Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 14701.60 
• Atom Count: 1027 
• Residue Count: 130 
• Unique protein chains: 1

2HEB

CONTRIBUTION OF WATER MOLECULES IN THE INTERIOR OF A PROTEIN TO THE CONFORMATIONAL STABILITY

• DOI: 10.2210/pdb2HEB/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Saccharomyces cerevisiae
• Mutation(s): 1 


• Deposited: 1997-09-16 Released: 1998-01-28 
• Deposition Author(s): Takano, K., Funahashi, J., Yamagata, Y., Fujii, S., Yutani, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.2 Å
• R-Value Work: 0.124 

Literature

Contribution of water molecules in the interior of a protein to the conformational stability.

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

(1997) J.Mol.Biol. 274: 132-142

• PubMed: 9398521 
• DOI: 10.1006/jmbi.1997.1365
• Primary Citation of Related Structures:  
  2HEF, 2HEE, 2HED, 2HEC, 2HEA


• PubMed Abstract: 
  

Water molecules frequently occur in the interior of globular proteins. To elucidate the contribution of buried water molecules to the conformational stability of a protein, we examined the crystal structures and the thermodynamic parameters of denaturation of six Ile to Ala/Gly mutant human lysozymes, in which a cavity is created at each mutation site by the substitution of a smaller side-chain for a larger one. One or two ordered water molecules were found in the cavities created in some mutants (I106A, I59A and I59G). The cavity volumes for these three mutants were bigger than those that remained empty in the other mutants. The stability of the mutant proteins with the newly introduced water molecules was about 8 kJ/mol higher than that expected from the change in hydrophobic surface area (DeltaDeltaASAHP) exposed upon denaturation. It was concluded that a water molecule in a cavity created in the interior of a protein contributes favorably to the stability.

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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
• 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




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Organizational Affiliation: 

Institute for Protein Research, Osaka University, Japan.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
LYSOZYME	A	130	Homo sapiens	Mutation(s): 1  Gene Names: LYZ (LZM) EC: 3.2.1.17
Find proteins for P61626 (Homo sapiens) Go to Gene View: LYZ Go to UniProtKB:  P61626

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
NA	A	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.2 Å
• R-Value Work: 0.124 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 56.800	α = 90.00
b = 61.220	β = 90.00
c = 33.760	γ = 90.00

Software Package:

Software Name	Purpose
X-PLOR	phasing
X-PLOR	model building
DENZO	data reduction
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1997-09-16 
• Released Date: 1998-01-28 
• Deposition Author(s): Takano, K., Funahashi, J., Yamagata, Y., Fujii, S., Yutani, K.

Revision History 

• Version 1.0: 1998-01-28
  Type: Initial release
• Version 1.1: 2008-03-24
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance