5V2D

Crystal structure of Pseudomonas brassicacearum lignostilbene dioxygenase

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.163 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Structure and function of a lignostilbene-alpha , beta-dioxygenase orthologue from Pseudomonas brassicacearum.

Loewen, P.C., Switala, J., Wells, J.P., Huang, F., Zara, A.T., Allingham, J.S., Loewen, M.C.

(2018) BMC Biochem 19: 8-8

  • DOI: https://doi.org/10.1186/s12858-018-0098-4
  • Primary Citation of Related Structures:  
    5V2D

  • PubMed Abstract: 

    Stilbene cleaving oxygenases (SCOs), also known as lignostilbene-α,β-dioxygenases (LSDs) mediate the oxidative cleavage of the olefinic double bonds of lignin-derived intermediate phenolic stilbenes, yielding small modified benzaldehyde compounds. SCOs represent one branch of the larger carotenoid cleavage oxygenases family. Here, we describe the structural and functional characterization of an SCO-like enzyme from the soil-born, bio-control agent Pseudomonas brassicacearum.

    • Organizational Affiliation: 

    Department of Microbiology, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada.


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dioxygenase
A, B, C, D
501Pseudomonas brassicacearumMutation(s): 0 
Gene Names: CD58_10895
UniProt
Find proteins for W8QAY8 (Pseudomonas brassicacearum)
Explore W8QAY8 
Go to UniProtKB:  W8QAY8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupW8QAY8
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.163 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.397α = 90
b = 104.673β = 94.79
c = 104.709γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)CanadaD9600

Revision History  (Full details and data files)

  • Version 1.0: 2018-03-07
    Type: Initial release
  • Version 1.1: 2019-03-20
    Changes: Data collection, Database references, Structure summary
  • Version 1.2: 2020-01-08
    Changes: Author supporting evidence
  • Version 1.3: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description