2M30
Solution NMR refinement of a metal ion bound protein using quantum mechanical/molecular mechanical and molecular dynamics methods
SOLUTION NMR
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. |