Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 14.72 kDa 
• Atom Count: 1237 
• Modelled Residue Count: 130 
• Deposited Residue Count: 130 
• Unique protein chains: 1

1OUI

CONTRIBUTION OF HYDROPHOBIC RESIDUES TO THE STABILITY OF HUMAN LYSOZYME: X-RAY STRUCTURE OF THE V93A MUTANT

• PDB DOI: 10.2210/pdb1OUI/pdb

• Classification: HYDROLASE (O-GLYCOSYL)
• Organism(s): Homo sapiens
• Expression System: Saccharomyces cerevisiae
• Mutation(s): Yes 


• Deposited: 1996-08-23 Released: 1997-02-12 
• Deposition Author(s): Takano, K., Yamagata, Y., Fujii, S., Yutani, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Work: 0.159 
• R-Value Observed: 0.159 

Literature

Contribution of the hydrophobic effect to the stability of human lysozyme: calorimetric studies and X-ray structural analyses of the nine valine to alanine mutants.

Takano, K., Yamagata, Y., Fujii, S., Yutani, K.

(1997) Biochemistry 36: 688-698

• PubMed: 9020766 
• DOI: 10.1021/bi9621829
• Primary Citation of Related Structures:  
  1OUB, 1OUC, 1OUD, 1OUE, 1OUF, 1OUG, 1OUH, 1OUI, 1OUJ


• PubMed Abstract: 
  

To clarify the contribution of the hydrophobic effect to the conformational stability of human lysozyme, a series of Val to Ala mutants were constructed. The thermodynamic parameters for the denaturation of these nine mutant proteins were determined using differential scanning calorimetry (DSC), and the crystal structures were solved at high resolution. The denaturation Gibbs energy (delta delta G) and enthalpy (delta delta H) values of the mutant proteins ranged from +2.2 to- 6.3 kJ/mol and from +7 to -17 kJ/mol, respectively. The structural analyses showed that the mutation site and/or the residues around it in some proteins shifted toward the created cavity, and the substitutions affected not only the mutations site but also other parts far from the site, although the structural changes were not as great. Correlation between the changes in the thermodynamic parameters and the structural features of mutant proteins was examined, including the five Ile to Val mutant human lysozymes [Takano et al. (1995) J. Mol. Biol. 254, 62-76]. There was no simple general correlation between delta delta G and the changes in hydrophobic surface area exposed upon denaturation (delta delta ASAHP). We found only a new correlation between the delta delta G and delta delta ASAHP of all of the hydrophobic residues if the effect of the secondary structure propensity was taken into account.

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Related Citations: 

• Contribution of Hydrophobic Residues to the Stability of Human Lysozyme: Calorimetric Studies and X-Ray Structural Analysis of the Five Isoleucine to Valine Mutants
  Takano, K., Ogasahara, K., Kaneda, H., Yamagata, Y., Fujii, S., Kanaya, E., Kikuchi, M., Oobatake, M., Yutani, K.
  (1995) J Mol Biol 254: 62

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Organizational Affiliation: 

Institute for Protein Research, Osaka University, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LYSOZYME	A	130	Homo sapiens	Mutation(s): 1  Gene Names: HUMAN LYSOZYME WITH VAL 93 REP, LYZ, LZM EC: 3.2.1.17
UniProt & NIH Common Fund Data Resources
Find proteins for P61626 (Homo sapiens) Explore P61626  Go to UniProtKB:  P61626
PHAROS:  P61626

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA	B [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Work: 0.159 
• R-Value Observed: 0.159 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.65	α = 90
b = 60.85	β = 90
c = 33.86	γ = 90

Software Package:

Software Name	Purpose
RIGAKU	data collection
RIGAKU	data reduction
X-PLOR	model building
X-PLOR	refinement
RIGAKU	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1996-08-23 
• Released Date: 1997-02-12 
Deposition Author(s): Takano, K., Yamagata, Y., Fujii, S., Yutani, K.

Revision History  

• Version 1.0: 1997-02-12
  Type: Initial release
  
• Version 1.1: 2008-03-04
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-11-29
  Changes: Derived calculations, Other
• Version 1.4: 2021-11-03
  Changes: Database references, Derived calculations