High-resolution solution structure of the LM5-1 FYVE domain from Leishmania major
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 3D_13C-separated_NOESY | 0.8mM LM5-1 U-15N, 13C; 50mM sodium phosphate buffer, 50mM KCl, 1mM DTT, 1mM AEBSF, 0.05% sodium azide; 90% H2O, 10% D2O | 90% H2O/10% D2O | 7.4 | 1 atm | 293 | ||
| 2 | 3D_15N-separated_NOESY | 0.8mM LM5-1 U-15N, 13C; 50mM sodium phosphate buffer, 50mM KCl, 1mM DTT, 1mM AEBSF, 0.05% sodium azide; 90% H2O, 10% D2O | 90% H2O/10% D2O | 7.4 | 1 atm | 293 | ||
| 3 | HNHA | 0.8mM LM5-1 U-15N, 13C; 50mM sodium phosphate buffer, 50mM KCl, 1mM DTT, 1mM AEBSF, 0.05% sodium azide; 90% H2O, 10% D2O | 90% H2O/10% D2O | 7.4 | 1 atm | 293 | ||
| 4 | 3D_13C-separated_NOESY | 0.8mM LM5-1 U-15N,13C; 50mM sodium phosphate buffer, 50mM KCl, 1mM DTT, 1mM AEBSF,0.05% sodium azide; 100% D2O | 99.99% D2O | 7.4 | 1 atm | 293 | ||
| 5 | 2D_13C-ct-HSQC | 0.8mM LM5-1 ~10% 13C; 50mM sodium phosphate buffer, 50mM KCl, 1mM DTT, 1mM AEBSF, 0.05% sodium azide; 100% D2O | 90% H2O/10% D2O | 7.4 | 1 atm | 293 | ||
| 6 | 2D_15N-HSQC-TROSY, 2D_HN(a/b-NC-J)-TROSY, 2D_HN(CO-a/b-C'CA-J)-TROSY, 3D_1H-dec_HN(CO)CA | 0.8mM LM5-1 U-15N,13C; 50mM sodium phosphate buffer, 50mM KCl, 1mM DTT, 1mM AEBSF, 0.05% sodium azide; 10mg/ml PF1; 90% H2O, 10% D2O | 90% H2O/10% D2O | 7.4 | 1 atm | 293 | ||
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Varian | INOVA | 500 |
| 2 | Varian | INOVA | 600 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| torsion angle dynamics, simulated annealing. | Structures based on 545 NOE-derived distance constraints, 101 dihedral angle restraints, and 259 residual dipolar couplings. | VNMR |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | structures with the least restraint violations, structures with the lowest energy |
| Conformers Calculated Total Number | 100 |
| Conformers Submitted Total Number | 21 |
| Representative Model | 21 (minimized average structure) |
| Additional NMR Experimental Information | |
|---|---|
| Details | 2 x Zn2+ ions not included in calculations, ligating cysteines treated as protonated sulfhydryl groups during simulated annealing. |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | collection | VNMR | 6.1c | Varian inc. |
| 2 | processing | NMRPipe | 2.2 | Delaglio |
| 3 | data analysis | XEASY | 1.3 | Bartels |
| 4 | structure solution | CYANA | 1.0.7 | Guntert |
| 5 | refinement | Xplor-NIH | 2.9.1 | |
