› 6xy9

X-ray diffraction
2.2Å resolution

Crystal structure of haloalkane dehalogenase DbeA-M1 loop variant from Bradyrhizobium elkanii

Released:
DOI: 10.2210/pdb6xy9/pdb
PDB entry 6xy9 coloured by chain, front view.
PDB entry 6xy9 coloured by chain, side view.
PDB entry 6xy9 coloured by chain, top view.
Source organism: Bradyrhizobium elkanii USDA 94
Primary publication:
Structural and catalytic effects of surface loop-helix transplantation within haloalkane dehalogenase family.
Marek M, Chaloupkova R, Prudnikova T, Sato Y, Rezacova P, Nagata Y, Kuta Smatanova I, Damborsky J
Comput Struct Biotechnol J 18 1352-1362 (2020)
PMID: 32612758

Function and Biology Details

Reaction catalysed: 
1-haloalkane + H(2)O = a primary alcohol + halide
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-122863 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Haloalkane dehalogenase Chains: A, B
Molecule details ›
Chains: A, B
Length: 309 amino acids
Theoretical weight: 33.73 KDa
Source organism: Bradyrhizobium elkanii USDA 94
Expression system: Escherichia coli
UniProt:
  • Canonical: E2RV62 (Residues: 5-142, 143-302; Coverage: 96%)
Gene names: dbeA, dhaA
Sequence domains: alpha/beta hydrolase fold

Ligands and Environments

2 bound ligands:
Ligand CL 4 x CL
Ligand ACT 2 x ACT
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: EMBL/DESY, HAMBURG BEAMLINE X11
Spacegroup: C2
Unit cell:
a: 133.75Å b: 75.13Å c: 77.6Å
α: 90° β: 91.9° γ: 90°
R-values:
R R work R free
0.178 0.175 0.235
Expression system: Escherichia coli

Quick links

Citations

1 citations in other articles

LoopGrafter: a web tool for transplanting dynamical loops for protein engineering.
Planas-Iglesias et al. (2022)

1 mention without citation

Structural and catalytic effects of surface loop-helix transplantation within haloalkane dehalogenase family.
Marek et al. (2020)