2LTD

Solution NMR Structure of apo YdbC from Lactococcus lactis, Northeast Structural Genomics Consortium (NESG) Target KR150

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	1.1 mM [U-100% 13C; U-100% 15N] KR150.020, 0.02 % NaN3, 10 mM DTT, 100 mM NaCL, 10 % D2O, 50 uM DSS, 10 mM TRIS-HCl	90% H2O/10% D2O		7.5	ambient	298
2	2D 1H-13C HSQC	1.1 mM [U-100% 13C; U-100% 15N] KR150.020, 0.02 % NaN3, 10 mM DTT, 100 mM NaCL, 10 % D2O, 50 uM DSS, 10 mM TRIS-HCl	90% H2O/10% D2O		7.5	ambient	298
3	3D HNCO	1.1 mM [U-100% 13C; U-100% 15N] KR150.020, 0.02 % NaN3, 10 mM DTT, 100 mM NaCL, 10 % D2O, 50 uM DSS, 10 mM TRIS-HCl	90% H2O/10% D2O		7.5	ambient	298
4	3D CBCA(CO)NH	1.1 mM [U-100% 13C; U-100% 15N] KR150.020, 0.02 % NaN3, 10 mM DTT, 100 mM NaCL, 10 % D2O, 50 uM DSS, 10 mM TRIS-HCl	90% H2O/10% D2O		7.5	ambient	298
5	3D HNCACB	1.1 mM [U-100% 13C; U-100% 15N] KR150.020, 0.02 % NaN3, 10 mM DTT, 100 mM NaCL, 10 % D2O, 50 uM DSS, 10 mM TRIS-HCl	90% H2O/10% D2O		7.5	ambient	298
6	3D 1H-13C arom NOESY	1.1 mM [U-100% 13C; U-100% 15N] KR150.020, 0.02 % NaN3, 10 mM DTT, 100 mM NaCL, 10 % D2O, 50 uM DSS, 10 mM TRIS-HCl	90% H2O/10% D2O		7.5	ambient	298
7	3D 1H-13C NOESY aliphatic	1.1 mM [U-100% 13C; U-100% 15N] KR150.020, 0.02 % NaN3, 10 mM DTT, 100 mM NaCL, 10 % D2O, 50 uM DSS, 10 mM TRIS-HCl	90% H2O/10% D2O		7.5	ambient	298
8	3D 1H-13C NOESY aromatic	1.1 mM [U-100% 13C; U-100% 15N] KR150.020, 0.02 % NaN3, 10 mM DTT, 100 mM NaCL, 10 % D2O, 50 uM DSS, 10 mM TRIS-HCl	90% H2O/10% D2O		7.5	ambient	298
9	3D 1H-15N NOESY	1.1 mM [U-100% 13C; U-100% 15N] KR150.020, 0.02 % NaN3, 10 mM DTT, 100 mM NaCL, 10 % D2O, 50 uM DSS, 10 mM TRIS-HCl	90% H2O/10% D2O		7.5	ambient	298
10	3D-X-filt-13C-editedNOESY	1.2 mM KR150.019, 0.02 % NaN3, 10 mM DTT, 100 mM NaCL, 10 % D2O, 50 uM DSS, 10 mM TRIS-HCl	90% H2O/10% D2O		7.5	ambient	298
11	3D HCCH-TOCSY	1.1 mM [U-100% 13C; U-100% 15N] KR150.020, 0.02 % NaN3, 10 mM DTT, 100 mM NaCL, 10 % D2O, 50 uM DSS, 10 mM TRIS-HCl	90% H2O/10% D2O		7.5	ambient	298
12	3D HBHA(CO)NH	1.1 mM [U-100% 13C; U-100% 15N] KR150.020, 0.02 % NaN3, 10 mM DTT, 100 mM NaCL, 10 % D2O, 50 uM DSS, 10 mM TRIS-HCl	90% H2O/10% D2O		7.5	ambient	298
13	3D HN(CA)CO	1.1 mM [U-100% 13C; U-100% 15N] KR150.020, 0.02 % NaN3, 10 mM DTT, 100 mM NaCL, 10 % D2O, 50 uM DSS, 10 mM TRIS-HCl	90% H2O/10% D2O		7.5	ambient	298
14	3D HCCH-COSY	1.1 mM [U-100% 13C; U-100% 15N] KR150.020, 0.02 % NaN3, 10 mM DTT, 100 mM NaCL, 10 % D2O, 50 uM DSS, 10 mM TRIS-HCl	90% H2O/10% D2O		7.5	ambient	298
15	3D CCH-TOCSY	1.1 mM [U-100% 13C; U-100% 15N] KR150.020, 0.02 % NaN3, 10 mM DTT, 100 mM NaCL, 10 % D2O, 50 uM DSS, 10 mM TRIS-HCl	90% H2O/10% D2O		7.5	ambient	298
16	1H-15N Hetnoe	0.697 mM [U-5% 13C; U-100% 15N] KR150.020, 0.02 % NaN3, 10 mM DTT, 100 mM NaCL, 10 % D2O, 50 uM DSS, 10 mM TRIS-HCl	90% H2O/10% D2O		7.5	ambient	298
17	1D T1	1.1 mM [U-100% 13C; U-100% 15N] KR150.020, 0.02 % NaN3, 10 mM DTT, 100 mM NaCL, 10 % D2O, 50 uM DSS, 10 mM TRIS-HCl	90% H2O/10% D2O		7.5	ambient	298
18	1D T2(cpmg)	1.1 mM [U-100% 13C; U-100% 15N] KR150.020, 0.02 % NaN3, 10 mM DTT, 100 mM NaCL, 10 % D2O, 50 uM DSS, 10 mM TRIS-HCl	90% H2O/10% D2O		7.5	ambient	298
19	j-mod HSQC (rdc)	0.697 mM [U-5% 13C; U-100% 15N] KR150.020, 0.02 % NaN3, 10 mM DTT, 100 mM NaCL, 10 % D2O, 50 uM DSS, 10 mM TRIS-HCl	90% H2O/10% D2O		7.5	ambient	298

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

NMR Refinement
Method	Details	Software
molecular dynamics	RESTRAINED MD IN WATER BATH, PARAM19, NCS SYMMETRY	CNS

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	refinement	CNS		Brunger, Adams, Clore, Gros, Nilges and Read
2	structure solution	CNS		Brunger, Adams, Clore, Gros, Nilges and Read
3	geometry optimization	CNS		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	processing	NMRPipe		Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
8	collection	TopSpin		Bruker Biospin
9	collection	VnmrJ		Varian
10	chemical shift assignment	PINE		Bahrami, Markley, Assadi, and Eghbalnia
11	data analysis	Sparky		Goddard
12	geometry optimization	TALOS+		Shen, Cornilescu, Delaglio and Bax
13	geometry optimization	PALES		PALES (Zweckstetter, Bax)
14	structure validation	PSVS		Bhattacharya, Montelione