SASDDG6: Photoreceptor sensory box 1 dark-state (SB1-LOV-R66I)

Basic information

• Entry: Database: SASBDB / ID: SASDDG6

Sample

Photoreceptor sensory box 1 dark-state (SB1-LOV-R66I)

• Sensory box protein dark-state (protein), Pseudomonas putida (strain ATCC 47054 / DSM 6125 / NCIMB 11950 / KT2440)

Function / homology

Function:

nucleotide binding

Domain/homology:

PAS domain / PAS-associated, C-terminal / PAC domain profile. / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily

Component:

Sensory box protein

• Biological species: Pseudomonas putida (strain ATCC 47054 / DSM 6125 / NCIMB 11950 / KT2440) (bacteria)
• Citation: Journal: PLoS One / Year: 2018; Title: Small-angle X-ray scattering study of the kinetics of light-dark transition in a LOV protein.; Authors: Katrin Röllen / Joachim Granzin / Renu Batra-Safferling / Andreas Maximilian Stadler / ; Abstract: Light, oxygen, voltage (LOV) photoreceptors consist of conserved photo-responsive domains in bacteria, archaea, plants and fungi, and detect blue-light via a flavin cofactor. We investigated the blue-light induced conformational transition of the dimeric photoreceptor PpSB1-LOV-R66I from Pseudomonas putida in solution by using small-angle X-ray scattering (SAXS). SAXS experiments of the fully populated light- and dark-states under steady-state conditions revealed significant structural differences between the two states that are in agreement with the known structures determined by crystallography. We followed the transition from the light- to the dark-state by using SAXS measurements in real-time. A two-state model based on the light- and dark-state conformations could describe the measured time-course SAXS data with a relaxation time τREC of ~ 34 to 35 min being larger than the recovery time found with UV/vis spectroscopy. Unlike the flavin chromophore-based UV/vis method that is sensitive to the local chromophore environment in flavoproteins, SAXS-based assay depends on protein conformational changes and provides with an alternative to measure the recovery kinetics.

Contact author

• Andreas Stadler (Forschungszentrum Jülich)

Models

• Model #1986: ; Type: dummy / Software: (2.8.3) / Radius of dummy atoms: 2.00 A / Symmetry: P2 / Chi-square value: 0.833; Search similar-shape structures of this assembly by Omokage search (details)
• Model #1975: ; Type: mix / Radius of dummy atoms: 1.90 A / Chi-square value: 1.049 / P-value: 0.000001; Search similar-shape structures of this assembly by Omokage search (details)
• Model #1981: ; Type: mix / Radius of dummy atoms: 1.90 A / Chi-square value: 1.049 / P-value: 0.000001; Search similar-shape structures of this assembly by Omokage search (details)
• Model #1982: ; Type: mix / Radius of dummy atoms: 1.90 A / Chi-square value: 1.049 / P-value: 0.000001; Search similar-shape structures of this assembly by Omokage search (details)
• Model #1983: ; Type: mix / Radius of dummy atoms: 1.90 A / Chi-square value: 1.049 / P-value: 0.000001; Search similar-shape structures of this assembly by Omokage search (details)
• Model #1984: ; Type: mix / Radius of dummy atoms: 1.90 A / Chi-square value: 1.049 / P-value: 0.000001; Search similar-shape structures of this assembly by Omokage search (details)
• Model #1985: ; Type: mix / Radius of dummy atoms: 1.90 A / Chi-square value: 1.049 / P-value: 0.000001; Search similar-shape structures of this assembly by Omokage search (details)
• Model #1996: ; Type: mix / Radius of dummy atoms: 1.90 A / Chi-square value: 4.38; Search similar-shape structures of this assembly by Omokage search (details)

Sample

• Sample: Name: Photoreceptor sensory box 1 dark-state (SB1-LOV-R66I) / Specimen concentration: 2.50-6.10
• Buffer: Name: 10mM Tris, 10 mM NaCl / pH: 7

Entity #1061

Type: protein / Description: Sensory box protein dark-state / Formula weight: 18.588 / Num. of mol.: 2
Source: Pseudomonas putida (strain ATCC 47054 / DSM 6125 / NCIMB 11950 / KT2440)
References: UniProt: Q88E39
Sequence:

MGSSHHHHHH SSGLVPRGSH MINAQLLQSM VDASNDGIVV AEKEGDDTIL IYVNAAFEYL TGYSRDEILY QDCRFLQGDD RDQLGRARIR KAMAEGRPCR EVLRNYRKDG SAFWNELSIT PVKSDFDQRT YFIGIQKDVS RQVELERELA ELRARPKPDE RA

Experimental information

• Beam: Instrument name: ESRF BM29 / City: Grenoble / 国: France / Type of source: X-ray synchrotron / Wavelength: 0.099 Å / Dist. spec. to detc.: 2.867 mm
• Detector: Name: Pilatus 1M / Pixsize x: 172 mm

Scan

Title: Photoreceptor sensory box 1 dark-state (SB1-LOV-R66I)
Measurement date: Dec 2, 2014 / Storage temperature: 10 °C / Cell temperature: 10 °C / Exposure time: 1 sec. / Number of frames: 10 / Unit: 1/nm /

	Min	Max
Q	0.1074	4.9693

Distance distribution function P(R)

Sofotware P(R): GNOM 5.0 / Number of points: 612 /

	Min	Max
Q	0.225707	3.11828
P(R) point	1	612
R	0	7.95

Result

Type of curve: merged

	Experimental	Standard	Standard error	Porod
MW	37.4 kDa	42.23 kDa	0.029	33.4 kDa
Volume	-	-	-	56.83 nm3

	P(R)	Guinier	Guinier error
Forward scattering, I0	41.92	42.23	0.029
Radius of gyration, Rg	2.543 nm	2.56 nm	0.01

	Min	Max
D	-	7.95
Guinier point	26	84