2HEB

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Work: 0.124 
  • R-Value Observed: 0.124 

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This is version 1.2 of the entry. See complete history. 


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

  • DOI: 10.1006/jmbi.1997.1365
  • Primary Citation of Related Structures:  
    2HEF, 2HEE, 2HED, 2HEC, 2HEB, 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 denatu ...

    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.

    Related Citations: 
    • 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
    • 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
    Organizational Affiliation: 

    Institute for Protein Research, Osaka University, Japan.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
LYSOZYMEA130Homo sapiensMutation(s): 1 
Gene Names: HUMAN LYSOZYME WITH ILE 23 REP, LYZ, LZM
EC: 3.2.1.17
Find proteins for P61626 (Homo sapiens)
Explore P61626 
Go to UniProtKB:  P61626
NIH Common Fund Data Resources
PHAROS  P61626
GTEx  ENSG00000090382
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA
Download Ideal Coordinates CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Work: 0.124 
  • R-Value Observed: 0.124 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.8α = 90
b = 61.22β = 90
c = 33.76γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

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