› 4ras

X-ray diffraction
2.3Å resolution

Reductive dehalogenase structure suggests a mechanism for B12-dependent dehalogenation

Released:
DOI: 10.2210/pdb4ras/pdb
PDB entry 4ras coloured by chain, front view.
PDB entry 4ras coloured by chain, side view.
PDB entry 4ras coloured by chain, top view.
Source organism: Nitratireductor pacificus pht-3B
Primary publication:
Reductive dehalogenase structure suggests a mechanism for B12-dependent dehalogenation.
Payne KA, Quezada CP, Fisher K, Dunstan MS, Collins FA, Sjuts H, Levy C, Hay S, Rigby SE, Leys D
Nature 517 513-516 (2015)
PMID: 25327251

Function and Biology Details

Biochemical function:
Biological process:
  • not assigned
Cellular component:
Sequence domains:

Structure analysis Details

Assemblies composition:
monomeric (preferred)
homo dimer
Assembly name:
PDBe Complex ID:
PDB-CPX-125509 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
4Fe-4S ferredoxin-type domain-containing protein Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 704 amino acids
Theoretical weight: 77.43 KDa
Source organism: Nitratireductor pacificus pht-3B
Expression system: Priestia megaterium
UniProt:
  • Canonical: K2MB66 (Residues: 1-698; Coverage: 100%)
Gene name: NA2_14372
Sequence domains:

Ligands and Environments

4 bound ligands:
Ligand SF4 6 x SF4
Ligand B12 3 x B12
Ligand CL 3 x CL
Ligand NA 3 x NA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04
Spacegroup: C2
Unit cell:
a: 177.34Å b: 171.51Å c: 109.02Å
α: 90° β: 98.87° γ: 90°
R-values:
R R work R free
0.182 0.181 0.207
Expression system: Priestia megaterium

Quick links

Citations

26 review citations

Vitamin B12 catalysed reactions.
Giedyk et al. (2015)
25 more

8 mentions without citation

Enzymatic Halogenation and Dehalogenation Reactions: Pervasive and Mechanistically Diverse.
Agarwal et al. (2017)
7 more