2LZ6 | pdb_00002lz6

Distinct ubiquitin binding modes exhibited by sh3 domains: molecular determinants and functional implications

SOLUTION NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D 1H-15N HSQC	0.2 mM [U-99% 15N] CD2AP SH3-C, 1 mM Ubiquitin	90% H2O/10% D2O	0	6.0	1 atm	298
2	3D HNCO JNH, JCC, JCH, JCAHA	0.9 mM [U-99% 13C; U-99% 15N] CD2AP SH3-C, 0.46 mM [U-99% 15N] Ubiquitin	90% H2O/10% D2O	0	6.0	1 atm	298
3	3D HNCO JNH, JCC, JCH, JCAHA	0.828 mM [U-99% 13C; U-99% 15N] CD2AP SH3-C, 1.37 mM [U-99% 15N] Ubiquitin	90% H2O/10% D2O	0	6.0	1 atm	298
4	3D HNCO JNH, JCC, JCH, JCAHA	0.78 mM [U-99% 13C; U-99% 15N] CD2AP SH3-C, 1.75 mM [U-99% 15N] Ubiquitin	90% H2O/10% D2O	0	6.0	1 atm	298
5	2D 1H-15N HSQC FILTERED DIPSAP	0.25 mM [U-99% 13C; U-99% 15N] CD2AP SH3-C, 1.75 mM [U-99% 15N] Ubiquitin	90% H2O/10% D2O	0	6.0	1 atm	298
6	2D 1H-15N HSQC	0.25 mM [U-99% 15N] Ubiquitin, 1 mM CD2AP SH3-C	90% H2O/10% D2O	0	6.0	1 atm	298

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Varian	Uniform NMR System	600
2	Varian	Uniform NMR System	800

NMR Refinement
Method	Details	Software
SIMULATED ANNEALING, MOLECULAR DYNAMICS	DOCKING	HADDOCK

NMR Ensemble Information
Conformer Selection Criteria	target function
Conformers Calculated Total Number	200
Conformers Submitted Total Number	10
Representative Model	1 (lowest energy)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	refinement	HADDOCK		Alexandre Bonvin
2	refinement	CNS/SCULPTOR		Brunger, Adams, Clore, Gros, Nilges and Read
3	structure solution	CNS/SCULPTOR		Brunger, Adams, Clore, Gros, Nilges and Read
4	structure solution	NMRView		Johnson, One Moon Scientific
5	structure solution	HADDOCK		Alexandre Bonvin

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.