2KY9

Solution NMR Structure of ydhK C-terminal Domain from B.subtilis, Northeast Structural Genomics Consortium Target Target SR518

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	0.4 mM [U-100% 13C; U-100% 15N] SR518, 100 mM sodium chloride, 5 mM DTT, 10 mM TRIS, 0.02 % sodium azide, 20 uM DSS	95% H2O/5% D2O	100	7.5	ambient	298
2	2D 1H-13C HSQC aliphatic	0.4 mM [U-100% 13C; U-100% 15N] SR518, 100 mM sodium chloride, 5 mM DTT, 10 mM TRIS, 0.02 % sodium azide, 20 uM DSS	95% H2O/5% D2O	100	7.5	ambient	298
3	3D HNCO	0.4 mM [U-100% 13C; U-100% 15N] SR518, 100 mM sodium chloride, 5 mM DTT, 10 mM TRIS, 0.02 % sodium azide, 20 uM DSS	95% H2O/5% D2O	100	7.5	ambient	298
4	3D CBCA(CO)NH	0.4 mM [U-100% 13C; U-100% 15N] SR518, 100 mM sodium chloride, 5 mM DTT, 10 mM TRIS, 0.02 % sodium azide, 20 uM DSS	95% H2O/5% D2O	100	7.5	ambient	298
5	3D HNCACB	0.4 mM [U-100% 13C; U-100% 15N] SR518, 100 mM sodium chloride, 5 mM DTT, 10 mM TRIS, 0.02 % sodium azide, 20 uM DSS	95% H2O/5% D2O	100	7.5	ambient	298
6	3D HN(CA)CO	0.4 mM [U-100% 13C; U-100% 15N] SR518, 100 mM sodium chloride, 5 mM DTT, 10 mM TRIS, 0.02 % sodium azide, 20 uM DSS	95% H2O/5% D2O	100	7.5	ambient	298
7	3D simutaneous 13C-aromatic,13C-aliphatic,15N edited 1H-1H NOESY	0.4 mM [U-100% 13C; U-100% 15N] SR518, 100 mM sodium chloride, 5 mM DTT, 10 mM TRIS, 0.02 % sodium azide, 20 uM DSS	95% H2O/5% D2O	100	7.5	ambient	298
8	3D HBHA(CO)NH	0.4 mM [U-100% 13C; U-100% 15N] SR518, 100 mM sodium chloride, 5 mM DTT, 10 mM TRIS, 0.02 % sodium azide, 20 uM DSS	95% H2O/5% D2O	100	7.5	ambient	298
9	2D 1H-13C CT-HSQC aliphatic	0.4 mM [U-100% 13C; U-100% 15N] SR518, 100 mM sodium chloride, 5 mM DTT, 10 mM TRIS, 0.02 % sodium azide, 20 uM DSS	95% H2O/5% D2O	100	7.5	ambient	298
10	2D 1H-13C CT-HSQC aromatic	0.4 mM [U-100% 13C; U-100% 15N] SR518, 100 mM sodium chloride, 5 mM DTT, 10 mM TRIS, 0.02 % sodium azide, 20 uM DSS	95% H2O/5% D2O	100	7.5	ambient	298
11	3D (H)CCH-COSY aliphatic	0.4 mM [U-100% 13C; U-100% 15N] SR518, 100 mM sodium chloride, 5 mM DTT, 10 mM TRIS, 0.02 % sodium azide, 20 uM DSS	95% H2O/5% D2O	100	7.5	ambient	298
12	3D (H)CCH-TOCSY aliphatic	0.4 mM [U-100% 13C; U-100% 15N] SR518, 100 mM sodium chloride, 5 mM DTT, 10 mM TRIS, 0.02 % sodium azide, 20 uM DSS	95% H2O/5% D2O	100	7.5	ambient	298
13	3D (H)CCH-COSY aromatic	0.4 mM [U-100% 13C; U-100% 15N] SR518, 100 mM sodium chloride, 5 mM DTT, 10 mM TRIS, 0.02 % sodium azide, 20 uM DSS	95% H2O/5% D2O	100	7.5	ambient	298
14	2D 1H-13C CT-HSQC methyl	0.7 mM [U-5% 13C; U-100% 15N] SR518, 100 mM sodium chloride, 5 mM DTT, 10 mM TRIS, 0.02 % sodium azide, 20 uM DSS	95% H2O/5% D2O	100	7.5	ambient	298
15	2D 1H-15N LR-HSQC for Histidine	0.7 mM [U-5% 13C; U-100% 15N] SR518, 100 mM sodium chloride, 5 mM DTT, 10 mM TRIS, 0.02 % sodium azide, 20 uM DSS	95% H2O/5% D2O	100	7.5	ambient	298
16	2D 1H-15N J-modulated HSQC	0.7 mM [U-5% 13C; U-100% 15N] SR518, 100 mM sodium chloride, 5 mM DTT, 10 mM TRIS, 0.02 % sodium azide, 20 uM DSS	95% H2O/5% D2O	100	7.5	ambient	298
17	2D 1H-15N J-modulated HSQC	0.5 mM [U-5% 13C; U-100% 15N] SR518, 100 mM sodium chloride, 5 mM DTT, 10 mM TRIS, 0.02 % sodium azide, 20 uM DSS, 3.5 % PEG	88% H2O/12% D2O	100	7.5	ambient	298
18	2D 1H-15N J-modulated HSQC	0.5 mM [U-5% 13C; U-100% 15N] SR518, 180 mM sodium chloride, 3.5 mM DTT, 7 mM TRIS, 0.014 % sodium azide, 14 uM DSS, 10.5 g/L Pf1 phage	88% H2O/12% D2O	180	7.5	ambient	298

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	AVANCE	900
2	Varian	INOVA	600
3	Varian	INOVA	750
4	Bruker	AVANCE	700

NMR Refinement
Method	Details	Software
simulated annealing	Structure determination was performed by running CYANA and AUTOSTRUCTURE in parallel using NOE-based constraints and PHI and PSI dihedral angle constraints from TALOS+. Consensus peak assignments were selected and used in iterative refinement with CYANA, with RDC constraints added at later stages. The 20 conformers out of 100 with the lowest target function were further refined by simulated annealing in explicit water bath using the program CNS with PARAM19 force field and upper limit constraints relaxed by 5%	CNS

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

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	refinement	CNS	1.2	Brunger, Adams, Clore, Gros, Nilges and Read
2	structure solution	CNS	1.2	Brunger, Adams, Clore, Gros, Nilges and Read
3	geometry optimization	CNS	1.2	Brunger, Adams, Clore, Gros, Nilges and Read
4	refinement	CYANA	3.0	Guntert, Mumenthaler and Wuthrich
5	geometry optimization	CYANA	3.0	Guntert, Mumenthaler and Wuthrich
6	structure solution	CYANA	3.0	Guntert, Mumenthaler and Wuthrich
7	data analysis	AutoStructure	2.2.1	Huang, Tejero, Powers and Montelione
8	structure calculation	AutoStructure	2.2.1	Huang, Tejero, Powers and Montelione
9	data analysis	AutoAssign	2.3.0	Zimmerman, Moseley, Kulikowski and Montelione
10	chemical shift assignment	AutoAssign	2.3.0	Zimmerman, Moseley, Kulikowski and Montelione
11	processing	NMRPipe		Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
12	data analysis	XEASY		Bartels et al.
13	collection	TopSpin	2.1	Bruker Biospin
14	collection	VnmrJ		Varian
15	data analysis	CARA	1.8.4	Keller and Wuthrich
16	peak picking	CARA	1.8.4	Keller and Wuthrich
17	chemical shift assignment	CARA	1.8.4	Keller and Wuthrich
18	processing	PROSA	6.4	Guntert
19	visualization	MOLMOL	2K.2	Koradi, Billeter and Wuthrich
20	data analysis	TALOS+	1.2009.0721.18	Shen, Cornilescu, Delaglio and Bax
21	validation	PSVS	1.3	Bhattacharya and Montelione