4KUK

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.130 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

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

  • DOI: 10.1186/s12866-015-0365-0
  • Primary Citation of Related Structures:  

  • 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 formatio ...

    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.


    Organizational Affiliation

    Institute of Complex Systems, ICS-6: Structural Biochemistry, Forschungszentrum Jülich, D-52425, Jülich, Germany. D.Willbold@fz-juelich.de.,Institute of Molecular Enzyme Technology, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich, D-52425, Jülich, Germany. karl-erich.jaeger@fz-juelich.de.,Institute of Complex Systems, ICS-6: Structural Biochemistry, Forschungszentrum Jülich, D-52425, Jülich, Germany. r.batra-safferling@fz-juelich.de.,Institute of Molecular Enzyme Technology, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich, D-52425, Jülich, Germany. u.krauss@fz-juelich.de.,Institute of Complex Systems, ICS-6: Structural Biochemistry, Forschungszentrum Jülich, D-52425, Jülich, Germany. j.granzin@fz-juelich.de.,Institute for Microbiology, Technische Universität Braunschweig, D-38106, Braunschweig, Germany. p.tielen@tu-bs.de.,Juelich Centre for Neutron Science JCNS (JCNS-1) & Institute for Complex Systems (ICS-1), Forschungszentrum Jülich, D-52425, Jülich, Germany. a.stadler@fz-juelich.de.,Institute of Molecular Enzyme Technology, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich, D-52425, Jülich, Germany. t.drepper@fz-juelich.de.,Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, D-52425, Jülich, Germany. karl-erich.jaeger@fz-juelich.de.,Institute of Complex Systems, ICS-6: Structural Biochemistry, Forschungszentrum Jülich, D-52425, Jülich, Germany. a.cousin@fz-juelich.de.,Institute of Molecular Enzyme Technology, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich, D-52425, Jülich, Germany. v.svensson@fz-juelich.de.,Institute of Molecular Enzyme Technology, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich, D-52425, Jülich, Germany. a.wirtz@fz-juelich.de.,Institute of Molecular Enzyme Technology, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich, D-52425, Jülich, Germany. e.knieps@fz-juelich.de.,Institute of Physical Biology, Heinrich-Heine-Universität Düsseldorf, D-40225, Düsseldorf, Germany. D.Willbold@fz-juelich.de.,Institute of Molecular Enzyme Technology, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich, D-52425, Jülich, Germany. f.circolone@fz-juelich.de.,Institute of Molecular Enzyme Technology, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich, D-52425, Jülich, Germany. s.endres@fz-juelich.de.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
blue-light photoreceptor
A
146Dinoroseobacter shibae (strain DSM 16493 / NCIMB 14021 / DFL 12)Mutation(s): 0 
Find proteins for A8LP63 (Dinoroseobacter shibae (strain DSM 16493 / NCIMB 14021 / DFL 12))
Go to UniProtKB:  A8LP63
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RBF
Query on RBF

Download SDF File 
Download CCD File 
A
RIBOFLAVIN
RIBOFLAVINE; VITAMIN B2
C17 H20 N4 O6
AUNGANRZJHBGPY-SCRDCRAPSA-N
 Ligand Interaction
ACY
Query on ACY

Download SDF File 
Download CCD File 
A
ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
NMM
Query on NMM
A
L-PEPTIDE LINKINGC7 H16 N4 O2ARG
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.130 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 89.978α = 90.00
b = 30.595β = 113.03
c = 49.332γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
PHENIXrefinement
ADSCdata collection
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-11-26
    Type: Initial release
  • Version 1.1: 2015-03-04
    Type: Database references
  • Version 1.2: 2015-04-01
    Type: Database references
  • Version 1.3: 2015-04-29
    Type: Database references