2KNB | pdb_00002knb

Solution NMR structure of the parkin Ubl domain in complex with the endophilin-A1 SH3 domain

SOLUTION NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	3D CBCA(CO)NH	0.8 mM [U-99% 13C; U-99% 15N] Ubl, 1.6 mM SH3	95% H2O/5% D2O	50	7.0	ambient	303
2	3D HNCACB	0.8 mM [U-99% 13C; U-99% 15N] Ubl, 1.6 mM SH3	95% H2O/5% D2O	50	7.0	ambient	303
3	3D CBCA(CO)NH	0.8 mM [U-99% 13C; U-99% 15N] SH3, 1.6 mM Ubl	95% H2O/5% D2O	50	7.0	ambient	303
4	3D HNCACB	0.8 mM [U-99% 13C; U-99% 15N] SH3, 1.6 mM Ubl	95% H2O/5% D2O	50	7.0	ambient	303
5	2D 1H-15N HSQC	0.8 mM [U-99% 13C; U-99% 15N] Ubl, 1.6 mM SH3	95% H2O/5% D2O	50	7.0	ambient	303
6	2D 1H-15N HSQC	0.8 mM [U-99% 13C; U-99% 15N] SH3, 1.6 mM Ubl	95% H2O/5% D2O	50	7.0	ambient	303
7	3D HCCH-COSY	1.2 mM [U-99% 13C; U-99% 15N] Ubl, 1.2 mM SH3	100% D2O	50	7.0	ambient	303
8	3D HCCH-COSY	1.2 mM [U-99% 13C; U-99% 15N] SH3, 1.2 mM Ubl	100% D2O	50	7.0	ambient	303
9	3D 1H-13C NOESY	1.2 mM [U-99% 13C; U-99% 15N] Ubl, 1.2 mM SH3	100% D2O	50	7.0	ambient	303
10	3D 1H-13C NOESY	1.2 mM [U-99% 13C; U-99% 15N] SH3, 1.2 mM Ubl	100% D2O	50	7.0	ambient	303
11	2D 1H-13C HSQC	1.2 mM [U-99% 13C; U-99% 15N] Ubl, 1.2 mM SH3	100% D2O	50	7.0	ambient	303
12	2D 1H-13C HSQC	1.2 mM [U-99% 13C; U-99% 15N] SH3, 1.2 mM Ubl	100% D2O	50	7.0	ambient	303
13	2D 1H-15N IPAP-HSQC	0.8 mM [U-99% 15N] Ubl, 1.6 mM SH3	95% H2O/5% D2O	50	7.0	ambient	303
14	2D 1H-15N IPAP-HSQC	0.8 mM [U-99% 15N] SH3, 1.6 mM Ubl	95% H2O/5% D2O	50	7.0	ambient	303
15	2D 1H-15N IPAP-HSQC	0.8 mM [U-99% 15N] Ubl, 1.6 mM SH3	95% H2O/5% D2O	50	7.0	ambient	303
16	2D 1H-15N IPAP-HSQC	0.8 mM [U-99% 15N] SH3, 1.6 mM Ubl	95% H2O/5% D2O	50	7.0	ambient	303
17	3D 1H-13C NOESY coupled	1.2 mM [U-99% 13C; U-99% 15N] Ubl, 1.2 mM SH3	100% D2O	50	7.0	ambient	303
18	3D 1H-13C NOESY coupled	1.2 mM [U-99% 13C; U-99% 15N] SH3, 1.2 mM Ubl	100% D2O	50	7.0	ambient	303

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

NMR Refinement
Method	Details	Software
simulated annealing	HADDOCK used to dock Ubl and SH3 crystal structures using intermolecular NOEs and RDCs	NMRPipe

NMR Ensemble Information
Conformer Selection Criteria	structures with the lowest energy
Conformers Calculated Total Number	200
Conformers Submitted Total Number	20
Representative Model	1 (lowest energy)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	processing	NMRPipe	2.5	Delaglio, F. et al.
2	chemical shift assignment	Sparky	3.115	Goddard, T. et al.
3	peak picking	Sparky	3.115	Goddard, T. et al.
4	structure solution	CNS	1.2	Brunger, A. et al.
5	refinement	CNS	1.2	Brunger, A. et al.

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729.