8H3W

Crystal structure of chicken egg lysozyme at ambient temperature

  • Classification: HYDROLASE
  • Organism(s): Gallus gallus
  • Mutation(s): No 

  • Deposited: 2022-10-09 Released: 2023-03-22 
  • Deposition Author(s): DeMirci, H.
  • Funding Organization(s): Other government

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.179 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Rapid and efficient ambient temperature X-ray crystal structure determination at Turkish Light Source.

Gul, M.Ayan, E.Destan, E.Johnson, J.A.Shafiei, A.Kepceoglu, A.Yilmaz, M.Ertem, F.B.Yapici, I.Tosun, B.Baldir, N.Tokay, N.Nergiz, Z.Karakadioglu, G.Paydos, S.S.Kulakman, C.Ferah, C.K.Guven, O.Atalay, N.Akcan, E.K.Cetinok, H.Arslan, N.E.Sabanoglu, K.Asci, B.Tavli, S.Gumusboga, H.Altuntas, S.Otsuka, M.Fujita, M.Teki N, S.Ci Ftci, H.Durdagi, S.Karaca, E.Kaplan Turkoz, B.Kabasakal, B.V.Kati, A.DeMi Rci, H.

(2023) Sci Rep 13: 8123-8123

  • DOI: https://doi.org/10.1038/s41598-023-33989-0
  • Primary Citation of Related Structures:  
    8H3W

  • PubMed Abstract: 

    High-resolution biomacromolecular structure determination is essential to better understand protein function and dynamics. Serial crystallography is an emerging structural biology technique which has fundamental limitations due to either sample volume requirements or immediate access to the competitive X-ray beamtime. Obtaining a high volume of well-diffracting, sufficient-size crystals while mitigating radiation damage remains a critical bottleneck of serial crystallography. As an alternative, we introduce the plate-reader module adapted for using a 72-well Terasaki plate for biomacromolecule structure determination at a convenience of a home X-ray source. We also present the first ambient temperature lysozyme structure determined at the Turkish light source (Turkish DeLight). The complete dataset was collected in 18.5 min with resolution extending to 2.39 Å and 100% completeness. Combined with our previous cryogenic structure (PDB ID: 7Y6A), the ambient temperature structure provides invaluable information about the structural dynamics of the lysozyme. Turkish DeLight provides robust and rapid ambient temperature biomacromolecular structure determination with limited radiation damage.


  • Organizational Affiliation

    Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lysozyme C129Gallus gallusMutation(s): 0 
EC: 3.2.1.17
UniProt
Find proteins for P00698 (Gallus gallus)
Explore P00698 
Go to UniProtKB:  P00698
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00698
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.179 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.03α = 90
b = 79.03β = 90
c = 38.089γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
CrysalisProdata reduction
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Released Date: 2023-03-22 
  • Deposition Author(s): DeMirci, H.

Funding OrganizationLocationGrant Number
Other governmentTurkey118C270

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-22
    Type: Initial release
  • Version 1.1: 2023-10-04
    Changes: Data collection, Database references
  • Version 1.2: 2023-11-29
    Changes: Refinement description
  • Version 1.3: 2024-05-08
    Changes: Database references