2JVE

Solution structure of the extracellular domain of Prod1, a protein implicated in proximodistal identity during amphibian limb regeneration

SOLUTION NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D 1H-15N HSQC	1 mM [U-15N] Prod1, 50 mM sodium phosphate, 150 mM sodium chloride, 1 mM EDTA	90% H2O/10% D2O	0.2	6.5	ambient	298
2	2D 1H-13C HSQC	1 mM [U-13C; U-15N] Prod1, 50 mM sodium phosphate, 150 mM sodium chloride, 1 mM EDTA	100% D2O	0.2	6.5	ambient	298
3	3D 1H-15N NOESY	1 mM [U-15N] Prod1, 50 mM sodium phosphate, 150 mM sodium chloride, 1 mM EDTA	90% H2O/10% D2O	0.2	6.5	ambient	298
4	3D 1H-13C NOESY	1 mM [U-13C; U-15N] Prod1, 50 mM sodium phosphate, 150 mM sodium chloride, 1 mM EDTA	100% D2O	0.2	6.5	ambient	298
5	3D 1H-13C aromatic NOESY	1 mM [U-13C; U-15N] Prod1, 50 mM sodium phosphate, 150 mM sodium chloride, 1 mM EDTA	100% D2O	0.2	6.5	ambient	298
6	3D CBCA(CO)NH	1 mM [U-13C; U-15N] Prod1, 50 mM sodium phosphate, 150 mM sodium chloride, 1 mM EDTA	90% H2O/10% D2O	0.2	6.5	ambient	298
7	3D HNCO	1 mM [U-13C; U-15N] Prod1, 50 mM sodium phosphate, 150 mM sodium chloride, 1 mM EDTA	90% H2O/10% D2O	0.2	6.5	ambient	298
8	3D HNCA	1 mM [U-13C; U-15N] Prod1, 50 mM sodium phosphate, 150 mM sodium chloride, 1 mM EDTA	90% H2O/10% D2O	0.2	6.5	ambient	298
9	3D HNCACB	1 mM [U-13C; U-15N] Prod1, 50 mM sodium phosphate, 150 mM sodium chloride, 1 mM EDTA	90% H2O/10% D2O	0.2	6.5	ambient	298
10	3D HN(CO)CA	1 mM [U-13C; U-15N] Prod1, 50 mM sodium phosphate, 150 mM sodium chloride, 1 mM EDTA	90% H2O/10% D2O	0.2	6.5	ambient	298
11	3D HN(CA)CO	1 mM [U-13C; U-15N] Prod1, 50 mM sodium phosphate, 150 mM sodium chloride, 1 mM EDTA	90% H2O/10% D2O	0.2	6.5	ambient	298
12	3D HA(CA)NH	1 mM [U-13C; U-15N] Prod1, 50 mM sodium phosphate, 150 mM sodium chloride, 1 mM EDTA	90% H2O/10% D2O	0.2	6.5	ambient	298
13	3D HN(CACO)NH	1 mM [U-13C; U-15N] Prod1, 50 mM sodium phosphate, 150 mM sodium chloride, 1 mM EDTA	90% H2O/10% D2O	0.2	6.5	ambient	298
14	3D HCCH-TOCSY	1 mM [U-13C; U-15N] Prod1, 50 mM sodium phosphate, 150 mM sodium chloride, 1 mM EDTA	100% D2O	0.2	6.5	ambient	298
15	3D HCCH-COSY	1 mM [U-13C; U-15N] Prod1, 50 mM sodium phosphate, 150 mM sodium chloride, 1 mM EDTA	100% D2O	0.2	6.5	ambient	298
16	3D 1H-15N TOCSY	1 mM [U-15N] Prod1, 50 mM sodium phosphate, 150 mM sodium chloride, 1 mM EDTA	90% H2O/10% D2O	0.2	6.5	ambient	298

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Varian	INOVA	800
2	Varian	INOVA	600
3	Varian	INOVA	600
4	Varian	UNITYPLUS	500

NMR Refinement
Method	Details	Software
DGSA-distance geometry simulated annealing	the structures were calculated using an ab-initio simulated annealing protocol within the CNS/Xplor-NIH programs with PARALLHDG v5.3 parameter set and PROLSQ non-bonded energy function. Cartesian and torsion angle dynamics were used to refine the structures.	NMRPipe

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	processing	NMRPipe		Delaglio, F. et al.
2	data analysis	ANSIG		Kraulis, P.J.
3	refinement	X-PLOR NIH		Schwieters, C.D. et al.

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.