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Solution NMR refinement of a metal ion bound protein using quantum mechanical/molecular mechanical and molecular dynamics methods
NMR Experiment Experiment Type Sample Contents Solvent Ionic Strength pH Pressure Temperature (K) Spectrometer 1 2D 1H-15N TROSY 2 mM [U-100% 13C; U-100% 15N] CzrA, 2.4 mM Zinc ion, 10 mM [U-100% 2H] MES, 50 mM sodium chloride 95% H2O/5% D2O 50 6.0 1 atm 313 2 2D 1H-13C HMQC 2 mM [U-100% 13C; U-100% 15N] CzrA, 2.4 mM Zinc ion, 10 mM [U-100% 2H] MES, 50 mM sodium chloride 95% H2O/5% D2O 50 6.0 1 atm 313 3 3D CBCA(CO)NH 2 mM [U-100% 13C; U-100% 15N] CzrA, 2.4 mM Zinc ion, 10 mM [U-100% 2H] MES, 50 mM sodium chloride 95% H2O/5% D2O 50 6.0 1 atm 313 4 3D HNCACB 2 mM [U-100% 13C; U-100% 15N] CzrA, 2.4 mM Zinc ion, 10 mM [U-100% 2H] MES, 50 mM sodium chloride 95% H2O/5% D2O 50 6.0 1 atm 313 5 3D C(CO)NH 2 mM [U-100% 13C; U-100% 15N] CzrA, 2.4 mM Zinc ion, 10 mM [U-100% 2H] MES, 50 mM sodium chloride 95% H2O/5% D2O 50 6.0 1 atm 313 6 3D H(CCO)NH 2 mM [U-100% 13C; U-100% 15N] CzrA, 2.4 mM Zinc ion, 10 mM [U-100% 2H] MES, 50 mM sodium chloride 95% H2O/5% D2O 50 6.0 1 atm 313 7 3D HNCO 2 mM [U-100% 13C; U-100% 15N] CzrA, 2.4 mM Zinc ion, 10 mM [U-100% 2H] MES, 50 mM sodium chloride 95% H2O/5% D2O 50 6.0 1 atm 313 8 2D 1H-15N IPAP-HSQC 2 mM [U-100% 13C; U-100% 15N] CzrA, 2.4 mM Zinc ion, 10 mM [U-100% 2H] MES, 50 mM sodium chloride 95% H2O/5% D2O 50 6.0 1 atm 313 9 3D 1H-15N NOESY-TROSY 2 mM [U-100% 13C; U-100% 15N] CzrA, 2.4 mM Zinc ion, 10 mM [U-100% 2H] MES, 50 mM sodium chloride 95% H2O/5% D2O 50 6.0 1 atm 313
NMR Spectrometer Information Spectrometer Manufacturer Model Field Strength 1 Varian INOVA 600 2 Varian INOVA 800 3 Varian INOVA 900
NMR Refinement Method Details Software molecular dynamics and quantum mechanical molecular mechanical molecular dynamics 132 ns of combined NOE and RDC constrained molecular dynamics and quantum mechanical / molecular mechanical molecular dynamics NMRPipe
NMR Ensemble Information Conformer Selection Criteria Structures from 1 ns of independent QM/MM MD sampling Conformers Calculated Total Number 132000 Conformers Submitted Total Number 10 Representative Model 1 (fewest violations)
Additional NMR Experimental Information Details Residual Dipolar Couplings were measured in anisotropic environment using phage or gels.
Computation: NMR Software # Classification Version Software Name Author 1 processing NMRPipe Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax 2 peak picking Sparky Goddard 3 chemical shift assignment Sparky Goddard 4 data analysis Sparky Goddard 5 chemical shift assignment MARS (MARS)-Jung and Zweckstetter 6 structure solution Amber 11 David Case et al. 7 refinement Amber 11 David Case et al. 8 geometry optimization Amber 11 David Case et al. 9 data analysis Amber 11 David Case et al.