7D8M

Crystal structure of DyP

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 

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Literature

Revealing two important tryptophan residues with completely different roles in a dye-decolorizing peroxidase from Irpex lacteus F17.

Li, L., Wang, T., Chen, T., Huang, W., Zhang, Y., Jia, R., He, C.

(2021) Biotechnol Biofuels 14: 128-128

  • DOI: https://doi.org/10.1186/s13068-021-01978-y
  • Primary Citation of Related Structures:  
    7D8M

  • PubMed Abstract: 

    Dye-decolorizing peroxidases (DyPs) represent a novel family of heme peroxidases that use H 2 O 2 as the final electron acceptor to catalyze the oxidation of various organic compounds. A DyP from Irpex lacteus F17 (Il-DyP4, corresponding to GenBank MG209114), obtained by heterologous expression, exhibits a high catalytic efficiency for phenolic compounds and a strong decolorizing ability toward various synthetic dyes. However, the enzyme structure and the catalytic residues involved in substrate oxidation remain poorly understood.

    • Organizational Affiliation: 

    School of Life Science, Economic and Technology Development Zone, Anhui University, 111 jiulong Road, Hefei, Anhui, PR China, 230601.


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dye-decolorizing peroxidase458Irpex lacteusMutation(s): 0 
UniProt
Find proteins for A0A2P1C6N4 (Irpex lacteus)
Explore A0A2P1C6N4 
Go to UniProtKB:  A0A2P1C6N4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2P1C6N4
Sequence Annotations
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 118.959α = 90
b = 118.959β = 90
c = 65.347γ = 120
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-08-18
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description