6QBJ | pdb_00006qbj

Structure determination of transmembrane- C-terminal fragment of UL49.5 protein from bovine herpesvirus 1 by NMR spectroscopy and molecular dynamics

SOLUTION NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D 1H-1H TOCSY	2.7 mM TMC.BHV, 100 mM DPC, 0.01 mM acetic acid -d4, 90 % H2O, 10 % D2O	50% H2O/50% D2O	0.05 mM	5	1 atm	303	Agilent Uniform NMR System 800
2	2D 1H-1H NOESY	2.7 mM TMC.BHV, 100 mM DPC, 0.01 mM acetic acid -d4, 90 % H2O, 10 % D2O	50% H2O/50% D2O	0.05 mM	5	1 atm	303	Agilent Uniform NMR System 800
3	2D DQF-COSY	2.7 mM TMC.BHV, 100 mM DPC, 0.01 mM acetic acid -d4, 90 % H2O, 10 % D2O	50% H2O/50% D2O	0.05 mM	5	1 atm	303	Agilent Uniform NMR System 800
4	2D 1H-1H ROESY	2.7 mM TMC.BHV, 100 mM DPC, 0.01 mM acetic acid -d4, 90 % H2O, 10 % D2O	50% H2O/50% D2O	0.05 mM	5	1 atm	303	Agilent Uniform NMR System 800

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Agilent	Uniform NMR System	800

NMR Refinement
Method	Details	Software
molecular dynamics		Amber

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	refinement	Amber		Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman
2	structure calculation	CYANA		Guntert, Mumenthaler and Wuthrich
3	chemical shift assignment	Sparky		Goddard
4	peak picking	Sparky		Goddard

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.