THE SOLUTION STRUCTURE OF YBCJ FROM E. COLI REVEALS A RECENTLY DISCOVERED ALFAL MOTIF INVOLVED IN RNA-BINDING
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D NOESY | 4-7mM YbcJ U-15N,13C; 50mM phosphate buffer, 300mM NaCl, 15mM DTT, 1mM sodium azide, pH 6.8 | 90% H2O/10% D2O | 50mM Phosphate, 300mM NaCl | 6.8 | ambient | 313 | |
| 2 | DQF-COSY | 4-7mM YbcJ U-15N,13C; 50mM phosphate buffer, 300mM NaCl, 15mM DTT, 1mM sodium azide, pH 6.8 | 90% H2O/10% D2O | 50mM Phosphate, 300mM NaCl | 6.8 | ambient | 313 | |
| 3 | HNHA | 4-7mM YbcJ U-15N,13C; 50mM phosphate buffer, 300mM NaCl, 15mM DTT, 1mM sodium azide, pH 6.8 | 90% H2O/10% D2O | 50mM Phosphate, 300mM NaCl | 6.8 | ambient | 313 | |
| 4 | 3D_15N-separated_NOESY | 4-7mM YbcJ U-15N,13C; 50mM phosphate buffer, 300mM NaCl, 15mM DTT, 1mM sodium azide, pH 6.8 | 90% H2O/10% D2O | 50mM Phosphate, 300mM NaCl | 6.8 | ambient | 313 | |
| 5 | IPAP-HSQC | 4-7mM YbcJ U-15N,13C; 50mM phosphate buffer, 300mM NaCl, 15mM DTT, 1mM sodium azide, pH 6.8, 8mg/mL of Pf1 phage | 90% H2O/10% D2O | 50mM Phosphate, 300mM NaCl | 6.8 | ambient | 313 | |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Bruker | DRX | 500 |
| 2 | Bruker | AVANCE | 600 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| simulated annealing | The structures are based on a total of 1205 restraints, 1011 are NOE-derived distance constraints, 89 dihedral angle restraints, 54 distance restraints from hydrogen bonds (27 hydrogen bonds), and 51 15N-1H residual dipolar couplings. | Gifa |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | structures with the least restraint violations,structures with the lowest energy |
| Conformers Calculated Total Number | 60 |
| Conformers Submitted Total Number | 20 |
| Representative Model | 7 (closest to the average) |
| Additional NMR Experimental Information | |
|---|---|
| Details | This structure was determined using standard 2D homonuclear and 3D heteronuclear techniques. |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | processing | Gifa | 4.31 | Delsuc |
| 2 | collection | XwinNMR | 2.1 | Bruker |
| 3 | data analysis | XEASY | 1.3.13 | Bartels |
| 4 | refinement | TALOS | 2003.027.13.05 | Bax |
| 5 | refinement | ARIA | 1.1 | Nilges |
| 6 | refinement | CNS | 1.1 | Brunger |
