› 8rc9

X-ray diffraction
2.06Å resolution

W-formate dehydrogenase from Desulfovibrio vulgaris - Co-crystallized with Formate and Exposed to air for 2 h

Released:
DOI: 10.2210/pdb8rc9/pdb
PDB entry 8rc9 coloured by chain, front view.
PDB entry 8rc9 coloured by chain, side view.
PDB entry 8rc9 coloured by chain, top view.
Source organism: Nitratidesulfovibrio vulgaris str. Hildenborough
Primary publication:
Substrate-dependent oxidative inactivation of a W-dependent formate dehydrogenase involving selenocysteine displacement.
Vilela-Alves G, Manuel RR, Viegas A, Carpentier P, Biaso F, Guigliarelli B, Pereira IAC, Romão MJ, Mota C
Chem Sci 15 13090-13101 (2024)
PMID: 39148770

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-180797 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
4Fe-4S Mo/W bis-MGD-type domain-containing protein Chain: A
Molecule details ›
Chain: A
Length: 1013 amino acids
Theoretical weight: 112.44 KDa
Source organism: Nitratidesulfovibrio vulgaris str. Hildenborough
Expression system: Desulfovibrio vulgaris str. Hildenborough
UniProt:
  • Canonical: Q72EJ1 (Residues: 1-1005; Coverage: 100%)
Gene names: DVU_0587, fdnG-1
Sequence domains:
4Fe-4S ferredoxin-type domain-containing protein Chain: B
Molecule details ›
Chain: B
Length: 214 amino acids
Theoretical weight: 23.86 KDa
Source organism: Nitratidesulfovibrio vulgaris str. Hildenborough
Expression system: Desulfovibrio vulgaris str. Hildenborough
UniProt:
  • Canonical: Q72EJ0 (Residues: 2-215; Coverage: 91%)
Gene name: DVU_0588
Sequence domains: 4Fe-4S dicluster domain

Ligands and Environments


Cofactor: Ligand MGD 2 x MGD
6 bound ligands:
Ligand SF4 4 x SF4
Ligand W 1 x W
Ligand H2S 1 x H2S
Ligand GOL 2 x GOL
Ligand EDO 2 x EDO
Ligand OXY 1 x OXY
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID30B
Spacegroup: P212121
Unit cell:
a: 65.18Å b: 127.926Å c: 149.467Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.209 0.206 0.255
Expression system: Desulfovibrio vulgaris str. Hildenborough

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