Solution NMR structure of the UPF0346 protein yozE from Bacillus subtilis. Northeast Structural Genomics target SR391.
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 3D_15N-separated_NOESY | 1.5mM U-13C,15N SR391, 5mM CaCl2, 100mM NaCl, 20mM NH4OAc, 10mM DTT, 0.02% NaN3 | 5% D2O, 95% H2O | 100 mM NaCl | 5.5 | atmospheric atm | 293 | |
| 2 | 3D_13C-separated_NOESY | 1.5mM U-13C,15N SR391, 5mM CaCl2, 100mM NaCl, 20mM NH4OAc, 10mM DTT, 0.02% NaN3 | 5% D2O, 95% H2O | 100 mM NaCl | 5.5 | atmospheric atm | 293 | |
| 3 | HNCA-J | 1.35mM 5%-13C,U-15N SR391, 5mM CaCl2, 100mM NaCl, 20mM NH4OAc, 10mM DTT, 0.02% NaN3 | 5% D2O, 95% H2O | 100 mM NaCl | 5.5 | atmospheric atm | 293 | |
| 4 | HiRes-CH_HSQC for stereospec. VL Methyl assign. | 1.35mM 5%-13C,U-15N SR391, 5mM CaCl2, 100mM NaCl, 20mM NH4OAc, 10mM DTT, 0.02% NaN3 | 5% D2O, 95% H2O | 100 mM NaCl | 5.5 | atmospheric atm | 293 | |
| 5 | HNCACB, HNcoCACB, HNCO,HNCA | 1.5mM U-13C,15N SR391, 5mM CaCl2, 100mM NaCl, 20mM NH4OAc, 10mM DTT, 0.02% NaN3 | 5% D2O, 95% H2O | 100 mM NaCl | 5.5 | atmospheric atm | 293 | |
| 6 | CccoNH_tocsy, HCCH-COSY | 1.5mM U-13C,15N SR391, 5mM CaCl2, 100mM NaCl, 20mM NH4OAc, 10mM DTT, 0.02% NaN3 | 5% D2O, 95% H2O | 100 mM NaCl | 5.5 | atmospheric atm | 293 | |
| 7 | HAcacoNH single transfer | 1.5mM U-13C,15N SR391, 5mM CaCl2, 100mM NaCl, 20mM NH4OAc, 10mM DTT, 0.02% NaN3 | 5% D2O, 95% H2O | 100 mM NaCl | 5.5 | atmospheric atm | 293 | |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Varian | INOVA | 600 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| Noesy assignments using AutoStructure, dyana and xplor for simulated annealing with a total of 1096 NOE distances. An average of 16.6 constraints/restrained res, 3.7 of which long range. 208 dihedral angle constraints and 42 h-bond constraints. | VNMR | |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | structures with the lowest energy |
| Conformers Calculated Total Number | 56 |
| Conformers Submitted Total Number | 10 |
| Representative Model | 1 (lowest energy) |
| Additional NMR Experimental Information | |
|---|---|
| Details | Automated backbone assignement using AutoAssign, manual sidechain assignment. Completeness: 95.3% BB, 88.2% SC, and 100% stereospecific Methyl assignments. Dihe. constr. determined with Talos and Hyper. RPF scores for NOE data consistency: Recall=0.932, Precision=0.874, F-measure=0.902 final DP score=0.738. RMSD ordered residues: 0.5 all BB, 1.0 all heavy atoms. Raw Procheck: psi-phi=0.1, all=-0.2, MolProbity 16.16. N-term tag included. |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | collection | VNMR | 6.1c | Varian Inc. |
| 2 | refinement | xplor-nih | 2.0.6 | Clore et. al. |
| 3 | processing | NMRPipe | 2.5 | Delaglio et. al. |
| 4 | data analysis | Sparky | 2.11 | Goddard, Kneller |
| 5 | structure solution | AutoStructure | 2.1.1 | Huang, Montelione |
| 6 | data analysis | AutoAssign | 1.17 | Zimmerman, Moseley, Montelione |
