7X9U
Type-II KH motif of human mitochondrial RbfA
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 3D_13C,15N-SEPARATED_NOESY SPECTRA | 0.79 mM [U-99% 13C; U-99% 15N] human mitochondrial RbfA, 100 mM non NaCl, 1 mM [U-99% 2H] d-DTT, 20 mM [U-99% 2H] d-Tris HCl, 0.02 % w/v non NaN3 | 90% H2O/10% D2O | 100 mM | 7 | 1 atm | 298 | Bruker AVANCE 800 |
2 | 3D CBCA(CO)NH | 0.79 mM [U-99% 13C; U-99% 15N] human mitochondrial RbfA, 100 mM non NaCl, 1 mM [U-99% 2H] d-DTT, 20 mM [U-99% 2H] d-Tris HCl, 0.02 % w/v non NaN3 | 90% H2O/10% D2O | 100 mM | 7 | 1 atm | 298 | Bruker AVANCE 600 |
3 | 3D HNCACB | 0.79 mM [U-99% 13C; U-99% 15N] human mitochondrial RbfA, 100 mM non NaCl, 1 mM [U-99% 2H] d-DTT, 20 mM [U-99% 2H] d-Tris HCl, 0.02 % w/v non NaN3 | 90% H2O/10% D2O | 100 mM | 7 | 1 atm | 298 | Bruker AVANCE 600 |
4 | 3D HCCH-COSY | 0.79 mM [U-99% 13C; U-99% 15N] human mitochondrial RbfA, 100 mM non NaCl, 1 mM [U-99% 2H] d-DTT, 20 mM [U-99% 2H] d-Tris HCl, 0.02 % w/v non NaN3 | 90% H2O/10% D2O | 100 mM | 7 | 1 atm | 298 | Bruker AVANCE 600 |
5 | 3D HCCH-TOCSY | 0.79 mM [U-99% 13C; U-99% 15N] human mitochondrial RbfA, 100 mM non NaCl, 1 mM [U-99% 2H] d-DTT, 20 mM [U-99% 2H] d-Tris HCl, 0.02 % w/v non NaN3 | 90% H2O/10% D2O | 100 mM | 7 | 1 atm | 298 | Bruker AVANCE 600 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | AVANCE | 600 |
2 | Bruker | AVANCE | 800 |
NMR Refinement | ||
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Method | Details | Software |
simulated annealing | The structures are refined based on 1463 distant constraints derived from NOE and estimated hydrogen bonds, and 212 dihedral constraints estimated from NOE data and TALOS program. | Amber |
NMR Ensemble Information | |
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Conformer Selection Criteria | structures with the least restraint violations |
Conformers Calculated Total Number | 200 |
Conformers Submitted Total Number | 20 |
Representative Model | 1 (lowest energy) |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | refinement | Amber | 12 | Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman |
2 | structure calculation | CYANA | 2-1 | Guntert, Mumenthaler and Wuthrich |
3 | chemical shift assignment | KUJIRA | 0.863 | N. Kobayashi, T. Kigawa, S. Yokoyama |
5 | peak picking | NMRView | 5.0.4 | Johnson, One Moon Scientific |
6 | processing | NMRPipe | 2007 | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax |
4 | geometry optimization | TALOS | 2007 | Cornilescu, Delaglio and Bax |