Find PDB structures and Computed Structure Models (CSM) by combining queries from tools in this suite: Attribute Search, Sequence Similarity, Sequence Motif, 3D Similarity, and 3D Motif with 'AND' logic.
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.