8RLG

Perdeuterated hen egg-white lysozyme at room temperature


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.07 Å
  • R-Value Free: 
    0.129 (Depositor) 
  • R-Value Work: 
    0.096 (Depositor), 0.090 (DCC) 

Starting Model: experimental
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Literature

Structure and dynamics of the active site of hen egg-white lysozyme from atomic resolution neutron crystallography.

Ramos, J.Laux, V.Mason, S.A.Lemee, M.H.Bowler, M.W.Diederichs, K.Haertlein, M.Forsyth, V.T.Mossou, E.Larsen, S.Langkilde, A.E.

(2025) Structure 33: 136-148.e3

  • DOI: https://doi.org/10.1016/j.str.2024.10.030
  • Primary Citation of Related Structures:  
    8RLF, 8RLG, 8RLH, 8RLI

  • PubMed Abstract: 

    Hen egg-white lysozyme (HEWL) is a widely used model protein in crystallographic studies and its enzymatic mechanism has been extensively investigated for decades. Despite this, the interaction between the reaction intermediate and the catalytic Asp52, as well as the orientation of Asn44 and Asn46 side chains, remain ambiguous. Here, we report the crystal structures of perdeuterated HEWL and D 2 O buffer-exchanged HEWL from 0.91 and 1.1 Å resolution neutron diffraction data, respectively. These structures were obtained at room temperature and acidic pH, representing the active state of the enzyme. The unambiguous assignment of hydrogen positions based on the neutron scattering length density maps elucidates the roles of Asn44, Asn46, Asn59, and nearby water molecules in the stabilization of Asp52. Additionally, the identification of hydrogen positions reveals unique details of lysozyme's folding, hydrogen (H)/deuterium (D) exchange, and side chain disorder.


  • Organizational Affiliation

    Institut Laue-Langevin, 71 avenue des Martyrs CS20156, 38042 Grenoble Cedex, France; Partnership for Structural Biology (PSB), 71 avenue des Martyrs CS 90181, 38042 Grenoble Cedex, France; Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark. Electronic address: ramosj@mbg.au.dk.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lysozyme C130Gallus gallusMutation(s): 0 
Gene Names: LYZ
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
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NO3
Query on NO3

Download Ideal Coordinates CCD File 
B [auth A]
C [auth A]
D [auth A]
E [auth A]
F [auth A]
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
K [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.07 Å
  • R-Value Free:  0.129 (Depositor) 
  • R-Value Work:  0.096 (Depositor), 0.090 (DCC) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 27.15α = 88.75
b = 31.76β = 71.71
c = 34.07γ = 67.99
Software Package:
Software NamePurpose
SHELXrefinement
XSCALEdata scaling
XDSdata reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-06
    Type: Initial release
  • Version 1.1: 2025-01-29
    Changes: Database references