2KDI

Solution structure of a Ubiquitin/UIM fusion protein

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% 15N] Ubiquitin/UIM fusion protein-5, 3 mM sodium azide-6, 20 mM sodium phosphate-7, 50 mM sodium chloride-8	95% H2O/5% D2O	0.103	6	ambient	300
2	2D 1H-13C HSQC	1.24 mM [U-100% 13C; U-100% 15N] Ubiquitin/UIM fusion protein-1, 3 mM sodium azide-2, 20 mM sodium phosphate-3, 50 mM sodium chloride-4	95% H2O/5% D2O	0.103	6	ambient	300
3	3D HN(COCA)CB	1.24 mM [U-100% 13C; U-100% 15N] Ubiquitin/UIM fusion protein-1, 3 mM sodium azide-2, 20 mM sodium phosphate-3, 50 mM sodium chloride-4	95% H2O/5% D2O	0.103	6	ambient	300
4	3D HNCACB	1.24 mM [U-100% 13C; U-100% 15N] Ubiquitin/UIM fusion protein-1, 3 mM sodium azide-2, 20 mM sodium phosphate-3, 50 mM sodium chloride-4	95% H2O/5% D2O	0.103	6	ambient	300
5	3D 1H-15N NOESY	1.1 mM [U-100% 15N] Ubiquitin/UIM fusion protein-5, 3 mM sodium azide-6, 20 mM sodium phosphate-7, 50 mM sodium chloride-8	95% H2O/5% D2O	0.103	6	ambient	300
6	3D 1H-13C NOESY	1.24 mM [U-100% 13C; U-100% 15N] Ubiquitin/UIM fusion protein-1, 3 mM sodium azide-2, 20 mM sodium phosphate-3, 50 mM sodium chloride-4	95% H2O/5% D2O	0.103	6	ambient	300
7	3D HCCH-COSY	1.24 mM [U-100% 13C; U-100% 15N] Ubiquitin/UIM fusion protein-1, 3 mM sodium azide-2, 20 mM sodium phosphate-3, 50 mM sodium chloride-4	95% H2O/5% D2O	0.103	6	ambient	300
8	3D HNCO	1.24 mM [U-100% 13C; U-100% 15N] Ubiquitin/UIM fusion protein-1, 3 mM sodium azide-2, 20 mM sodium phosphate-3, 50 mM sodium chloride-4	95% H2O/5% D2O	0.103	6	ambient	300
9	3D H(CCO)NH	1.24 mM [U-100% 13C; U-100% 15N] Ubiquitin/UIM fusion protein-1, 3 mM sodium azide-2, 20 mM sodium phosphate-3, 50 mM sodium chloride-4	95% H2O/5% D2O	0.103	6	ambient	300
10	2D HN-IPAP	0.5 mM [U-100% 15N] Ubiquitin/UIM fusion protein-9, 3 mM sodium azide-10, 20 mM sodium phosphate-11, 50 mM sodium chloride-12	95% H2O/5% D2O	0.103	6	ambient	300
11	3D 1H-15N TOCSY	1.1 mM [U-100% 15N] Ubiquitin/UIM fusion protein-5, 3 mM sodium azide-6, 20 mM sodium phosphate-7, 50 mM sodium chloride-8	95% H2O/5% D2O	0.103	6	ambient	300
12	3D HCCH-TOCSY	1.24 mM [U-100% 13C; U-100% 15N] Ubiquitin/UIM fusion protein-1, 3 mM sodium azide-2, 20 mM sodium phosphate-3, 50 mM sodium chloride-4	95% H2O/5% D2O	0.103	6	ambient	300
13	3D (H)C(CCO)NH-TOCSY	1.24 mM [U-100% 13C; U-100% 15N] Ubiquitin/UIM fusion protein-1, 3 mM sodium azide-2, 20 mM sodium phosphate-3, 50 mM sodium chloride-4	95% H2O/5% D2O	0.103	6	ambient	300
14	2D 1H-15N HSQC	0.5 mM [U-100% 15N] Ubiquitin/UIM fusion protein-9, 3 mM sodium azide-10, 20 mM sodium phosphate-11, 50 mM sodium chloride-12	95% H2O/5% D2O	0.103	6	ambient	300
15	2D HN-IPAP	1.1 mM [U-100% 15N] Ubiquitin/UIM fusion protein-5, 3 mM sodium azide-6, 20 mM sodium phosphate-7, 50 mM sodium chloride-8	95% H2O/5% D2O	0.103	6	ambient	300

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

NMR Refinement
Method	Details	Software
simulated annealing, torsion angle dynamics, molecular dynamics, energy minimization		CYANA

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	CYANA	2.1	Guntert, Mumenthaler and Wuthrich
2	peak picking	Sparky	3.111	Goddard
3	chemical shift assignment	Sparky	3.111	Goddard
4	data analysis	Sparky	3.111	Goddard
5	geometry optimization	X-PLOR	2.18	Brunger
6	structure solution	X-PLOR	2.18	Brunger
7	refinement	X-PLOR	2.18	Brunger
8	data analysis	X-PLOR	2.18	Brunger
9	data analysis	TALOS	2003.027.13.05	Cornilescu, Delaglio and Bax
10	structure solution	TALOS	2003.027.13.05	Cornilescu, Delaglio and Bax
11	data analysis	PALES		Markus Zweckstetter and Ad Bax