7KNK | pdb_00007knk

STRUCTURE OF HEN EGG-WHITE LYSOZYME grown with Kitchen recipe

• PDB DOI: https://doi.org/10.2210/pdb7KNK/pdb

• Classification: HYDROLASE
• Organism(s): Gallus gallus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-11-04 Released: 2021-12-01 
• Deposition Author(s): Fox, A.L., Mathews, I.I.
• Funding Organization(s): Department of Energy (DOE, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 
  0.213 (Depositor), 0.222 (DCC) 
• R-Value Work: 
  0.157 (Depositor), 0.157 (DCC) 
• R-Value Observed: 
  0.160 (Depositor) 

Starting Model: experimental

Literature

Remote laboratory training for high school students: grocery store based hands-on project in protein crystallography.

Fox, A.L., Teteris, A.R., Mathews, I.I.

(2023) J Appl Crystallogr 56: 1557-1568

• PubMed: 37791367 
• DOI: https://doi.org/10.1107/S1600576723006805
• Primary Citation Related Structures: 
  7KNK


• PubMed Abstract: 
  

  The COVID-19 pandemic measures forced students to stay home and confined them to remote learning. This had a large impact on laboratory experiments, which are often impossible to complete from home. This article is a resource for instructors/educators to introduce the topic of structural biology and crystallographic methods. The main focus is to describe a hands-on crystallization laboratory exercise that can be carried out remotely at home with safe household products. X-ray crystallography is a vital technique for determining protein structure and function. This information can be used to understand fundamental biological processes and to help in the design of life-saving medications. Here, a method was developed to teach crystallography using reagents and equipment that can be found in grocery stores. The steps involved in a crystallography experiment are detailed with links and references to additional resources.

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Organizational Affiliation: 
• Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 14.39 kDa 
• Atom Count: 1,136 
• Modeled Residue Count: 129 
• Deposited Residue Count: 129 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysozyme C	A	129	Gallus gallus	Mutation(s): 0  Gene Names: LYZ EC: 3.2.1.17
UniProt
Find proteins for P00698 (Gallus gallus) Explore P00698  Go to UniProtKB:  P00698

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free:  0.213 (Depositor), 0.222 (DCC) 
• R-Value Work:  0.157 (Depositor), 0.157 (DCC) 
• R-Value Observed: 0.160 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.483	α = 90
b = 78.483	β = 90
c = 37.104	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-12-01 
Deposition Author(s): Fox, A.L., Mathews, I.I.

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Funding Organization	Location	Grant Number
Department of Energy (DOE, United States)	United States	DE-AC02-76SF00515
Department of Energy (DOE, United States)	United States	SULI program

Revision History  

• Version 1.0: 2021-12-01
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description
• Version 1.2: 2024-11-20
  Changes: Structure summary
• Version 1.3: 2025-02-05
  Changes: Database references