloride; 3 mM hexammine cobalt chloride; 10 mM phosphate buffer; 90% H2O, 10% D2O | 90% H2O/10% D2O | 100 mM Na, 3 mM Co(NH3)6 | 6.5 | ambient | 288 | |
5 | DQF-COSY | 2 mM P4m RNA; 100 mM sodium chloride; 10 mM phosphate buffer; 99.96% D2O | 99.96% D2O | 100 mM Na | 6.5 | ambient | 288 | |
6 | 31P-1H-COSY | 2 mM P4m RNA; 100 mM sodium chloride; 10 mM phosphate buffer; 99.96% D2O | 99.96% D2O | 100 mM Na | 6.5 | ambient | 288 | |
7 | 13C-1H-HMQC | 2 mM P4m RNA; 100 mM sodium chloride; 10 mM phosphate buffer; 99.96% D2O | 99.96% D2O | 100 mM Na | 6.5 | ambient | 288 |
NMR Spectrometer Information | |||
---|---|---|---|
Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | AMX | 600 |
2 | Bruker | DRX | 500 |
NMR Refinement | ||
---|---|---|
Method | Details | Software |
restrained molecular dynamics and simulated annealing | The average structure is based on superposition of 12 converged structures after refinement. The average RMS deviation between the ensemble and the average structure is 1.5 Angstrom. A total of 268 NOE-derived intramolecular distance constraints, 171 dihedral restraint and 49 distance restraints from hydrogen bonds were used in the refinement. 12 NOE derived intermolecular distance constraints were used to localize the bound cobalt (III) hexammine | XwinNMR |
NMR Ensemble Information | |
---|---|
Conformer Selection Criteria | |
Conformers Calculated Total Number | |
Conformers Submitted Total Number | 1 |
Representative Model | (minimized average structure) |
Additional NMR Experimental Information | |
---|---|
Details | This structure was determined using standard 2D homonuclear techniques and 13C and 31P heteronuclear techniques at natural abundance. Intermolecular NOE crosspeaks between RNA protons and cobalt (III) hexammine protons and derived intermolecular distance constraints were used to determine the site of cobalt (III) hexammine binding in the complex structure |
Computation: NMR Software | ||||
---|---|---|---|---|
# | Classification | Version | Software Name | Author |
1 | collection | XwinNMR | 3.1 | Bruker |
2 | processing | Felix | 95 | MSI |
3 | structure solution | X-PLOR | 3.841 | Brunger |
4 | refinement | X-PLOR | 3.841 | Brunger |