Structural Model for the interaction between RPA32 C-terminal domain and SV40 T antigen origin binding domain.
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D 15N-1H HSQC | 0.2mM RPA32C U-15N, 0.6mM Tag-OBD, 20mM Tris buffer pH 7.0, 2 mM DTT, 5mM MgCl2, 90% H2O, 10% D2O | 90% H2O/10% D2O | 0.03 M | 7.0 | ambient | 298 | |
| 2 | 2D 15N-1H HSQC | 0.2mM Tag-OBD U-15N, 0.6mM RPA32C, 20mM Tris buffer pH 7.0, 2mM DTT, 5mM MgCl2, 90% H2O, 10% D2O | 90% H2O/10% D2O | 0.03 M | 7.0 | ambient | 298 | |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Bruker | AVANCE | 600 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| Rigid body docking, Semi-flexible simulated annealing, Refinement using explicit water | 1500 conformers were obtained in the rigid body docking and 200 best conformers were selected for semi-flexible simulated annealing followed by refinement. | UXNMR |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | structures with acceptable covalent geometry,structures with favorable non-bond energy |
| Conformers Calculated Total Number | 200 |
| Conformers Submitted Total Number | 20 |
| Representative Model | 1 (lowest energy) |
| Additional NMR Experimental Information | |
|---|---|
| Details | This model structure was obtained using ambigous chemical shift pertubation constraints and validated using residual dipolar couplings and point mutations on the interface |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | collection | UXNMR | 2.3 | Bruker software |
| 2 | data analysis | Felix | 2000 | Accelrys, Inc |
| 3 | structure solution | HADDOCK | 1.3 | Bonvin, A.M. |
| 4 | refinement | HADDOCK | 1.3 | Bonvin, A.M. |
