Solution NMR structure of the YjcQ protein from Bacillus subtilis. Northeast Structural Genomics target SR346.
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 3D_13C-separated_NOESY | 0.85 mM U-13C,15N SR346, 5mM CaCl2, 100mM NaCl, 20mM NH4OAc, 10mM DTT, 0.02% NaN3 | 5% D2O, 95% H2O | 0.1 M NaCl | 5.5 | atmospheric atm | 293 | |
| 2 | 3D_15N-separated_NOESY | 0.85 mM U-13C,15N SR346, 5mM CaCl2, 100mM NaCl, 20mM NH4OAc, 10mM DTT, 0.02% NaN3 | 5% D2O, 95% H2O | 0.1 M NaCl | 5.5 | atmospheric atm | 293 | |
| 3 | HcCH-TOCSY, HcCH-COSY,CccoNH-TOCSY | 0.85 mM U-13C,15N SR346, 5mM CaCl2, 100mM NaCl, 20mM NH4OAc, 10mM DTT, 0.02% NaN3 | 5% D2O, 95% H2O | 0.1 M NaCl | 5.5 | atmospheric atm | 293 | |
| 4 | 3D-HNCACB, HNcoCACB, HBHAcoNH, HNCO | 0.85 mM U-13C,15N SR346, 5mM CaCl2, 100mM NaCl, 20mM NH4OAc, 10mM DTT, 0.02% NaN3 | 5% D2O, 95% H2O | 0.1 M NaCl | 5.5 | atmospheric atm | 293 | |
| 5 | C13_HSQC_noct Stereospecific VL Me assign. | 0.77 mM 5%-13C,U-15N SR346, 5mM CaCl2, 100mM NaCl, 20mM NH4OAc, 10mM DTT, 0.02% NaN3 | 5% D2O, 95% H2O | 0.1 M NaCl | 5.5 | atmospheric atm | 293 | |
| 6 | Het-NOE, T1/T1rho | 0.85 mM U-13C,15N SR346, 5mM CaCl2, 100mM NaCl, 20mM NH4OAc, 10mM DTT, 0.02% NaN3 | 5% D2O, 95% H2O | 0.1 M NaCl | 5.5 | atmospheric atm | 293 | |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Bruker | AVANCE | 600 |
| 2 | Varian | INOVA | 600 |
| 3 | Varian | INOVA | 750 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| Noesy assignments made with iterative method using CS, 3J, Hyper (dihedral), and Dyana for simulated annealing MD. Converged structures are further refined using NIH-xplor followed by CNS in explicit water shell (Nielges) . Full lenght sequence was carried through the refinement protocol, the disordered regions and hexHIS tag are not reported. Structure based on 595 constraints, 249 long range, 163 dihedral constraints and 36 H-bond constraints. | VNMR | |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | structures with the lowest energy |
| Conformers Calculated Total Number | 100 |
| Conformers Submitted Total Number | 20 |
| Representative Model | 1 (lowest energy) |
| Additional NMR Experimental Information | |
|---|---|
| Details | Structure determined by Triple resonance NMR spectroscopy. Monomer in solution by NMR Tc = 8.6 +/- 0.1 ns (1D T1/T1rho +/- fit std). CIS peptide res. 19T-20P. Structure determined by triple resonance NMR spectroscopy. Coordinates reported from residue 5 to 82 section based on order parameter. AutoAssign used for backbone assignment, manually completed sidechain. 13C and 15N NOESY were assigned with AutoStructure. Dihedral angle restraints determined by HYPER . Assignment stats (excluding C-term tag): backbone 84.6%, sidechain 74.7%, aromatic (sc) 89.36%, VL methyl stereospecific 100%, unambiguous sidechain NH2 85.7%. Structure quality factor PSVS 1.3: ordered residues ranges alpha helix (7-17, 23-26,30-43, 67-76), b-strand (46-47, 64-65, 50-51, 56-57) [S(phi)+S(psi)]>1.8. RMSD 0.6 bb, 1.2 all heavy atoms. Rama: 95.8% most fav, 3.7% addtl. all., 0.3 gen. all.,0.3% disall. Procheck (psi-phi): 0.03/0.43 (raw/Z), Procheck (all): 1.18/-1.18 (raw/Z), MolProbity Clash: 27.67/-3.22 (raw/Z). RPF scores all assigned residues (fit of noesy peaklists to structure): Recall: 0.896, Precision: 0.90, F-measure: 0.898, DP-score: 0.70. Monomer by light scattering. |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | collection | VNMR | 6.1C | Varian Inc. |
| 2 | collection | XwinNMR | 3.5 | Bruker Biospin |
| 3 | structure solution | DYANA | 1.2 | Gunthert |
| 4 | refinement | X-PLOR | 2.11.2 | Clore |
| 5 | processing | NMRPipe | 2005 | Delaglio |
| 6 | data analysis | Sparky | 3.11 | Goddard & Kneller |
| 7 | data analysis | AutoAssign | 2.2.1 | Zimmerman, Moseley, Montelione |
| 8 | structure solution | AutoStructure | 2.1.1 | Huang, Montelione |
| 9 | structure solution | HYPER | 2.1 | Tejero, Montelione |
| 10 | data analysis | PdbStat | 4.1 | Tejero, Montelione |
| 11 | refinement | PSVS | 1.3 | Bhattacharya, Montelione |
| 12 | refinement | Procheck NMR | 3.51 | Laskowski, MacArthur |
| 13 | refinement | MolProbity | 3.01 | Lovell, Richardson et. al. |
