› 6ojr

X-ray diffraction
2.3Å resolution

Crystal structure of Sphingomonas paucimobilis TMY1009 apo-LsdA

Released:
DOI: 10.2210/pdb6ojr/pdb
PDB entry 6ojr coloured by chain, front view.
PDB entry 6ojr coloured by chain, side view.
PDB entry 6ojr coloured by chain, top view.
Source organism: Sphingomonas paucimobilis
Primary publication:
Identification of functionally important residues and structural features in a bacterial lignostilbene dioxygenase.
Kuatsjah E, Verstraete MM, Kobylarz MJ, Liu AKN, Murphy MEP, Eltis LD
J Biol Chem 294 12911-12920 (2019)
PMID: 31292192

Function and Biology Details

Reaction catalysed: 
1,2-bis(4-hydroxy-3-methoxyphenyl)ethylene + O(2) = 2 vanillin
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domain:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-176052 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Lignostilbene-alpha,beta-dioxygenase isozyme I Chains: A, B
Molecule details ›
Chains: A, B
Length: 482 amino acids
Theoretical weight: 54.2 KDa
Source organism: Sphingomonas paucimobilis
Expression system: Escherichia coli
UniProt:
  • Canonical: Q53353 (Residues: 2-483; Coverage: 99%)
Sequence domains: Retinal pigment epithelial membrane protein

Ligands and Environments

2 bound ligands:
Ligand GOL 5 x GOL
Ligand MG 3 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL7-1
Spacegroup: P3221
Unit cell:
a: 181.364Å b: 181.364Å c: 94.983Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.183 0.182 0.205
Expression system: Escherichia coli

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Citations

4 review citations

The molecular aspects of absorption and metabolism of carotenoids and retinoids in vertebrates.
Widjaja-Adhi et al. (2020)
3 more

2 mentions without citation

Identification of functionally important residues and structural features in a bacterial lignostilbene dioxygenase.
Kuatsjah et al. (2019)
1 more