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