6TEY
Solution Structure of the DNA-binding TubR fragment from Clostridium Botulinum
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 3D HNCO | 80.13 mM | 6.4 | 1 atm | 298 | Bruker AVANCE 600 | ||
| 2 | 3D HN(CO)CA | 80.13 mM | 6.4 | 1 atm | 298 | Bruker AVANCE 600 | ||
| 3 | 3D HNCA | 80.13 mM | 6.4 | 1 atm | 298 | Bruker AVANCE 600 | ||
| 4 | 3D CBCA(CO)NH | 80.13 mM | 6.4 | 1 atm | 298 | Bruker AVANCE 600 | ||
| 5 | 3D HNCACB | 80.13 mM | 6.4 | 1 atm | 298 | Bruker AVANCE 600 | ||
| 6 | 3D H(CCO)NH | 80.13 mM | 6.4 | 1 atm | 298 | Bruker AVANCE 600 | ||
| 7 | 2D 1H-1H NOESY | 225 uM [U-15N] TubR, 25 mM potassium phosphate, 50 mM potassium chloride, 2 mM D-10 DTT | 90% H2O/10% D2O | 80.13 mM | 6.4 | 1 atm | 298 | Bruker AVANCE 600 |
| 9 | 2D 1H-15N HSQC | 80.13 mM | 6.4 | 1 atm | 298 | Bruker AVANCE 600 | ||
| 8 | 2D 1H-13C HSQC | 80.13 mM | 6.4 | 1 atm | 298 | Bruker AVANCE 600 | ||
| 10 | 2D 1H-13C HSQC aromatic | 80.13 mM | 6.4 | 1 atm | 298 | Bruker AVANCE 600 | ||
| 11 | 3D C(CO)NH | 80.13 mM | 6.4 | 1 atm | 298 | Bruker AVANCE 600 | ||
| 12 | 3D HCCH-TOCSY | 80.13 mM | 6.4 | 1 atm | 298 | Bruker AVANCE 600 | ||
| 13 | 3D HCCH-TOCSY | 80.13 mM | 6.4 | 1 atm | 298 | Bruker AVANCE 600 | ||
| 14 | 3D 1H-15N NOESY | 225 uM [U-15N] TubR, 25 mM potassium phosphate, 50 mM potassium chloride, 2 mM D-10 DTT | 90% H2O/10% D2O | 80.13 mM | 6.4 | 1 atm | 298 | Bruker AVANCE 600 |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Bruker | AVANCE | 600 |
| 2 | Bruker | AVANCE | 600 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| torsion angle dynamics | CYANA | |
| molecular dynamics | Amber | |
| distance geometry | MolProbity | |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | target function |
| Conformers Calculated Total Number | 150 |
| Conformers Submitted Total Number | 20 |
| Representative Model | 1 (medoid) |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | collection | TopSpin | Bruker Biospin | |
| 2 | data analysis | CARA | Keller and Wuthrich | |
| 3 | chemical shift assignment | CARA | Keller and Wuthrich | |
| 4 | peak picking | CARA | Keller and Wuthrich | |
| 5 | structure calculation | CYANA | Guntert, Mumenthaler and Wuthrich | |
| 6 | refinement | MolProbity | Richardson | |
| 7 | geometry optimization | MolProbity | Richardson | |
| 8 | processing | TopSpin | Bruker Biospin | |
| 9 | refinement | Amber | Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman | |
