Structure of the complex of ubiquitin and the UBA domain from DNA-damage-inducible 1 protein (Ddi1)
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D 1H-15N HSQC | 1 mM [U-100% 15N] Ub-1, 20 mM sodium phosphate-2, 7 % [U-99% 2H] D2O-3, 93 % H2O-4 | 93% H2O/7% D2O | 20 | 6.8 | ambient | 298.2 | |
| 2 | 2D 1H-15N HSQC | 1 mM [U-100% 15N] UBA-5, 20 mM sodium phosphate-6, 7 % [U-99% 2H] D2O-7, 93 % H2O-8 | 93% H2O/7% D2O | 20 | 6.8 | ambient | 298.2 | |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Bruker | AVANCE | 600 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| simulated annealing | TopSpin | |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | structures with the least restraint violations |
| Conformers Calculated Total Number | 10 |
| Conformers Submitted Total Number | 10 |
| Representative Model | 1 (lowest energy) |
| Additional NMR Experimental Information | |
|---|---|
| Details | Two titration experiments were conducted. Basically unlabeled ligand protein was added stepwise to N15-Labeled protein solution. |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | collection | TopSpin | 2.1 | Bruker Biospin |
| 2 | processing | TopSpin | 2.1 | Bruker Biospin |
| 3 | chemical shift assignment | CARA | 1.8.1 | Keller and Wuthrich |
| 4 | geometry optimization | HADDOCK | 2.1 | Alexandre Bonvin |
| 5 | refinement | HADDOCK | 2.1 | Alexandre Bonvin |
| 6 | structure solution | HADDOCK | 2.1 | Alexandre Bonvin |
