2KR0
Solution structure of the proteasome ubiquitin receptor Rpn13
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 | 0.1 mM [U-15N] protein, 0.1 mM [U-15N; U-50% 2H] protein | 90% H2O/10% D2O | 20 mM phosphate, 50 mM NaCl | 6.5 | 298 | ||
2 | 3D 1H-15N NOESY | 0.1 mM [U-15N] protein, 0.1 mM [U-15N; U-50% 2H] protein | 90% H2O/10% D2O | 20 mM phosphate, 50 mM NaCl | 6.5 | 298 | ||
3 | 2D 1H-15N HSQC | 0.1 mM [U-15N] protein, 0.1 mM [U-15N; U-50% 2H] protein | 90% H2O/10% D2O | 20 mM phosphate, 50 mM NaCl | 6.5 | 298 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Varian | INOVA | 800 |
2 | Varian | INOVA | 900 |
3 | Bruker | AVANCE | 700 |
NMR Refinement | ||
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Method | Details | Software |
simulated annealing | The structure of two functional domain of the protein is calculated based on their NOE-derived distance constraints, hydrogen bonds and dihedral angle restraints. The paramagnetic relaxation enhancement from spin-labeling experiments and inter-domain NOE help define the structure of full protein. | VnmrJ |
NMR Ensemble Information | |
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Conformer Selection Criteria | structures with the lowest energy |
Conformers Calculated Total Number | 50 |
Conformers Submitted Total Number | 31 |
Representative Model | 1 (lowest energy) |
Additional NMR Experimental Information | |
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Details | The Spectra took in Bruker Advance 700 MHz are a set of spin-labeling experiments to achieve PRE data. |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | collection | VnmrJ | Varian | |
2 | collection | TopSpin | Bruker Biospin | |
3 | processing | NMRPipe | 2.5 | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax |
4 | chemical shift assignment | XEASY | 6.4 | Bartels et al. |
5 | data analysis | XEASY | 6.4 | Bartels et al. |
6 | peak picking | XEASY | 6.4 | Bartels et al. |
7 | chemical shift assignment | CARA | 1.8.4 | Keller and Wuthrich |
8 | data analysis | CARA | 1.8.4 | Keller and Wuthrich |
9 | refinement | X-PLOR NIH | Schwieters, Kuszewski, Tjandra and Clore | |
10 | structure solution | X-PLOR NIH | Schwieters, Kuszewski, Tjandra and Clore |