The tetrameric structure of haloalkane dehalogenase DpaA from Paraglaciecola agarilytica NO2

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.178 

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The tetrameric structure of the novel haloalkane dehalogenase DpaA from Paraglaciecola agarilytica NO2.

Mazur, A.Prudnikova, T.Grinkevich, P.Mesters, J.R.Mrazova, D.Chaloupkova, R.Damborsky, J.Kuty, M.Kolenko, P.Kuta Smatanova, I.

(2021) Acta Crystallogr D Struct Biol 77: 347-356

  • DOI: https://doi.org/10.1107/S2059798321000486
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Haloalkane dehalogenases (EC are microbial enzymes that catalyse the hydrolytic conversion of halogenated compounds, resulting in a halide ion, a proton and an alcohol. These enzymes are used in industrial biocatalysis, bioremediation and biosensing of environmental pollutants or for molecular tagging in cell biology. The novel haloalkane dehalogenase DpaA described here was isolated from the psychrophilic and halophilic bacterium Paraglaciecola agarilytica NO2, which was found in marine sediment collected from the East Sea near Korea. Gel-filtration experiments and size-exclusion chromatography provided information about the dimeric composition of the enzyme in solution. The DpaA enzyme was crystallized using the sitting-drop vapour-diffusion method, yielding rod-like crystals that diffracted X-rays to 2.0 Å resolution. Diffraction data analysis revealed a case of merohedral twinning, and subsequent structure modelling and refinement resulted in a tetrameric model of DpaA, highlighting an uncommon multimeric nature for a protein belonging to haloalkane dehalogenase subfamily I.

  • Organizational Affiliation

    Faculty of Science, University of South Bohemia in Ceske Budejovice, Branisovska 1760, 370 05 Ceske Budejovice, Czech Republic.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Haloalkane dehalogenase 1
A, B, C, D, E
A, B, C, D, E, F, G, H
307Paraglaciecola agarilytica NO2Mutation(s): 0 
Gene Names: dhmA1GAGA_3124
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on CL

Download Ideal Coordinates CCD File 
I [auth A]
J [auth B]
K [auth C]
L [auth C]
M [auth C]
I [auth A],
J [auth B],
K [auth C],
L [auth C],
M [auth C],
N [auth D],
O [auth E],
P [auth E],
Q [auth F],
R [auth F],
S [auth F],
T [auth F],
U [auth F],
V [auth F],
W [auth G],
X [auth G],
Y [auth G],
Z [auth H]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.178 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.385α = 90
b = 155.506β = 90
c = 155.611γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Grant Agency of the Czech RepublicCzech Republic17-24321S
German Research Foundation (DFG)GermanyDAAD-16-09
European Regional Development FundCzech RepublicCZ.02.1.01/0.0/0.0/15_003/0000441
European Regional Development FundCzech RepublicCZ.02.1.01/0.0/0.0/16_019/0000778
European Regional Development FundCzech RepublicLM2015047
European Regional Development FundCzech RepublicLM2018121
Ministry of Education (MoE, Czech Republic)Czech RepublicCZ.02.1.01/0.0/0.0/16_026/0008451

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-17
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Advisory, Data collection, Database references, Refinement description