8XXB | pdb_00008xxb

Crystal Structure of a triple-mutant (A69F/M124P/R127G) of halohydrin dehalogenase HheD8 complexed with chloride


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.190 (Depositor), 0.191 (DCC) 
  • R-Value Work: 
    0.185 (Depositor), 0.186 (DCC) 
  • R-Value Observed: 
    0.185 (Depositor) 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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Literature

Biocatalytic enantioselective formation and ring-opening of oxetanes.

Hua, X.Wang, Y.F.Jin, X.Yu, H.Y.Wang, H.H.Chen, Y.Z.Wan, N.W.

(2025) Nat Commun 16: 1170-1170

  • DOI: https://doi.org/10.1038/s41467-025-56463-z
  • Primary Citation Related Structures: 
    8XXB

  • PubMed Abstract: 

    Although biocatalysis offers complementary or alternative approaches to traditional synthetic methods, the limited range of available enzymatic reactions currently poses challenges in synthesizing a diverse array of desired compounds. Consequently, there is a significant demand for developing novel biocatalytic processes to enable reactions that were previously unattainable. Herein, we report the discovery and subsequent protein engineering of a unique halohydrin dehalogenase to develop a biocatalytic platform for enantioselective formation and ring-opening of oxetanes. This biocatalytic platform, exhibiting high efficiency, excellent enantioselectivity, and broad scopes, facilitates the preparative-scale synthesis of chiral oxetanes and a variety of chiral γ-substituted alcohols. Additionally, both the enantioselective oxetane formation and ring-opening processes are proven scalable for large-scale transformations at high substrate concentrations, and can be integrated efficiently in a one-pot, one-catalyst cascade system. This work expands the enzymatic toolbox for non-natural reactions and will promote further exploration of the catalytic repertoire of halohydrin dehalogenases in synthetic and pharmaceutical chemistry.


  • Organizational Affiliation
    • School of Pharmacy, Zunyi Medical University, Zunyi, 563000, China.

Macromolecule Content 

  • Total Structure Weight: 24.76 kDa 
  • Atom Count: 1,692 
  • Modeled Residue Count: 222 
  • Deposited Residue Count: 233 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Short-chain dehydrogenase/reductase SDR233Thauera aminoaromatica S2Mutation(s): 3 
Gene Names: C665_05478
UniProt
Find proteins for N6YXW4 (Thauera aminoaromatica S2)
Explore N6YXW4 
Go to UniProtKB:  N6YXW4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupN6YXW4
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CL

Query on CL



Download:Ideal Coordinates CCD File
B [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.190 (Depositor), 0.191 (DCC) 
  • R-Value Work:  0.185 (Depositor), 0.186 (DCC) 
  • R-Value Observed: 0.185 (Depositor) 
Space Group: P 62 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 138.564α = 90
b = 138.564β = 90
c = 66.822γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data

  • Released Date: 2024-01-31 
  • Deposition Author(s): Wan, N.W.

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2024-01-31
    Type: Initial release
  • Version 1.1: 2025-02-26
    Changes: Database references, Structure summary