2JQQ | pdb_00002jqq

Solution structure of Saccharomyces cerevisiae conserved oligomeric Golgi subunit 2 protein (Cog2p)

SOLUTION NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	3D HNCO	1 mM [U-100% 13C; U-100% 15N] Cog2p, 3 mM TRIS, 50 uM EDTA, 10 mM sodium chloride, 0.0025 % sodium azide	95% H2O/5% D2O	0.01	7	ambient	303
2	3D HNCACB	1 mM [U-100% 13C; U-100% 15N] Cog2p, 3 mM TRIS, 50 uM EDTA, 10 mM sodium chloride, 0.0025 % sodium azide	95% H2O/5% D2O	0.01	7	ambient	303
3	3D CBCA(CO)NH	1 mM [U-100% 13C; U-100% 15N] Cog2p, 3 mM TRIS, 50 uM EDTA, 10 mM sodium chloride, 0.0025 % sodium azide	95% H2O/5% D2O	0.01	7	ambient	303
4	2D DQF-COSY	1 mM [U-100% 13C; U-100% 15N] Cog2p, 3 mM TRIS, 50 uM EDTA, 10 mM sodium chloride, 0.0025 % sodium azide	100% D2O	0.01	7	ambient	303
5	2D 1H-15N HSQC	1 mM [U-100% 13C; U-100% 15N] Cog2p, 3 mM TRIS, 50 uM EDTA, 10 mM sodium chloride, 0.0025 % sodium azide	95% H2O/5% D2O	0.01	7	ambient	303
6	3D HCCH-TOCSY	1 mM [U-100% 13C; U-100% 15N] Cog2p, 3 mM TRIS, 50 uM EDTA, 10 mM sodium chloride, 0.0025 % sodium azide	95% H2O/5% D2O	0.01	7	ambient	303
7	3D C(CO)NH	1 mM [U-100% 13C; U-100% 15N] Cog2p, 3 mM TRIS, 50 uM EDTA, 10 mM sodium chloride, 0.0025 % sodium azide	95% H2O/5% D2O	0.01	7	ambient	303
8	3D 1H-15N NOESY	1 mM [U-100% 13C; U-100% 15N] Cog2p, 3 mM TRIS, 50 uM EDTA, 10 mM sodium chloride, 0.0025 % sodium azide	95% H2O/5% D2O	0.01	7	ambient	303
9	3D 1H-13C NOESY	1 mM [U-100% 13C; U-100% 15N] Cog2p, 3 mM TRIS, 50 uM EDTA, 10 mM sodium chloride, 0.0025 % sodium azide	95% H2O/5% D2O	0.01	7	ambient	303
10	2D 1H-13C CT-HSQC	1 mM [U-100% 13C; U-100% 15N] Cog2p, 3 mM TRIS, 50 uM EDTA, 10 mM sodium chloride, 0.0025 % sodium azide	95% H2O/5% D2O	0.01	7	ambient	303

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Varian	INOVA	800
2	Varian	INOVA	750
3	Varian	INOVA	600

NMR Refinement
Method	Details	Software
DGSA-distance geometry simulated annealing		CNS

NMR Ensemble Information
Conformer Selection Criteria	structures with the lowest energy
Conformers Calculated Total Number	1200
Conformers Submitted Total Number	20
Representative Model	1 (lowest energy)

Additional NMR Experimental Information
Details	Experiments collected at the EMSL at PNNL. Residues 59-108 were present in the Cog2 protein used in this NMR study; however a lack of long-range contacts prevented the inclusion of these residues in the final models.

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	structure solution	CNS	1.1	A Brunger, P Adams, M Clore, P Gros, M Nilges and R Read
2	refinement	CNS	1.1	A Brunger, P Adams, M Clore, P Gros, M Nilges and R Read
3	processing	NMRPipe		F Delaglio, S Grzesiek, GW Vuister, G Zhu, J Pfeifer and A Bax
4	refinement	AQUA		T Rullmann, JF Doreleijers and R Kaptein
5	peak picking	NMRView		B Johnson, One Moon Scientific
6	chemical shift assignment	NMRView		B Johnson, One Moon Scientific
7	data analysis	NMRView		B Johnson, One Moon Scientific
8	geometry optimization	TALOS		G Cornilescu, F Delaglio and A Bax
9	collection	XwinNMR		Bruker Biospin
10	refinement	ProcheckNMR		RA Laskowski and M MacArthur

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.