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.

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.