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HtrA1 bound to an optimized peptide: NMR assignment of PDZ domain and ligand resonances
NMR Experiment Experiment Type Sample Contents Solvent Ionic Strength pH Pressure Temperature (K) Spectrometer 1 2D 1H-15N HSQC 2 mM [U-15N] HtrA1-PDZ, 4 mM synthetic peptide H1-C1 90% H2O/10% D2O 0.025 6.0 ambient 298 2 3D HNCA 2 mM [U-13C; U-15N] HtrA1-PDZ, 4 mM synthetic peptide H1-C1 90% H2O/10% D2O 0.025 6.0 ambient 298 3 3D HNCO 2 mM [U-13C; U-15N] HtrA1-PDZ, 4 mM synthetic peptide H1-C1 90% H2O/10% D2O 0.025 6.0 ambient 298 4 3D HNCACB 2 mM [U-13C; U-15N] HtrA1-PDZ, 4 mM synthetic peptide H1-C1 90% H2O/10% D2O 0.025 6.0 ambient 298 5 3D CBCA(CO)NH 2 mM [U-13C; U-15N] HtrA1-PDZ, 4 mM synthetic peptide H1-C1 90% H2O/10% D2O 0.025 6.0 ambient 298 6 3D HN(CO)CA 2 mM [U-13C; U-15N] HtrA1-PDZ, 4 mM synthetic peptide H1-C1 90% H2O/10% D2O 0.025 6.0 ambient 298 7 2D 1H-13C HSQC 2 mM [U-10% 13C; U-99% 15N] HtrA1-PDZ, 4 mM synthetic peptide H1-C1 100% D2O 0.025 6.0 ambient 298 8 3D 1H-15N NOESY 2 mM [U-15N] HtrA1-PDZ, 4 mM synthetic peptide H1-C1 90% H2O/10% D2O 0.025 6.0 ambient 298 9 3D 1H-13C NOESY 2 mM [U-13C; U-15N] HtrA1-PDZ, 4 mM synthetic peptide H1-C1 100% D2O 0.025 6.0 ambient 298 10 3D HCCH-TOCSY 2 mM [U-13C; U-15N] HtrA1-PDZ, 4 mM synthetic peptide H1-C1 100% D2O 0.025 6.0 ambient 298 11 2D 1H-1H NOESY 13C,15N-filtered in F1 2 mM [U-13C; U-15N] HtrA1-PDZ, 1.8 mM synthetic peptide H1-C1 90% H2O/10% D2O 0.025 6.0 ambient 298 12 2D 1H-1H TOCSY,13C,15N-filtered in F1 2 mM [U-13C; U-15N] HtrA1-PDZ, 1.8 mM synthetic peptide H1-C1 90% H2O/10% D2O 0.025 6.0 ambient 298 13 3D 1H-13C NOESY, 13C-filtered in F1 2 mM [U-13C; U-15N] HtrA1-PDZ, 1.8 mM synthetic peptide H1-C1 100% D2O 0.025 6.0 ambient 298
NMR Spectrometer Information Spectrometer Manufacturer Model Field Strength 1 Bruker DRX 600 2 Bruker DRX 800
NMR Refinement Method Details Software torsion angle dynamics followed by cartesian dynamics and minimization NMRPipe
NMR Ensemble Information Conformer Selection Criteria structures with the least restraint violations Conformers Calculated Total Number 100 Conformers Submitted Total Number 20 Representative Model 1 (lowest energy)
Computation: NMR Software # Classification Version Software Name Author 1 processing NMRPipe 2005 for LINUX Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax 2 data analysis Sparky 3.11 Goddard 3 chemical shift assignment Monte 2.02 Hitchens, T.K., Lukin, J.A., Zhan, Y. and Rule, G.S. 4 automated noe assignment CYANA 2.0 Guntert, Mumenthaler and Wuthrich 5 collection TopSpin 1.3 Bruker Biospin 6 dihedral angle restraints TALOS Cornilescu, Delaglio and Bax 7 structure solution CNX 2002 Accelrys Software Inc. 8 refinement CNX 2002 Accelrys Software Inc.