› 6zxx

X-ray diffraction
1.99Å resolution

Catabolic reductive dehalogenase NpRdhA, N-terminally tagged.

Released:
DOI: 10.2210/pdb6zxx/pdb
PDB entry 6zxx coloured by chain, front view.
PDB entry 6zxx coloured by chain, side view.
PDB entry 6zxx coloured by chain, top view.
Source organism: Nitratireductor pacificus pht-3B
Primary publication:
Catabolic Reductive Dehalogenase Substrate Complex Structures Underpin Rational Repurposing of Substrate Scope.
Halliwell T, Fisher K, Payne KAP, Rigby SEJ, Leys D
Microorganisms 8 (2020)
PMID: 32887524

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
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: 725 amino acids
Theoretical weight: 79.72 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

6 bound ligands:
Ligand SF4 6 x SF4
Ligand B12 3 x B12
Ligand NA 3 x NA
Ligand QSH 3 x QSH
Ligand QSB 3 x QSB
Ligand BR 3 x BR
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04-1
Spacegroup: C2
Unit cell:
a: 180.182Å b: 170.391Å c: 107.957Å
α: 90° β: 99.16° γ: 90°
R-values:
R R work R free
0.184 0.182 0.218
Expression system: Priestia megaterium

Quick links

Citations

2 citation in other articles

Accurate prediction by AlphaFold2 for ligand binding in a reductive dehalogenase and implications for PFAS (per- and polyfluoroalkyl substance) biodegradation.
Guo et al. (2023)
1 more

1 mention without citation

Catabolic Reductive Dehalogenase Substrate Complex Structures Underpin Rational Repurposing of Substrate Scope.
Halliwell et al. (2020)