7BHK

Crystal structure of hen egg white lysozyme using drop-on-drop SFX method.

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

  • Deposited: 2021-01-11 Released: 2021-07-21 
  • Deposition Author(s): Butryn, A., Orville, A.M.
  • Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC), Wellcome Trust, Royal Society

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

An on-demand, drop-on-drop method for studying enzyme catalysis by serial crystallography.

Butryn, A.Simon, P.S.Aller, P.Hinchliffe, P.Massad, R.N.Leen, G.Tooke, C.L.Bogacz, I.Kim, I.S.Bhowmick, A.Brewster, A.S.Devenish, N.E.Brem, J.Kamps, J.J.A.G.Lang, P.A.Rabe, P.Axford, D.Beale, J.H.Davy, B.Ebrahim, A.Orlans, J.Storm, S.L.S.Zhou, T.Owada, S.Tanaka, R.Tono, K.Evans, G.Owen, R.L.Houle, F.A.Sauter, N.K.Schofield, C.J.Spencer, J.Yachandra, V.K.Yano, J.Kern, J.F.Orville, A.M.

(2021) Nat Commun 12: 4461-4461

  • DOI: https://doi.org/10.1038/s41467-021-24757-7
  • Primary Citation of Related Structures:  
    7BH3, 7BH4, 7BH5, 7BH6, 7BH7, 7BHK, 7BHL, 7BHM, 7BHN

  • PubMed Abstract: 

    Serial femtosecond crystallography has opened up many new opportunities in structural biology. In recent years, several approaches employing light-inducible systems have emerged to enable time-resolved experiments that reveal protein dynamics at high atomic and temporal resolutions. However, very few enzymes are light-dependent, whereas macromolecules requiring ligand diffusion into an active site are ubiquitous. In this work we present a drop-on-drop sample delivery system that enables the study of enzyme-catalyzed reactions in microcrystal slurries. The system delivers ligand solutions in bursts of multiple picoliter-sized drops on top of a larger crystal-containing drop inducing turbulent mixing and transports the mixture to the X-ray interaction region with temporal resolution. We demonstrate mixing using fluorescent dyes, numerical simulations and time-resolved serial femtosecond crystallography, which show rapid ligand diffusion through microdroplets. The drop-on-drop method has the potential to be widely applicable to serial crystallography studies, particularly of enzyme reactions with small molecule substrates.


  • Organizational Affiliation

    Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lysozyme129Gallus 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: 1.45 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.804α = 90
b = 78.804β = 90
c = 38.002γ = 90
Software Package:
Software NamePurpose
cctbx.xfeldata processing
PHASERphasing
PHENIXrefinement

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)United Kingdom102593
Wellcome TrustUnited Kingdom210734/Z/18/Z
Royal SocietyUnited Kingdom182017

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-21
    Type: Initial release
  • Version 1.1: 2021-08-04
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Database references, Refinement description