Solution structure of LARG PDZ domain in complex with C-terminal octa-peptide of Plexin B1
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 3D_15N-separated_NOESY | 0.8mM 15N, 13C-labeled LARG PDZ domain, 5mM EDTA, 1mM DTT, 7.6mM synthetic peptide | 50mM phosphate buffer, 90% H2O, 10% D2O | 50 mM phosphate buffer, 50mM NaCl | 6.0 | 1 atm | 293 | |
| 2 | 3D_13C-separated_NOESY | 0.8mM 15N, 13C-labeled LARG PDZ domain, 5mM EDTA, 1mM DTT, 7.6mM synthetic peptide | 50mM phosphate buffer, 99.9% D2O | 50 mM phosphate buffer, 50mM NaCl | 6.0 | 1 atm | 293 | |
| 3 | 2D, 13C, 15N-filtered, 13C-edited NOESY | 0.8mM 15N, 13C-labeled LARG PDZ domain, 5mM EDTA, 1mM DTT, 7.6mM synthetic peptide | 50mM phosphate buffer, 99.9% D2O | 50 mM phosphate buffer, 50mM NaCl | 6.0 | 1 atm | 293 | |
| 4 | DQF-COSY | 0.8mM 15N, 13C-labeled LARG PDZ domain, 5mM EDTA, 1mM DTT, 7.6mM synthetic peptide | 50mM phosphate buffer, 99.9% D2O | 50 mM phosphate buffer, 50mM NaCl | 6.0 | 1 atm | 293 | |
| 5 | 2D TOCSY | 0.8mM 15N, 13C-labeled LARG PDZ domain, 5mM EDTA, 1mM DTT, 7.6mM synthetic peptide | 50mM phosphate buffer, 99.9% D2O | 50 mM phosphate buffer, 50mM NaCl | 6.0 | 1 atm | 293 | |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Bruker | DMX | 500 |
| 2 | Bruker | DMX | 600 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| Distance geometry, simulated annealing, molecular dynamics, torsion angle dynamics | The complex structure is solved using a total of 1306 experimental restraints that include 1155 intramolecular NOEs, 90 dihedral angle restraints and 61 intermolecular NOEs derived from NMR spectroscopy | CNS |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | structures with the lowest energy |
| Conformers Calculated Total Number | 200 |
| Conformers Submitted Total Number | 20 |
| Representative Model | 1 (closest to the average) |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | structure solution | CNS | Cns 1.1 | Brunger A. T. etall |
| 2 | processing | NMRPipe | Nmrpipe 2.2 | F.Delaglio |
| 3 | data analysis | Sparky 3 | Sparky 3 | T.D.Goddard and D.G.Kneller |
| 4 | processing | Molmol 2k.2 | Molmol 2k.2 | Koradi |
| 5 | refinement | Csi 1.0 | Csi 1.0 | David S. Wishart |
