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Cell transformation by the myc oncogene activates expression of a lipocalin: analysis of the gene (Q83) and solution structure of its protein product
NMR Experiment Experiment Type Sample Contents Solvent Ionic Strength pH Pressure Temperature (K) Spectrometer 1 3D HCCH-TOCSY 3mM lipocalin Q83 U-15N,13C; 20 mM potassium phosphate; 50 mM potassium chloride; 0.5mM dithiothreitol; 90% H2O, 10% D2O 90% H2O/10% D2O 20mM potassium phosphate; 50mM potassium chloride; 0.5mM dithiothreitol 6.4 ambient 299 2 3D_CCH-TOCSY-NNH 3mM lipocalin Q83 U-15N,13C; 20 mM potassium phosphate; 50 mM potassium chloride; 0.5mM dithiothreitol; 90% H2O, 10% D2O 90% H2O/10% D2O 20mM potassium phosphate; 50mM potassium chloride; 0.5mM dithiothreitol 6.4 ambient 299 3 3D_NOESY-HSQC:(two_13C,Ca/methyl-centered,15N) 3mM lipocalin Q83 U-15N,13C; 20 mM potassium phosphate; 50 mM potassium chloride; 0.5mM dithiothreitol; 90% H2O, 10% D2O 90% H2O/10% D2O 20mM potassium phosphate; 50mM potassium chloride; 0.5mM dithiothreitol 6.4 ambient 299 4 3D HNHA 3mM lipocalin Q83 U-15N,13C; 20 mM potassium phosphate; 50 mM potassium chloride; 0.5mM dithiothreitol; 90% H2O, 10% D2O 90% H2O/10% D2O 20mM potassium phosphate; 50mM potassium chloride; 0.5mM dithiothreitol 6.4 ambient 299 5 Cross-correlated_relaxation_rates_Ca(i)Ha(i)-DD/C'(i)-CSA 3mM lipocalin Q83 U-15N,13C; 20 mM potassium phosphate; 50 mM potassium chloride; 0.5mM dithiothreitol; 90% H2O, 10% D2O 90% H2O/10% D2O 20mM potassium phosphate; 50mM potassium chloride; 0.5mM dithiothreitol 6.4 ambient 299 6 Cross-correlated_relaxation_rates_Ca(i)Ha(i)-DD/C'(i-1)-CSA 3mM lipocalin Q83 U-15N,13C; 20 mM potassium phosphate; 50 mM potassium chloride; 0.5mM dithiothreitol; 90% H2O, 10% D2O 90% H2O/10% D2O 20mM potassium phosphate; 50mM potassium chloride; 0.5mM dithiothreitol 6.4 ambient 299
NMR Spectrometer Information Spectrometer Manufacturer Model Field Strength 1 Varian UNITYPLUS 500
NMR Refinement Method Details Software ARIA/CNS automated refinement using also ambiguous NOE distance constraints;
simulated annealing (torsion angle dynamics) 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 20 Representative Model 15 (closest to the average)
Computation: NMR Software # Classification Version Software Name Author 1 collection VNMR 6.1 Rev B Varian Associates, Inc. 2 processing NMRPipe 1.8 Rev 2001.030.21.27 Delaglio 3 data analysis ANSIG 3.3 Kraulis 4 data analysis NMRView 4.1.3 Johnson (Merck and Co., Inc.) 5 structure solution ARIA/CNS 1.0 Linge, Nilges, Brunger 6 refinement CNS 1.0 Brunger