Solution NMR Structure of Q5LLS5 from Silicibacter pomeroyi. Northeast Structural Genomics Consortium target SiR90
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D 1H-15N HSQC | 0.65 mM 5% 13C, 100% 15N SiR90, 10 mM Tris, 5 mM DTT, 100 mM NaCl, 95% H2O/5% D2O | 100 | 6.5 | ambient | 293 | ||
| 2 | 2D 1H-13C HSQC | 0.65 mM 5% 13C, 100% 15N SiR90, 10 mM Tris, 5 mM DTT, 100 mM NaCl, 95% H2O/5% D2O | 100 | 6.5 | ambient | 293 | ||
| 3 | 2D 1H-15N HSQC | 0.65 mM [U-100% 13C; U-100% 15N] SiR90, 10 mM Tris, 5 mM DTT, 100 mM NaCl, 95% H2O/5% D2O | 100 | 6.5 | ambient | 293 | ||
| 4 | 2D 1H-13C HSQC | 0.65 mM [U-100% 13C; U-100% 15N] SiR90, 10 mM Tris, 5 mM DTT, 100 mM NaCl, 95% H2O/5% D2O | 100 | 6.5 | ambient | 293 | ||
| 5 | 3D CBCA(CO)NH | 0.65 mM [U-100% 13C; U-100% 15N] SiR90, 10 mM Tris, 5 mM DTT, 100 mM NaCl, 95% H2O/5% D2O | 100 | 6.5 | ambient | 293 | ||
| 6 | 3D HNCACB | 0.65 mM [U-100% 13C; U-100% 15N] SiR90, 10 mM Tris, 5 mM DTT, 100 mM NaCl, 95% H2O/5% D2O | 100 | 6.5 | ambient | 293 | ||
| 7 | 3D HBHA(CO)NH | 0.65 mM [U-100% 13C; U-100% 15N] SiR90, 10 mM Tris, 5 mM DTT, 100 mM NaCl, 95% H2O/5% D2O | 100 | 6.5 | ambient | 293 | ||
| 8 | 3D HNHA | 0.65 mM [U-100% 13C; U-100% 15N] SiR90, 10 mM Tris, 5 mM DTT, 100 mM NaCl, 95% H2O/5% D2O | 100 | 6.5 | ambient | 293 | ||
| 9 | 3D HCCH-TOCSY | 0.65 mM [U-100% 13C; U-100% 15N] SiR90, 10 mM Tris, 5 mM DTT, 100 mM NaCl, 95% H2O/5% D2O | 100 | 6.5 | ambient | 293 | ||
| 10 | 3D 1H-15N NOESY | 0.65 mM [U-100% 13C; U-100% 15N] SiR90, 10 mM Tris, 5 mM DTT, 100 mM NaCl, 95% H2O/5% D2O | 100 | 6.5 | ambient | 293 | ||
| 11 | 3D 1H-13C NOESY | 0.65 mM [U-100% 13C; U-100% 15N] SiR90, 10 mM Tris, 5 mM DTT, 100 mM NaCl, 95% H2O/5% D2O | 100 | 6.5 | ambient | 293 | ||
| 12 | 2D 1H-15N HSQC | 0.65 mM [U-100% 13C; U-100% 15N] SiR90, 10 mM Tris, 5 mM DTT, 100 mM NaCl, 100% D2O | 100 | 6.5 | ambient | 293 | ||
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Varian | INOVA | 600 |
| 2 | Varian | INOVA | 500 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| simulated annealing | The structures are based on a total of 819 conformationally restricting NOE-derived distance constraints, 52 dihedral angle constraints, and 26 hydrogen bond constraints.(14.5 constraints per residue, 5.2 long-range constraints per residue, computed for residues 1-62 by PSVS 1.3). Residues 62-67 correspond to the Histidines of the C-terminal tag and could not be assigned. Structure determination was performed iteratively using AutoStructure (XPLOR-NIH). After a final XPLOR calculation using the constraints derived from AutoStructure, the 20 lowest energy structures out of 100 were further refined by restrained Molecular dynamics/Energy minimization in explicit water (CNS). The C-terminal HIS-tag residues of the protein were included in the calculations as well as the deposition. Coordinates for the following residues are not well determined: 1-7,18-29,46-48,58-67. The structure was determined using standard Triple resonance NMR experiments. Automated backbone assignments were made using AutoAssign and the sidechain assignments were completed manually. Automatic NOESY assignments as well as distance, dihedral angle and hydrogen-bond constraints were determined using AutoStructure. Structure quality factors, where ordered residues comprise: 8-17,30-45,49-57. RMSD of BB 0.5A, heavy atoms 1.0A. Ramachandran statistics for ordered residues: Most favoured: 91.1%, Additionally allowed: 8.9%, Generally allowed: 0.0%, Unfavourable: 0%. Procheck scores for ordered residues (raw/Z) phi-psi: -0.56/-1.89; all -0.33/-1.95. Molprobity clash score (raw/Z) 17.48/-1.47. RPF scores for goodness of fit to NOESY data: recall: 0.943, precision: 0.92, F-measure: 0.93. Final DP-score 0.795. | PSVS |
| 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) |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | structure validation | PSVS | 1.3 | Bhattacharya , Hang and Montelione |
| 2 | data analysis | PdbStat | 4.1 | Roberto Tejero and Montelione |
| 3 | refinement | CNS | 1.1 | Brunger, Adams, Clore, Gros, Nilges and Read |
| 4 | refinement | X-PLOR NIH | 2.11.2 | Schwieters, Kuszewski, Tjandra and Clore |
| 5 | refinement | AutoStructure | 2.1.1 | Huang, Tejero, Powers and Montelione |
| 6 | structure solution | AutoStructure | 2.1.1 | Huang, Tejero, Powers and Montelione |
| 7 | processing | NMRPipe | 2.3 | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax |
| 8 | data analysis | Sparky | 3.110 | Goddard |
| 9 | collection | VNMR | 6.1c | Varian |
| 10 | chemical shift assignment | AutoAssign | 2.2.1 | Zimmerman, Moseley, Kulikowski and Montelione |
