2HV4
NMR solution structure refinement of yeast iso-1-ferrocytochrome c
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D NOESY | 2-3 mM cytochrome c, 50 mM phosphate buffer, pH 7.0, 90% H2O, 10% D2O | 90% H2O/10% D2O | 50 mM phosphate buffer | 7 | ambient | 303 | |
2 | 2D TOCSY | 2-3 mM cytochrome c, 50 mM phosphate buffer, pH 7.0, 90% H2O, 10% D2O | 90% H2O/10% D2O | 50 mM phosphate buffer | 7 | ambient | 303 | |
3 | 3D_15N-separated_NOESY | 2-3 mM cytochrome c U-15N, 50 mM phosphate buffer, pH 7.0, 90% H2O, 10% D2O | 90% H2O/10% D2O | 50 mM phosphate buffer | 7 | ambient | 303 | |
4 | HNHA | 2-3 mM cytochrome c U-15N, 50 mM phosphate buffer, pH 7.0, 90% H2O, 10% D2O | 90% H2O/10% D2O | 50 mM phosphate buffer | 7 | ambient | 303 | |
5 | 3D_13C-separated_NOESY | 2-3 mM cytochrome c U-15N,13C, 50 mM phosphate buffer, pH 7.0, 90% H2O, 10% D2O | 90% H2O/10% D2O | 50 mM phosphate buffer | 7 | ambient | 303 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | AVANCE | 700 |
2 | Bruker | AVANCE | 800 |
NMR Refinement | ||
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Method | Details | Software |
simulated annealing in torsion angle space followed by restrained energy minimization | XwinNMR |
NMR Ensemble Information | |
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Conformer Selection Criteria | target function |
Conformers Calculated Total Number | 500 |
Conformers Submitted Total Number | 35 |
Representative Model | 1 (fewest violations) |
Additional NMR Experimental Information | |
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Details | The present structure is a refinement of 1YFC obtained through heteronuclear nmr experiments at higher magnetic field, and additional structural constraints. Resonances assignment was based on HNCA, HN(CO)CA, (H)CCH-TOCSY, H(C)CH-TOCSY, CBCA(CO)NH, and CCC(CO)NH experiments |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | data analysis | XwinNMR | 3.1 | Bruker |
2 | structure solution | DYANA | 1.5 | Guentert |
3 | refinement | Amber | 8.0 |