› 2yxd

X-ray diffraction
2.3Å resolution

Crystal Structure of Cobalamin biosynthesis precorrin 8W decarboxylase (cbiT)

Released:
DOI: 10.2210/pdb2yxd/pdb
PDB entry 2yxd coloured by chain, front view.
PDB entry 2yxd coloured by chain, side view.
PDB entry 2yxd coloured by chain, top view.
Source organism: Methanocaldococcus jannaschii DSM 2661
Entry authors: Padmanabhan B, Bessho Y, Yokoyama S, RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Function and Biology Details

Reaction catalysed: 
S-adenosyl-L-methionine + cobalt-precorrin-6B = S-adenosyl-L-homocysteine + cobalt-precorrin-7 + CO(2)
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assemblies composition:
homo dimer (preferred)
homo tetramer
Assembly name:
PDBe Complex ID:
PDB-CPX-176484 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Probable cobalt-precorrin-6B C(15)-methyltransferase (decarboxylating) Chains: A, B
Molecule details ›
Chains: A, B
Length: 183 amino acids
Theoretical weight: 20.72 KDa
Source organism: Methanocaldococcus jannaschii DSM 2661
Expression system: Escherichia coli
UniProt:
  • Canonical: Q57836 (Residues: 1-183; Coverage: 100%)
Gene names: MJ0391, cbiT
Sequence domains: Methyltransferase domain
Structure domains: Vaccinia Virus protein VP39

Ligands and Environments

2 bound ligands:
Ligand SO4 2 x SO4
Ligand MES 1 x MES
1 modified residue:
Ligand MSE 8 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL26B1
Spacegroup: P41212
Unit cell:
a: 93.442Å b: 93.442Å c: 81.042Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.202 0.198 0.273
Expression system: Escherichia coli

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