1XST
Solution structure of E.coli RNase P RNA P4 stem, U69A mutation, complexed with cobalt (III) hexammine.
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D NOESY | 2mM P4 U69A RNA; 100mM NaCl; 10mM phosphate buffer; 90% H2O, 10% D2O | 90% H2O/10% D2O | 100 mM NaCl | 6.4 | ambient | 288 | |
2 | 2D NOESY | 2mM P4 U69A RNA; 100mM NaCl; 10mM phosphate buffer; 100% D2O | 100% D2O | 100 mM NaCl | 6.4 | ambient | 288 | |
3 | 2D NOESY | 2mM P4 U69A RNA; 100mM NaCl; 6mM hexammine cobalt chloride; 10mM phosphate buffer; 90% H2O, 10% D2O | 90% H2O/10% D2O | 100 mM NaCl, 6 mM Co(NH3)6Cl | 6.4 | ambient | 288 | |
4 | DQF-COSY | 2mM P4 U69A RNA; 100mM NaCl; 10mM phosphate buffer; 100% D2O | 100% D2O | 100 mM NaCl | 6.4 | ambient | 288 | |
5 | 31P-1H-Hetero-COSY | 2mM P4 U69A RNA; 100mM NaCl; 10mM phosphate buffer; 100% D2O | 100% D2O | 100 mM NaCl | 6.4 | ambient | 288 | |
6 | 31P-1H-Hetero-TOCSY-NOESY | 2mM P4 U69A RNA; 100mM NaCl; 10mM phosphate buffer; 100% D2O | 100% D2O | 100 mM NaCl | 6.4 | ambient | 288 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | DMX | 600 |
NMR Refinement | ||
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Method | Details | Software |
restrained molecular dynamics and simulated annealing | The average structure is based on the superposition of 14 structures after refinement. The average RMS deviation between the ensemble and the average structure is 1.85 Angstrom. A total of 290 NOE-derived distance constraints, 245 dihedral constraints and 48 distance constraints from hydrogen bonds were used in refinement. 15 NOE derived intermolecular distance constraints were used to localize the bound cobalt (III) hexammine. | XwinNMR |
NMR Ensemble Information | |
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Conformer Selection Criteria | |
Conformers Calculated Total Number | |
Conformers Submitted Total Number | 1 |
Representative Model | 1 (minimized average structure) |
Additional NMR Experimental Information | |
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Details | The structure was determined using standard 2D homonuclear techniques as well as 13C and 31P heteronuclear experiments performed at natural abundance. Intermolecular NOE crosspeaks between RNA protons and cobalt (III) hexammine protons and intermolecular distance constraints derived thereof were used to determine the site of cobalt (III) hexammine binding. |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | collection | XwinNMR | 1.2 | Bruker |
2 | processing | NMRPipe | 2.1 | F. Delaglio |
3 | structure solution | X-PLOR | 3.1 | A. Bruenger |
4 | refinement | X-PLOR | 3.1 | A. Bruenger |