2K14

Solution structure of the soluble domain of the NfeD protein YuaF from Bacillus subtilis

SOLUTION NMR

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NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D 1H-15N HSQC	0.9 mM [U-13C; U-15N] YuaF, 50 mM TRIS, 300 mM sodium chloride, 4 mM sodium azide	95% H2O/5% D2O	300	7.5	ambient atm	280
2	2D 1H-13C HSQC	0.9 mM [U-13C; U-15N] YuaF, 50 mM TRIS, 300 mM sodium chloride, 4 mM sodium azide	100% D2O	300	7.5	ambient atm	280
3	3D CBCA(CO)NH	0.9 mM [U-13C; U-15N] YuaF, 50 mM TRIS, 300 mM sodium chloride, 4 mM sodium azide	95% H2O/5% D2O	300	7.5	ambient atm	280
4	3D HNCO	0.9 mM [U-13C; U-15N] YuaF, 50 mM TRIS, 300 mM sodium chloride, 4 mM sodium azide	95% H2O/5% D2O	300	7.5	ambient atm	280
5	3D HN(CA)CO	0.9 mM [U-13C; U-15N] YuaF, 50 mM TRIS, 300 mM sodium chloride, 4 mM sodium azide	95% H2O/5% D2O	300	7.5	ambient atm	280
6	3D HNCACB	0.9 mM [U-13C; U-15N] YuaF, 50 mM TRIS, 300 mM sodium chloride, 4 mM sodium azide	95% H2O/5% D2O	300	7.5	ambient atm	280
7	3D 1H-15N TOCSY	1 mM [U-15N] YuaF, 50 mM TRIS, 300 mM sodium chloride, 4 mM sodium azide	95% H2O/5% D2O	300	7.5	ambient atm	280
8	3D 1H-15N NOESY	1 mM [U-15N] YuaF, 50 mM TRIS, 300 mM sodium chloride, 4 mM sodium azide	95% H2O/5% D2O	300	7.5	ambient atm	280
9	3D HCCH-COSY	0.9 mM [U-13C; U-15N] YuaF, 50 mM TRIS, 300 mM sodium chloride, 4 mM sodium azide	100% D2O	300	7.5	ambient atm	280
10	3D HCCH-TOCSY	0.9 mM [U-13C; U-15N] YuaF, 50 mM TRIS, 300 mM sodium chloride, 4 mM sodium azide	100% D2O	300	7.5	ambient atm	280
11	3D 1H-13C NOESY	0.9 mM [U-13C; U-15N] YuaF, 50 mM TRIS, 300 mM sodium chloride, 4 mM sodium azide	100% D2O	300	7.5	ambient atm	280
12	(HB)CB(CGCD)HD	0.9 mM [U-13C; U-15N] YuaF, 50 mM TRIS, 300 mM sodium chloride, 4 mM sodium azide	100% D2O	300	7.5	ambient atm	280
13	(HB)CB(CGCDCE)HE	0.9 mM [U-13C; U-15N] YuaF, 50 mM TRIS, 300 mM sodium chloride, 4 mM sodium azide	100% D2O	300	7.5	ambient atm	280
14	2D 1H-13C HSQC aromatic	0.9 mM [U-13C; U-15N] YuaF, 50 mM TRIS, 300 mM sodium chloride, 4 mM sodium azide	100% D2O	300	7.5	ambient atm	280
15	3D 1H-13C NOESY aromatic	0.9 mM [U-13C; U-15N] YuaF, 50 mM TRIS, 300 mM sodium chloride, 4 mM sodium azide	100% D2O	300	7.5	ambient atm	280

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

NMR Refinement
Method	Details	Software
torsion angle dynamics, simulated annealing	400 Starting structures for refinement were generated with the final set of constraints by torsion angle dynamics in CYANA 2.0., Refinement of the final structural ensemble was carried out by molecular dynamics simulated annealing in AMBER 8. The 100 structures with lowest target function in CYANA 2.0 were imported into AMBER 8, minimized and subjected to simulated annealing in vacuum with charges reduced to 20% of their original value. The final round of simulated annealing was carried out within a generalized-Born solvation model with full charges followed by energy minimization. Constraints from CYANA were translated into AMBER 8 format taking stereospecific assignments, pseudoatom corrections and NOE-averaging into account.	CYANA

NMR Ensemble Information
Conformer Selection Criteria	structures with the least restraint violations
Conformers Calculated Total Number	400
Conformers Submitted Total Number	20
Representative Model	1 (fewest violations)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	structure solution	CYANA	2.0	Guntert, Mumenthaler and Wuthrich
2	refinement	Amber	8	Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollm
3	collection	XwinNMR	3.6	Bruker Biospin
4	chemical shift assignment	CARA	1.8.4	Keller and Wuthrich
5	processing	TopSpin	1.3.b.20	Bruker Biospin