2MWG

Full-Length Solution Structure Of YtvA, a LOV-Photoreceptor Protein and Regulator of Bacterial Stress Response

SOLUTION NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	3D HCCH-TOCSY	500 uM [U-13C; U-15N; U-2H; {ILE, LEU, VAL 1H-Met}] YtvA, 500 uM [U-75% 13C; U-75% 15N; U-75% 2H] FMN, 20 mM potassium phosphate, 50 mM sodium chloride, 0.1 % sodium azide	95% H2O/5% D2O	70	6.5	ambient	300
2	3D 1H-13C NOESY aliphatic	500 uM [U-15N; U-2H; {ILE, LEU, VAL 1H-Met}] YtvA, 500 uM [U-75% 15N; U-75% 2H] FMN, 20 mM potassium phosphate, 50 mM sodium chloride, 0.1 % sodium azide	95% H2O/5% D2O	70	6.5	ambient	300
3	2D 1H-15N TROSY	100 uM [U-15N; U-2H] YtvA, 100 uM [U-75% 15N; U-75% 2H] FMN, 20 mM potassium phosphate, 50 mM sodium chloride, 0.1 % sodium azide, 10 mg/mL Pf1 phage	95% H2O/5% D2O	70	6.5	ambient	300
4	2D 1H-15N TROSY	100 uM [U-15N; U-2H] YtvA, 100 uM [U-75% 15N; U-75% 2H] FMN, 20 mM potassium phosphate, 50 mM sodium chloride, 0.1 % sodium azide, 4 % C12E5, 1.5 % Hexanol	95% H2O/5% D2O	70	6.5	ambient	300

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

NMR Refinement
Method	Details	Software
monte-carlo simulated annealing using torsion angle dynamics, simulated annealing.	OWING TO THE RELATIVELY LOW NUMBER OF RESTRAINTS TO DETERMINE THE STRUCTURE AB INITIO, STRUCTURES OF THE FOUR MAJOR SEGMENTS WERE CALCULATED USING CS-ROSETTA. 12,000 AND 2,000 STRUCTURES WERE CALCULATED FOR LOV OR STAS AND NCAP OR JA, RESPECTIVELY. THE LOWEST ENERGY STRUCTURE WAS FURTHER USED. THE STRUCTURES OF THE FOUR SEGMENTS OBTAINED BY CS-ROSETTA WERE REFINED AGAINST THE RDCS USING LOW TEMPERATURE SA. 100 STRUCTURES WERE CALCULATED AND THE CLOSEST TO AN AVERAGE OF THE 10 LOWEST ENERGY STRUCTURES WAS USED IN THE NEXT STEP. ALL FOUR SEGMENTS (NCAP, LOV, JA, STAS) WERE COMBINED TO A DIMERIC FULL-LENGTH STRUCTURE. THE YF1 STRUCTURE (PDB 4GCZ) WAS USED AS A TEMPLATE FOR THE ALIGNMENT OF LOV AND NCAP IN THE DIMER. ALL FOUR SEGMENTS WERE TREATED AS RIGID BODIES IN A HIGH TEMPERATURE SIMULATED ANNEALING. 100 STRUCTURES WERE CALCULATED AND THE CLOSEST TO AN AVERAGE OF THE LOWEST 10 WAS USED IN THE LAST REFINEMENT STEP. THE FINAL STRUCTURAL ENSEMBLE WAS OBTAINED USING THE SAME REFINEMENT PROTOCOLS AS IN STEP 2. 100 STRUCTURES WERE CALCULATED AND THE LOWEST 10 ARE SUBMITTED.	TopSpin

NMR Ensemble Information
Conformer Selection Criteria	structures with the lowest energy
Conformers Calculated Total Number	100
Conformers Submitted Total Number	10
Representative Model	1 (closest to the average)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	collection	TopSpin	v2.1	Bruker Biospin
2	processing	TopSpin	v2.1	Bruker Biospin
3	chemical shift assignment	CCPN	v2.1.5	CCPN
4	data analysis	CCPN	v2.1.5	CCPN
5	peak picking	CCPN	v2.1.5	CCPN
6	structure solution	CS-ROSETTA	v3.2	Shen, Vernon, Baker and Bax
7	structure solution	X-PLOR NIH	v2.30	Schwieters, Kuszewski, Tjandra and Clore
8	refinement	X-PLOR NIH	v2.30	Schwieters, Kuszewski, Tjandra and Clore
9	geometry optimization	X-PLOR NIH	v2.30	Schwieters, Kuszewski, Tjandra and Clore

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.