2HED

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Work: 0.157 

wwPDB Validation 3D Report Full Report


This is version 1.3 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:  

  • 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 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


    Organizational Affiliation

    Institute for Protein Research, Osaka University, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LYSOZYME
A
130Homo sapiensMutation(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
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Work: 0.157 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 56.970α = 90.00
b = 60.360β = 90.00
c = 33.510γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
X-PLORphasing
X-PLORmodel building
PROCESSdata reduction
PROCESSdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-01-14
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other