2X8R | pdb_00002x8r

The structure of a family GH25 lysozyme from Aspergillus fumigatus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 
    0.207 (Depositor), 0.207 (DCC) 
  • R-Value Work: 
    0.169 (Depositor), 0.169 (DCC) 
  • R-Value Observed: 
    0.171 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

The Structure of a Family Gh25 Lysozyme from Aspergillus Fumigatus

Korczynska, J.E.Danielsen, S.Schagerlof, U.Turkenburg, J.P.Davies, G.J.Wilson, K.S.Taylor, E.J.

(2010) Acta Crystallogr Sect F Struct Biol Cryst Commun 66: 973

  • DOI: https://doi.org/10.1107/S1744309110025601
  • Primary Citation Related Structures: 
    2X8R

  • PubMed Abstract: 

    Lysins are important biomolecules which cleave the bacterial cell-wall polymer peptidoglycan. They are finding increasing commercial and medical application. In order to gain an insight into the mechanism by which these enzymes operate, the X-ray structure of a CAZy family GH25 ;lysozyme' from Aspergillus fumigatus was determined. This is the first fungal structure from the family and reveals a modified alpha/beta-barrel-like fold in which an eight-stranded beta-barrel is flanked by three alpha-helices. The active site lies toward the bottom of a negatively charged pocket and its layout has much in common with other solved members of the GH25 and related GH families. A conserved active-site DXE motif may be implicated in catalysis, lending further weight to the argument that this glycoside hydrolase family operates via a ;substrate-assisted' catalytic mechanism.


  • Organizational Affiliation
    • Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5YW, England.

Macromolecule Content 

  • Total Structure Weight: 140.52 kDa 
  • Atom Count: 11,208 
  • Modeled Residue Count: 1,257 
  • Deposited Residue Count: 1,260 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
GLYCOSYL HYDROLASE
A, B, C, D, E
A, B, C, D, E, F
210Aspergillus fumigatus Af293Mutation(s): 0 
EC: 3.2.1.17
UniProt
Find proteins for A4DA29 (Aspergillus fumigatus (strain ATCC MYA-4609 / CBS 101355 / FGSC A1100 / Af293))
Explore A4DA29 
Go to UniProtKB:  A4DA29
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA4DA29
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free:  0.207 (Depositor), 0.207 (DCC) 
  • R-Value Work:  0.169 (Depositor), 0.169 (DCC) 
  • R-Value Observed: 0.171 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.65α = 90
b = 111.72β = 90
c = 119.16γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-09-08
    Type: Initial release
  • Version 1.1: 2012-04-18
    Changes: Database references, Refinement description, Version format compliance
  • Version 1.2: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description
  • Version 1.3: 2024-10-09
    Changes: Structure summary