Solution structure of Iron-Sulfur cluster assembly protein IscU from Bacillus subtilis, with Zinc bound at the active site. Northeast Structural Genomics Consortium Target SR17
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 3D-TOCSYS | 20mM Sodium Phosphate, 50mM Sodium Chloride, 10mM DTT, 0.02% NaN3, 95% H2O, 5% D2O | 95% H2O/5% D2O | 100mM | 6.5 | ambient | 293 | |
| 2 | 13C,1H-HSQC | 20mM Sodium Phosphate, 50mM Sodium Chloride, 10mM DTT, 0.02% NaN3, 95% H2O, 5% D2O | 95% H2O/5% D2O | 100mM | 6.5 | ambient | 293 | |
| 3 | 15N,1H-HSQC | 20mM Sodium Phosphate, 50mM Sodium Chloride, 10mM DTT, 0.02% NaN3, 95% H2O, 5% D2O | 95% H2O/5% D2O | 100mM | 6.5 | ambient | 293 | |
| 4 | 13C,1H-HSQC | 100mM Potassium Phosphate, 200mM Glycerol, 1mM DTT, 0.02% NaN3 | 5% D2O, 95% H2O | 100mM | 6.5 | ambient | 293 | |
| 5 | 15N,1H-HSQC, 2D Homonuclear NOESY | 100mM Potassium Phosphate, 200mM Glycerol, 1mM DTT, 0.02% NaN3 | 5% D2O, 95% H2O | 100mM | 6.5 | ambient | 293 | |
| 6 | 4D_13C-separated_NOESY | 100mM Potassium Phosphate, 200mM Glycerol, 1mM DTT, 0.02% NaN3 | 5% D2O, 95% H2O | 100mM | 6.5 | ambient | 293 | |
| 7 | 3D_13C-separated_NOESY | 100mM Potassium Phosphate, 200mM Glycerol, 1mM DTT, 0.02% NaN3 | 5% D2O, 95% H2O | 100mM | 6.5 | ambient | 293 | |
| 8 | 3D_15N-separated_NOESY | 100mM Potassium Phosphate, 200mM Glycerol, 1mM DTT, 0.02% NaN3 | 5% D2O, 95% H2O | 100mM | 6.5 | ambient | 293 | |
| 9 | H/D exchange | 20mM Sodium Phosphate, 50mM Sodium Chloride, 10mM DTT, 0.02% NaN3, 95% H2O, 5% D2O | 95% H2O/5% D2O | 100mM | 6.5 | ambient | 293 | |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Varian | INOVA | 750 |
| 2 | Varian | INOVA | 800 |
| 3 | Varian | INOVA | 600 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| Minimal constraint structure contained 492 conformationally restricting NOE-derived distance constraints, 108 hydrogen bond constraints, and 197 dihedral angle constraints. This resulted in 5.9 constraints per residue and 1.2 long range constraints per residue. Structure determination was performed with the following steps: AutoStructure-Dyana was used to identify distance constraints. These distance constraints were used as input into a Simulated Annealing with Xplor-NIH. The top ten structures were energy minimized with water using CNS. | AutoAssign | |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | structures with the lowest energy |
| Conformers Calculated Total Number | 60 |
| Conformers Submitted Total Number | 10 |
| Representative Model | 1 (lowest energy) |
| Additional NMR Experimental Information | |
|---|---|
| Details | This structure was determined using a selective isotopic labeling strategy involving the protonation of specific residues in a perdeuterated background. Protonated atoms include: ile HD1, val HG*, leu HD*. All tyr and phe side-chains are protonated. In addition to the atoms mentioned above, exchangeable atoms were protonated. |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | data analysis | AutoAssign | 1.9 | Zimmerman, Moseley and Montelione |
| 2 | structure solution | AutoStructure | 2.0.0 | Huang and Montelione |
| 3 | structure solution | TALOS | 2.1 | Cornilescu, Delaglio and Bax |
| 4 | structure solution | Hyper & PDBstat | 3.2 and 3.32 | Tejero and Montelione |
| 5 | processing | NMRPipe | 2.1 | Delaglio et al. |
| 6 | refinement | X-PLOR | 2.0.6 | Schwieters, et al. |
| 7 | refinement | CNS | 1.0 | Brunger, et al. |
| 8 | data analysis | Sparky | 3.106 | Goddard |
