2LUP
RDC refined solution structure of double-stranded RNA binding domain of S. cerevisiae RNase III (rnt1p) in complex with the terminal RNA hairpin of snr47 precursor
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D 1H-15N HSQC | 1 mM [U-100% 13C; U-100% 15N] protein, 90 % H2O, 10 % [U-100% 2H] D2O, 20 mM sodium phosphate, 150 mM sodium chloride | 90% H2O/10% D2O | 150 | 6.5 | ambient | 298 | |
2 | 3D HNCACB | 1 mM [U-100% 13C; U-100% 15N] protein, 90 % H2O, 10 % [U-100% 2H] D2O, 20 mM sodium phosphate, 150 mM sodium chloride | 90% H2O/10% D2O | 150 | 6.5 | ambient | 298 | |
3 | 3D HBHA(CO)NH | 1 mM [U-100% 13C; U-100% 15N] protein, 90 % H2O, 10 % [U-100% 2H] D2O, 20 mM sodium phosphate, 150 mM sodium chloride | 90% H2O/10% D2O | 150 | 6.5 | ambient | 298 | |
4 | 3D HNCO | 1 mM [U-100% 13C; U-100% 15N] protein, 90 % H2O, 10 % [U-100% 2H] D2O, 20 mM sodium phosphate, 150 mM sodium chloride | 90% H2O/10% D2O | 150 | 6.5 | ambient | 298 | |
5 | 3D HCCH-TOCSY | 1 mM [U-100% 13C; U-100% 15N] protein, 90 % [U-100% 2H] D2O, 10 % sodium chloride, 150 mM sodium phosphate | 100% D2O | 150 | 6.5 | ambient | 298 | |
6 | 3D HCCH-COSY | 1 mM [U-100% 13C; U-100% 15N] protein, 90 % [U-100% 2H] D2O, 10 % sodium chloride, 150 mM sodium phosphate | 100% D2O | 150 | 6.5 | ambient | 298 | |
7 | 3D 1H-15N NOESY | 1 mM [U-100% 13C; U-100% 15N] protein, 90 % H2O, 10 % [U-100% 2H] D2O, 20 mM sodium phosphate, 150 mM sodium chloride | 90% H2O/10% D2O | 150 | 6.5 | ambient | 298 | |
8 | 3D 1H-13C NOESY | 1 mM [U-100% 13C; U-100% 15N] protein, 90 % [U-100% 2H] D2O, 10 % sodium chloride, 150 mM sodium phosphate | 100% D2O | 150 | 6.5 | ambient | 298 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | DRX | 500 |
2 | Bruker | DRX | 600 |
NMR Refinement | ||
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Method | Details | Software |
simulated annealing | THIS STRUCTURE IS AN RDC REFINED STRUCTURE OF PDB ENTRY 1T4L USING THE SAME RESTRAINTS PLUS ADDITIONAL RDCS [81 RDCS (REFINED) VS 43 RDCS (1T4L)]. | TopSpin |
NMR Ensemble Information | |
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Conformer Selection Criteria | structures with the lowest energy |
Conformers Calculated Total Number | 100 |
Conformers Submitted Total Number | 16 |
Representative Model | 1 (lowest energy) |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | collection | TopSpin | Bruker Biospin | |
2 | processing | NMRPipe | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax | |
3 | data analysis | NMRView | Johnson, One Moon Scientific | |
4 | chemical shift assignment | NMRView | Johnson, One Moon Scientific | |
5 | data analysis | TALOS | Cornilescu, Delaglio and Bax | |
6 | structure solution | X-PLOR NIH | Schwieters, Kuszewski, Tjandra and Clore | |
7 | refinement | X-PLOR NIH | Schwieters, Kuszewski, Tjandra and Clore |