☰ Navigation Tabs
High-resolution solution structure of the LM5-1 FYVE domain from Leishmania major
NMR Experiment Experiment Type Sample Contents Solvent Ionic Strength pH Pressure Temperature (K) Spectrometer 1 3D_13C-separated_NOESY 0.8mM LM5-1 U-15N, 13C; 50mM sodium phosphate buffer, 50mM KCl, 1mM DTT, 1mM AEBSF, 0.05% sodium azide; 90% H2O, 10% D2O 90% H2O/10% D2O 7.4 1 atm 293 2 3D_15N-separated_NOESY 0.8mM LM5-1 U-15N, 13C; 50mM sodium phosphate buffer, 50mM KCl, 1mM DTT, 1mM AEBSF, 0.05% sodium azide; 90% H2O, 10% D2O 90% H2O/10% D2O 7.4 1 atm 293 3 HNHA 0.8mM LM5-1 U-15N, 13C; 50mM sodium phosphate buffer, 50mM KCl, 1mM DTT, 1mM AEBSF, 0.05% sodium azide; 90% H2O, 10% D2O 90% H2O/10% D2O 7.4 1 atm 293 4 3D_13C-separated_NOESY 0.8mM LM5-1 U-15N,13C; 50mM sodium phosphate buffer, 50mM KCl, 1mM DTT, 1mM AEBSF,0.05% sodium azide; 100% D2O 99.99% D2O 7.4 1 atm 293 5 2D_13C-ct-HSQC 0.8mM LM5-1 ~10% 13C; 50mM sodium phosphate buffer, 50mM KCl, 1mM DTT, 1mM AEBSF, 0.05% sodium azide; 100% D2O 90% H2O/10% D2O 7.4 1 atm 293 6 2D_15N-HSQC-TROSY, 2D_HN(a/b-NC-J)-TROSY, 2D_HN(CO-a/b-C'CA-J)-TROSY, 3D_1H-dec_HN(CO)CA 0.8mM LM5-1 U-15N,13C; 50mM sodium phosphate buffer, 50mM KCl, 1mM DTT, 1mM AEBSF, 0.05% sodium azide; 10mg/ml PF1; 90% H2O, 10% D2O 90% H2O/10% D2O 7.4 1 atm 293
NMR Spectrometer Information Spectrometer Manufacturer Model Field Strength 1 Varian INOVA 500 2 Varian INOVA 600
NMR Refinement Method Details Software torsion angle dynamics, simulated annealing. Structures based on 545 NOE-derived distance constraints, 101 dihedral angle restraints, and 259 residual dipolar couplings. VNMR
NMR Ensemble Information Conformer Selection Criteria structures with the least restraint violations, structures with the lowest energy Conformers Calculated Total Number 100 Conformers Submitted Total Number 21 Representative Model 21 (minimized average structure)
Additional NMR Experimental Information Details 2 x Zn2+ ions not included in calculations, ligating cysteines treated as protonated sulfhydryl groups during simulated annealing.
Computation: NMR Software # Classification Version Software Name Author 1 collection VNMR 6.1c Varian inc. 2 processing NMRPipe 2.2 Delaglio 3 data analysis XEASY 1.3 Bartels 4 structure solution CYANA 1.0.7 Guntert 5 refinement Xplor-NIH 2.9.1