1IOT

STABILIZATION OF HEN EGG WHITE LYSOZYME BY A CAVITY-FILLING MUTATION

• PDB DOI: https://doi.org/10.2210/pdb1IOT/pdb

• Classification: HYDROLASE
• Organism(s): Gallus gallus
• Expression System: Saccharomyces cerevisiae
• Mutation(s): Yes 


• Deposited: 2001-03-28 Released: 2001-04-11 
• Deposition Author(s): Ohmura, T., Ueda, T., Ootsuka, K., Saito, M., Imoto, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Observed: 0.171 

Literature

Stabilization of hen egg white lysozyme by a cavity-filling mutation.

Ohmura, T., Ueda, T., Ootsuka, K., Saito, M., Imoto, T.

(2001) Protein Sci 10: 313-320

• PubMed: 11266617 
• DOI: https://doi.org/10.1110/ps.37401
• Primary Citation of Related Structures:  
  1IOQ, 1IOR, 1IOS, 1IOT


• PubMed Abstract: 
  

  Stabilization of a protein using cavity-filling strategy has hardly been successful because of unfavorable van der Waals contacts. We succeeded in stabilizing lysozymes by cavity-filling mutations. The mutations were checked by a simple energy minimization in advance. It was shown clearly that the sum of free energy change caused by the hydrophobicity and the cavity size was correlated very well with protein stability. We also considered the aromatic-aromatic interaction. It is reconfirmed that the cavity-filling mutation in a hydrophobic core is a very useful method to stabilize a protein when the mutation candidate is selected carefully.

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Organizational Affiliation: 

Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka 812-8582, Japan.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 14.31 kDa 
• Atom Count: 1,073 
• 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): 1  EC: 3.2.1.17
UniProt
Find proteins for P00698 (Gallus gallus) Explore P00698  Go to UniProtKB:  P00698

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Observed: 0.171 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.16	α = 90
b = 79.16	β = 90
c = 37.98	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-04-11 
Deposition Author(s): Ohmura, T., Ueda, T., Ootsuka, K., Saito, M., Imoto, T.

Revision History  

• Version 1.0: 2001-04-11
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-04
  Changes: Refinement description
• Version 1.4: 2021-11-10
  Changes: Database references
• Version 1.5: 2023-12-27
  Changes: Data collection
• Version 1.6: 2024-11-06
  Changes: Structure summary