› 5xen

X-ray diffraction
1.94Å resolution

Crystal structure of a hydrogen sulfide-producing enzyme (Fn1220) from Fusobacterium nucleatum in complex with L-serine-PLP Schiff base

Released:
DOI: 10.2210/pdb5xen/pdb
PDB entry 5xen coloured by chain, front view.
PDB entry 5xen coloured by chain, side view.
PDB entry 5xen coloured by chain, top view.
Source organism: Fusobacterium nucleatum subsp. nucleatum ATCC 25586
Entry authors: Kezuka Y, Yoshida Y, Nonaka T

Function and Biology Details

Reaction catalysed: 
O-acetyl-L-serine + hydrogen sulfide = L-cysteine + acetate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-185978 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Tryptophan synthase beta chain-like PALP domain-containing protein Chains: A, B
Molecule details ›
Chains: A, B
Length: 310 amino acids
Theoretical weight: 33.53 KDa
Source organism: Fusobacterium nucleatum subsp. nucleatum ATCC 25586
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q8RE94 (Residues: 12-316; Coverage: 97%)
Gene name: FN1220
Sequence domains: Pyridoxal-phosphate dependent enzyme
Structure domains: Rossmann fold

Ligands and Environments


Cofactor: Ligand PLP 4 x PLP
4 bound ligands:
Ligand SER 2 x SER
Ligand ACT 2 x ACT
Ligand CA 8 x CA
Ligand PEG 3 x PEG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-5A
Spacegroup: P43212
Unit cell:
a: 116.869Å b: 116.869Å c: 99.393Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.16 0.158 0.186
Expression system: Escherichia coli BL21(DE3)

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