2M5D

Solution Structure of the Bacillus cereus Metallo-Beta-Lactamase BcII in Complex with R-Thiomandelic Acid

SOLUTION NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D 1H-15N HSQC	1 mM [U-99% 15N] BcII-1, 1 mM R-Thiomandelic Acid-2, 20 mM MES-3, 100 mM sodium chloride-4	90% H2O/10% D2O	120	6.4	ambient	308
2	2D 1H-15N HSQC	1 mM [U-99% 13C; U-99% 15N] BcII-5, 1 mM R-Thiomandelic Acid-6, 20 mM MES-7, 100 mM sodium chloride-8	90% H2O/10% D2O	120	6.4	ambient	308
3	2D 1H-13C HSQC aliphatic	1 mM [U-99% 13C; U-99% 15N] BcII-5, 1 mM R-Thiomandelic Acid-6, 20 mM MES-7, 100 mM sodium chloride-8	90% H2O/10% D2O	120	6.4	ambient	308
4	2D 1H-13C HSQC aromatic	1 mM [U-99% 13C; U-99% 15N] BcII-5, 1 mM R-Thiomandelic Acid-6, 20 mM MES-7, 100 mM sodium chloride-8	90% H2O/10% D2O	120	6.4	ambient	308
5	3D CBCA(CO)NH	1 mM [U-99% 13C; U-99% 15N] BcII-5, 1 mM R-Thiomandelic Acid-6, 20 mM MES-7, 100 mM sodium chloride-8	90% H2O/10% D2O	120	6.4	ambient	308
6	3D HNCACB	1 mM [U-99% 13C; U-99% 15N] BcII-5, 1 mM R-Thiomandelic Acid-6, 20 mM MES-7, 100 mM sodium chloride-8	90% H2O/10% D2O	120	6.4	ambient	308
7	3D HNCA	1 mM [U-99% 13C; U-99% 15N] BcII-5, 1 mM R-Thiomandelic Acid-6, 20 mM MES-7, 100 mM sodium chloride-8	90% H2O/10% D2O	120	6.4	ambient	308
8	3D HN(CA)CO	1 mM [U-99% 13C; U-99% 15N] BcII-5, 1 mM R-Thiomandelic Acid-6, 20 mM MES-7, 100 mM sodium chloride-8	90% H2O/10% D2O	120	6.4	ambient	308
9	3D HNCO	1 mM [U-99% 13C; U-99% 15N] BcII-5, 1 mM R-Thiomandelic Acid-6, 20 mM MES-7, 100 mM sodium chloride-8	90% H2O/10% D2O	120	6.4	ambient	308
10	3D HCCH-TOCSY	1 mM [U-99% 13C; U-99% 15N] BcII-5, 1 mM R-Thiomandelic Acid-6, 20 mM MES-7, 100 mM sodium chloride-8	90% H2O/10% D2O	120	6.4	ambient	308
11	3D HCCH-TOCSY	1 mM [U-99% 13C; U-99% 15N] BcII-5, 1 mM R-Thiomandelic Acid-6, 20 mM MES-7, 100 mM sodium chloride-8	90% H2O/10% D2O	120	6.4	ambient	308
12	3D 1H-15N NOESY	1 mM [U-99% 15N] BcII-1, 1 mM R-Thiomandelic Acid-2, 20 mM MES-3, 100 mM sodium chloride-4	90% H2O/10% D2O	120	6.4	ambient	308
13	3D 1H-13C NOESY aliphatic	1 mM [U-99% 13C; U-99% 15N] BcII-5, 1 mM R-Thiomandelic Acid-6, 20 mM MES-7, 100 mM sodium chloride-8	90% H2O/10% D2O	120	6.4	ambient	308
14	3D 1H-13C NOESY aromatic	1 mM [U-99% 13C; U-99% 15N] BcII-5, 1 mM R-Thiomandelic Acid-6, 20 mM MES-7, 100 mM sodium chloride-8	90% H2O/10% D2O	120	6.4	ambient	308

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	AVANCE	800
2	Bruker	AVANCE	600
3	Bruker	AVANCE	600

NMR Refinement
Method	Details	Software
simulated annealing, torsion angle dynamics	The refinement protocol used consisted of five cycles of simulated annealing with a high start temperature (8000 K) and a gradual slow cooling to a low temperature (100 K) in a large number of steps (20,000). This standard torsion angle based simulating annealing protocol with all constraints applied simultaneously is combined with cycles of redundant dihedral angle constraints (REDAC; Guntert and Wuthrich, 1991). Several cycles of this combined refinement protocol, which eliminates violations and progressively reduces target function values while improving local and overall quality, were used to generate the final converged structures. Out of an ensemble of 100 converged structures generated, the 20 best (lowest CYANA target function during refinement) structures were selected.	CYANA

NMR Ensemble Information
Conformer Selection Criteria	structures with the lowest energy
Conformers Calculated Total Number	100
Conformers Submitted Total Number	20
Representative Model	1 (lowest energy)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	structure solution	CYANA		Guntert, Mumenthaler and Wuthrich
2	refinement	CYANA		Guntert, Mumenthaler and Wuthrich
3	structure solution	CANDID		Guntert, Mumenthaler and Wuthrich
4	automated noe assignment	CANDID		Guntert, Mumenthaler and Wuthrich
5	data analysis	Sparky		Goddard
6	peak picking	Sparky		Goddard
7	data analysis	MOLMOL		Koradi, Billeter and Wuthrich
8	processing	NMRPipe		Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
9	collection	TopSpin		Bruker Biospin
10	collection	XwinNMR		Bruker Biospin
11	validation	ProcheckNMR		Laskowski and MacArthur
12	validation	WHAT IF		Vriend
13	processing	NMRDraw		Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax

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.