› 9jer

X-ray diffraction
1.9Å resolution

Arginine decarboxylase in Aspergillus oryzae, ligand-free form

Released:
DOI: 10.2210/pdb9jer/pdb
PDB entry 9jer coloured by chain, front view.
PDB entry 9jer coloured by chain, side view.
PDB entry 9jer coloured by chain, top view.
Source organism: Aspergillus oryzae RIB40
Primary publication:
Unveiling the reaction mechanism of arginine decarboxylase in Aspergillus oryzae: Insights from crystal structure analysis.
Odagaki Y, Murakami Y, Takita T, Mizutani K, Mikami B, Fujiwara S, Yasukawa K
Biochem Biophys Res Commun 733 150728 (2024)
PMID: 39321488

Function and Biology Details

Reaction catalysed: 
L-arginine = agmatine + CO(2)
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-274685 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
L-tryptophan decarboxylase PsiD-like domain-containing protein Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 462 amino acids
Theoretical weight: 51.17 KDa
Source organism: Aspergillus oryzae RIB40
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: Q2UAM5 (Residues: 1-442; Coverage: 92%)
Gene name: AO090102000327
Sequence domains:
L-tryptophan decarboxylase PsiD-like domain-containing protein Chains: E, F, G, H
Molecule details ›
Chains: E, F, G, H
Length: 42 amino acids
Theoretical weight: 4.68 KDa
Source organism: Aspergillus oryzae RIB40
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: Q2UAM5 (Residues: 443-483; Coverage: 9%)
Gene name: AO090102000327

Ligands and Environments

2 bound ligands:
Ligand PEG 10 x PEG
Ligand EDO 128 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL26B1
Spacegroup: C2221
Unit cell:
a: 134.692Å b: 196.484Å c: 196.783Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.17 0.169 0.202
Expression system: Escherichia coli BL21

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