7FGV

H/D exchanged Hen egg-white lysozyme denatured in heat condition and refolded in solution

• PDB DOI: https://doi.org/10.2210/pdb7FGV/pdb

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


• Deposited: 2021-07-28 Released: 2022-02-09 
• Deposition Author(s): Kita, A., Morimoto, Y.
• Funding Organization(s): Ministry of Education, Culture, Sports, Science and Technology (Japan)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.182 
• R-Value Work: 0.141 
• R-Value Observed: 0.143 

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• Method: NEUTRON DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.250 
• R-Value Work: 0.224 

Literature

Hydrogen/Deuterium Exchange Behavior During Denaturing/Refolding Processes Determined in Tetragonal Hen Egg-White Lysozyme Crystals.

Kita, A., Morimoto, Y.

(2022) Mol Biotechnol 64: 590-597

• PubMed: 35028904 
• DOI: https://doi.org/10.1007/s12033-022-00447-7
• Primary Citation of Related Structures:  
  7FG8, 7FGU, 7FGV


• PubMed Abstract: 
  

  The hydrogen/deuterium (H/D) exchange of main-chain amide hydrogens in the protein that denatured and refolded in deuterated solvent is considered to contain the traces of hydrogen bond cleavages or the exposure to solvent of the buried part of the protein during the denaturing and refolding (denaturing/refolding) processes. Here, we report the H/D exchange behaviors in hen egg-white lysozymes denatured under acidic conditions, basic conditions, and thermal conditions and then refolded in deuterated solvents, using crystallographic methods. The results indicate that the space containing the Trp28 side chain was hardly exposed to the solvent in acidic conditions, but exposed under basic or heated conditions. Moreover, the β-bridges between Tyr53 and Ile58 in strands β2 and β3, which are in a highly conserved region, show some tolerance to changes in pD. The results indicate that crystallographic method is one of the powerful tools to analyze the denaturing/refolding processes of proteins.

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Organizational Affiliation: 

Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Sen-nan, Osaka, 590-0494, Japan.

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: 1,085 
• Modelled 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  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 (Subject of Investigation/LOI)	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA (Subject of Investigation/LOI)	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.182 
• R-Value Work: 0.141 
• R-Value Observed: 0.143 
• Space Group: P 4₃ 2₁ 2

• Method: NEUTRON DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.250 
• R-Value Work: 0.224 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.15	α = 90
b = 79.15	β = 90
c = 37.902	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-02-09 
Deposition Author(s): Kita, A., Morimoto, Y.

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Funding Organization	Location	Grant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	--

Revision History  

• Version 1.0: 2022-02-09
  Type: Initial release
  
• Version 1.1: 2022-05-11
  Changes: Database references
• Version 1.2: 2024-04-03
  Changes: Data collection, Refinement description