1Q56

NMR structure of the B0 isoform of the agrin G3 domain in its Ca2+ bound state

SOLUTION NMR

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NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	3D_15N-separated_NOESY (100 ms)	1 mM protein, 5 mM CaCl2, 10 mM d4-immidazole	90% H2O/10% D2O	5 mM CaCl2	6.5	ambient	298
2	HNHB (chi restraints)	1 mM protein, 5 mM CaCl2, 10 mM d4-immidazole	90% H2O/10% D2O	5 mM CaCl2	6.5	ambient	298
3	HSQC-NOESY-HSQC (tm = 200 ms / perdeuterated protein)	1 mM protein, 5 mM CaCl2, 10 mM d4-immidazole	90% H2O/10% D2O	5 mM CaCl2	6.5	ambient	298
4	HNCACB (TALOS restraints from HN,Ca, Cb shifts ), HNCO (Talos C' shifts), 3D-15N sep TOCSY (Talos Ha shifts)	1 mM protein, 5 mM CaCl2, 10 mM d4-immidazole	90% H2O/10% D2O	5 mM CaCl2	6.5	ambient	298
5	3D-13C separated NOESY (tm = 125 ms) and isotope exchange experiments to derive H-bond restraints	1 mM protein, 5 mM CaCl2, 10 mM d4-immidazole	99.9% D2O	5 mM CaCl2	6.5	ambient	298

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Varian	INOVA	600

NMR Refinement
Method	Details	Software
Torsion angle dynamics (Dyana 1.5) followed by simulated annealing (X-Plor 3.851)	Hydrogen bond restraints were assigned based on protection from solvent exchange, and consistency of hydrogen bonds with preliminary structures. Backbone phi and psi dihedral restraints were obtained from 1Ha, 13Ca, 13Cb, 13C and 15N chemical shifts using the program TALOS (Cornilescu et al., 1993). Side-chain chi1 restraints were from 3D HNHB data, in conjunction with HN-HBETA 2/HN-HBETA 3 and HALPHA-HBETA 2/HALPHA-HBETA 3 NOE intensity ratios. These data were also used to obtain stereospecific assignments for the C-BETA protons of 37 residues. NOEs involving the remainder of prochiral groups with non-degenerate chemical shifts were treated as ambiguous with respect to stereospecific assignments, and represented as 1/<SUM(R^-6)>^-1/6 sums using XPLOR 3.851 (Brunger, 1992). Initial structures calculated with this approach, were used to identify sites in which one of the stereospecific assignments was more consistent with the remaining distance and dihedral restraints. This enabled stereospecific assignment of a further 13 methylene groups, and 13 valine and leucine prochiral methyl groups. For the final NMR calculations, 400 random conformations were subjected to restrained torsion angle dynamics with the program Dyana 1.5 (Guentert et al., 1997). The 40 structures with the smallest Dyana target functions were refined with a published simulated annealing protocol (Nilges et al., 1991), using the program XPLOR 3.851 (Brunger, 1992). The 15 lowest-energy simulated annealing structures with no distance or dihedral violations larger than 4 were kept for analysis.	DYANA

NMR Ensemble Information
Conformer Selection Criteria	structures with the lowest energy
Conformers Calculated Total Number	400
Conformers Submitted Total Number	15
Representative Model	1 (closest to the average)

Additional NMR Experimental Information
Details	sample for 15N HSQC-NOESY 15N HSQC was 2H/13C/15N labeled.

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	structure solution	DYANA	1.5	Gntert
2	refinement	X-PLOR	3.851	Brunger
3	data analysis	Felix	2000?	accelerys