2OS6
Solution structure of LARG PDZ domain in complex with C-terminal octa-peptide of Plexin B1
SOLUTION NMR
NMR Experiment | ||||||||
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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 | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | DMX | 500 |
2 | Bruker | DMX | 600 |
NMR Refinement | ||
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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 | |
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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 | ||||
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# | 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 |