5V2D

Crystal structure of Pseudomonas brassicacearum lignostilbene dioxygenase

• PDB DOI:  https://doi.org/10.2210/pdb5V2D/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Pseudomonas brassicacearum
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2017-03-03 Released: 2018-03-07 
• Deposition Author(s): Loewen, P.C., Loewen, M.
• Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada)

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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 

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

• PubMed: 30115012 
• 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.

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Organizational Affiliation: 

Department of BioMedical and Molecular Sciences, Queen's University, Kingston, ON, K7L 3N6, Canada.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 224.51 kDa 
• Atom Count: 16,428 
• Modelled Residue Count: 1,931 
• Deposited Residue Count: 2,004 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dioxygenase	A, B, C, D	501	Pseudomonas brassicacearum	Mutation(s): 0  Gene Names: CD58_10895 EC: 1.13.11
UniProt
Find proteins for W8QAY8 (Pseudomonas brassicacearum) Explore W8QAY8  Go to UniProtKB:  W8QAY8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FE	E [auth A], F [auth B], G [auth C], H [auth D]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

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 = 96.397	α = 90
b = 104.673	β = 94.79
c = 104.709	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-03-07 
Deposition Author(s): Loewen, P.C., Loewen, M.

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Funding Organization	Location	Grant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	D9600

Revision History  

• 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