1F7H
SOLUTION STRUCTURE OF THE RNASE P RNA (M1 RNA) P4 STEM OLIGORIBONUCLEOTIDE COMPLEXED WITH COBALT (III) HEXAMINE, NMR, ENSEMBLE OF 11 STRUCTURES
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D NOESY | 2 mM P4 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 P4 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 P4 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 P4 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 P4 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 P4 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 P4 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 | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | AMX | 600 |
2 | Bruker | DRX | 500 |
NMR Refinement | ||
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Method | Details | Software |
restrained molecular dynamics; simulated annealing | The structures are based on a total of 266 NOE-derived distance constraints, 164 dihedral restraints and 48 distance restraints from hydrogen bonds. 12 NOE derived intermolecular distance constraints were used to localize the bound cobalt(III) hexammine. The 11 structures with lowest NOE and dihedral angle violation energies are presented | XwinNMR |
NMR Ensemble Information | |
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Conformer Selection Criteria | structures with the least restraint violations |
Conformers Calculated Total Number | 50 |
Conformers Submitted Total Number | 11 |
Representative Model | 2 (closest to the average) |
Additional NMR Experimental Information | |
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Details | This structure was determined using standard 2D homonuclear techniques and 13C and 31P heteronuclear techniques at natural abundance. Distance constraints derived from intermolecular NOE crosspeaks between RNA protons and cobalt (III) hexammine protons were used to determine the site of cobalt (III) hexammine binding in the complex structure |
Computation: NMR Software | ||||
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# | 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 |