4KUO

A superfast recovering full-length LOV protein from the marine phototrophic bacterium Dinoroseobacter shibae (Photoexcited state)

• PDB DOI: https://doi.org/10.2210/pdb4KUO/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Dinoroseobacter shibae DFL 12 = DSM 16493
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-05-22 Released: 2014-11-26 
• Deposition Author(s): Circolone, F., Granzin, J., Stadler, A., Krauss, U., Drepper, T., Endres, S., Knieps-Gruenhagen, E., Wirtz, A., Willbold, D., Batra-Safferling, R., Jaeger, K.-E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.182 
• R-Value Work: 0.163 
• R-Value Observed: 0.164 

Literature

Structure and function of a short LOV protein from the marine phototrophic bacterium Dinoroseobacter shibae.

Endres, S., Granzin, J., Circolone, F., Stadler, A., Krauss, U., Drepper, T., Svensson, V., Knieps-Grunhagen, E., Wirtz, A., Cousin, A., Tielen, P., Willbold, D., Jaeger, K.E., Batra-Safferling, R.

(2015) BMC Microbiol 15: 30-30

• PubMed: 25887755 
• DOI: https://doi.org/10.1186/s12866-015-0365-0
• Primary Citation of Related Structures:  
  4KUK, 4KUO


• PubMed Abstract: 
  

  Light, oxygen, voltage (LOV) domains are widely distributed in plants, algae, fungi, bacteria, and represent the photo-responsive domains of various blue-light photoreceptor proteins. Their photocycle involves the blue-light triggered adduct formation between the C(4a) atom of a non-covalently bound flavin chromophore and the sulfur atom of a conserved cysteine in the LOV sensor domain. LOV proteins show considerable variation in the structure of N- and C-terminal elements which flank the LOV core domain, as well as in the lifetime of the adduct state.

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Organizational Affiliation: 

Institute of Molecular Enzyme Technology, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich, D-52425, Jülich, Germany. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 17.24 kDa 
• Atom Count: 1,015 
• Modelled Residue Count: 115 
• Deposited Residue Count: 146 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
blue-light photoreceptor	A	146	Dinoroseobacter shibae DFL 12 = DSM 16493	Mutation(s): 0  Gene Names: Dshi_2006
UniProt
Find proteins for A8LP63 (Dinoroseobacter shibae (strain DSM 16493 / NCIMB 14021 / DFL 12)) Explore A8LP63  Go to UniProtKB:  A8LP63

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RBF	B [auth A]	RIBOFLAVIN C17 H20 N4 O6 AUNGANRZJHBGPY-SCRDCRAPSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.182 
• R-Value Work: 0.163 
• R-Value Observed: 0.164 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.78	α = 90
b = 30.936	β = 113.09
c = 49.538	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-11-26 
Deposition Author(s): Circolone, F., Granzin, J., Stadler, A., Krauss, U., Drepper, T., Endres, S., Knieps-Gruenhagen, E., Wirtz, A., Willbold, D., Batra-Safferling, R., Jaeger, K.-E.

Revision History  

• Version 1.0: 2014-11-26
  Type: Initial release
  
• Version 1.1: 2015-03-04
  Changes: Database references
• Version 1.2: 2015-04-01
  Changes: Database references
• Version 1.3: 2015-04-29
  Changes: Database references
• Version 1.4: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description