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 30DB | pdb_000030db

Hen egg white lysozyme complexed with PEG, ACT, and CL (in meso crystallization)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 
    0.206 (Depositor), 0.206 (DCC) 
  • R-Value Work: 
    0.177 (Depositor), 0.177 (DCC) 
  • R-Value Observed: 
    0.179 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 30DB

This is version 1.0 of the entry. See complete history. 

Literature

A low-cost, portable polarizing digital light microscope for monitoring crystal growth and for crystal harvesting.

Kennedy, S., Huang, R.H., Witek, W., Krawinski, P., Boland, C., Yang, L., Leddy, N., Caffrey, M.

(2026) J Appl Crystallogr 59: 1693-1706

  • DOI: https://doi.org/10.1107/S1600576726007880
  • Primary Citation Related Structures: 
    30DA, 30DB

  • PubMed Abstract: 

    Motivated by the need for a convenient way to demonstrate the growth of crystals in glass plates by the lipid cubic phase method at crystallization workshops and courses, we developed a lightweight, portable, compact and inexpensive digital microscope device. The device is built around hand-held Wi-Fi and hardwired digital microscopes that are available commercially at low cost and that can use cell phones and personal computers for imaging without the need for unwieldy eyepieces. The device provides illumination from above and below the crystallization plate over a range of brightness levels. It can be used with regular white light and with polarized light to detect birefringent crystals. While not the focus of this study, the new device has been shown to also work with batch and vapour-diffusion plates. Remote monitoring of crystallization plates in a cold cabinet or walk-in refrigerator at 4 °C is possible with the Wi-Fi microscope. Crystals grown in lipid cubic phase and vapour-diffusion crystallization plates were harvested with the aid of the new device and used for diffraction data collection, leading to structure determination at high resolution. Most parts of the device were 3D printed in polylactic acid plastic. The corresponding STL files, included as part of this publication, can be used to make replicates of the current microscope and to produce bespoke devices suited to the specific needs of the user. We envision using the new device for outreach activities at primary, secondary and third-level schools, and at science fairs in support of the citizen scientist. Relatedly, in this study examples are included of recorded images of plant and animal tissue sections. One reveals birefringent materials in a tomato leaf. Another shows optically active crystals of calcium oxalate in onion tunic tissue.


  • Organizational Affiliation: 
    • School of Medicine, Trinity College, Dublin 2, D02 R590, Ireland.

Macromolecule Content 

  • Total Structure Weight: 14.81 kDa 
  • Atom Count: 1,149 
  • Modeled Residue Count: 129 
  • Deposited Residue Count: 129 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PEG

Query on PEG



Download:Ideal Coordinates CCD File
B [auth A],
C [auth A],
E [auth A]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
ACT

Query on ACT



Download:Ideal Coordinates CCD File
D [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL

Query on CL



Download:Ideal Coordinates CCD File
F [auth A],
G [auth A],
H [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free:  0.206 (Depositor), 0.206 (DCC) 
  • R-Value Work:  0.177 (Depositor), 0.177 (DCC) 
  • R-Value Observed: 0.179 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.563α = 90
b = 77.563β = 90
c = 38.624γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Science Foundation IrelandIreland--

Revision History  (Full details and data files)

  • Version 1.0: 2026-10-28
    Type: Initial release