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Structure determination of N-terminal fragment of UL49.5 protein from bovine herpesvirus 1 by NMR spectroscopy and molecular dynamics
NMR Experiment Experiment Type Sample Contents Solvent Ionic Strength pH Pressure Temperature (K) Spectrometer 1 2D TOCSY 1.0 mM N.BHV 90% H2O/10% D2O 50 mM 6.5 1 bar 298 Bruker AVANCE III 700 7 2D NOESY 1.0 mM N.BHV 90% H2O/10% D2O 50 mM 6.5 1 bar 298 Bruker AVANCE III 700 8 2D DQF-COSY 1.0 mM N.BHV 90% H2O/10% D2O 50 mM 6.5 1 bar 298 Bruker AVANCE III 700 9 2D ROESY 1.0 mM N.BHV 90% H2O/10% D2O 50 mM 6.5 1 bar 298 Bruker AVANCE III 700 2 2D TOCSY 1.0 mM N.BHV 90% H2O/10% D2O 50 mM 6.5 1 bar 298 Varian Uniform NMR System 800 3 2D NOESY 1.0 mM N.BHV 90% H2O/10% D2O 50 mM 6.5 1 bar 298 Varian Uniform NMR System 800 4 2D 1H-15N HSQC 1.0 mM N.BHV 90% H2O/10% D2O 50 mM 6.5 1 bar 298 Varian Uniform NMR System 800 5 2D 1H-13C HSQC aliphatic 1.0 mM N.BHV 90% H2O/10% D2O 50 mM 6.5 1 bar 298 Varian Uniform NMR System 800 6 2D 1H-13C HSQC aromatic 1.0 mM N.BHV 90% H2O/10% D2O 50 mM 6.5 1 bar 298 Varian Uniform NMR System 800
NMR Spectrometer Information Spectrometer Manufacturer Model Field Strength 1 Bruker AVANCE III 700 2 Varian Uniform NMR System 800
NMR Refinement Method Details Software molecular dynamics Amber
NMR Ensemble Information Conformer Selection Criteria structures with the lowest energy Conformers Calculated Total Number 200 Conformers Submitted Total Number 18 Representative Model 1 (lowest energy)
Computation: NMR Software # Classification Version Software Name Author 1 chemical shift assignment Sparky 3.114 Goddard 2 processing NMRPipe Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax 3 peak picking Sparky Goddard 4 data analysis Sparky Goddard 5 structure calculation CYANA Guntert, Mumenthaler and Wuthrich 6 refinement Amber Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman