› 5gjm

X-ray diffraction
2.91Å resolution

Crystal structure of Lysine decarboxylase from Selenomonas ruminantium in C2 space group

Released:
DOI: 10.2210/pdb5gjm/pdb
PDB entry 5gjm coloured by chain, front view.
PDB entry 5gjm coloured by chain, side view.
PDB entry 5gjm coloured by chain, top view.
Source organism: Selenomonas ruminantium
Primary publication:
Crystal Structure and Pyridoxal 5-Phosphate Binding Property of Lysine Decarboxylase from Selenomonas ruminantium.
Sagong HY, Son HF, Kim S, Kim YH, Kim IK, Kim KJ
PLoS One 11 e0166667 (2016)
PMID: 27861532

Function and Biology Details

Reactions catalysed: 
L-ornithine = putrescine + CO(2)
L-lysine = cadaverine + CO(2)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-129333 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Lysine/ornithine decarboxylase Chains: A, B
Molecule details ›
Chains: A, B
Length: 393 amino acids
Theoretical weight: 43.26 KDa
Source organism: Selenomonas ruminantium
Expression system: Escherichia coli
UniProt:
  • Canonical: O50657 (Residues: 1-393; Coverage: 100%)
Gene name: ldc
Sequence domains:
Structure domains:

Ligands and Environments

1 bound ligand:
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PAL/PLS BEAMLINE 7A (6B, 6C1)
Spacegroup: C2
Unit cell:
a: 146.45Å b: 70.794Å c: 88.061Å
α: 90° β: 101.03° γ: 90°
R-values:
R R work R free
0.181 0.177 0.234
Expression system: Escherichia coli

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Citations

1 review citation

Glyphosate's Synergistic Toxicity in Combination with Other Factors as a Cause of Chronic Kidney Disease of Unknown Origin.
Gunatilake et al. (2019)
4 other articles

2 mentions without citation

Crystal Structure and Pyridoxal 5-Phosphate Binding Property of Lysine Decarboxylase from Selenomonas ruminantium.
Sagong et al. (2016)
1 more