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: 14798.59 
• Atom Count: 1031 
• Residue Count: 130 
• Unique protein chains: 1

1B5V

CONTRIBUTION OF HYDROGEN BONDS TO THE CONFORMATIONAL STABILITY OF HUMAN LYSOZYME: CALORIMETRY AND X-RAY ANALYSIS OF SIX SER->ALA MUTANTS

• DOI: 10.2210/pdb1B5V/pdb

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


• Deposited: 1999-01-11 Released: 1999-01-20 
• Deposition Author(s): Takano, K., Yamagata, Y., Kubota, M., Funahashi, J., Fujii, S., Yutani, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.17 Å
• R-Value Work: 0.161 

Literature

Contribution of hydrogen bonds to the conformational stability of human lysozyme: calorimetry and X-ray analysis of six Ser --> Ala mutants.

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

(1999) Biochemistry 38: 6623-6629

• PubMed: 10350481 
• DOI: 10.1021/bi9901228
• Primary Citation of Related Structures:  
  1B5Z, 1B5Y, 1B5X, 1B5W, 1B5U


• PubMed Abstract: 
  

To further examine the contribution of hydrogen bonds to the conformational stability of the human lysozyme, six Ser to Ala mutants were constructed. The thermodynamic parameters for denaturation of these six Ser mutant proteins were investigated by differential scanning calorimetry (DSC), and the crystal structures were determined by X-ray analysis. The denaturation Gibbs energy (DeltaG) of the Ser mutant proteins was changed from 2.0 to -5.7 kJ/mol, compared to that of the wild-type protein. With an analysis in which some factors that affected the stability due to mutation were considered, the contribution of hydrogen bonds to the stability (Delta DeltaGHB) was extracted on the basis of the structures of the mutant proteins. The results showed that hydrogen bonds between protein atoms and between a protein atom and a water bound with the protein molecule favorably contribute to the protein stability. The net contribution of one intramolecular hydrogen bond to protein stability (DeltaGHB) was 8.9 +/- 2.6 kJ/mol on average. However, the contribution to the protein stability of hydrogen bonds between a protein atom and a bound water molecule was smaller than that for a bond between protein atoms.

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Related Citations: 

• Contribution of Hydrophobic Effect Valine Mutants 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.,Ogasawaha, K.,Kaneda, H.,Yamagata, Y.,Fujii, S.,Kanaya, E.,Kikuchi, M.,Oobatake, M.,Yutani, K.
  (1995) J.Mol.Biol. 254: 62
• Contribution of Hydrogen Bonds to the Conformational Stability of Human Lysozyme: Calorimetry and X-Ray Analysis of Six Tyr->Phe Mutants
  Yamagata, Y.,Kubota, M.,Sumikawa, Y.,Funahashi, J.,Takano, K.,Fujii, S.,Yutani, K.
  (1998) Biochemistry 37: 9355
• A General Rule for the Relationship between Hydrophobic Effect and Conformational Stability of a Protein: Stability and Structure of a Series of Hydrophobic Mutants of Human Lysozyme
  Takano, K.,Yamagata, Y.,Yutani, K.
  (1998) J.Mol.Biol. 280: 749
• The Structure, Stability, and Folding Process of Amyloidogenic Mutant Human Lysozyme
  Funahashi, J.,Takano, K.,Ogasahara, K.,Yamagata, Y.,Yutani, K.
  (1996) J.Biochem.(TOKYO) 120: 1216
• Contribution of Water Molecules in the Interior of a Protein to the Conformational Stability
  Takano, K.,Funahasihi, J.F.,Yamagata, Y.,Fujii, S.,Yutani, K.
  (1997) J.Mol.Biol. 274: 132




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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
PROTEIN (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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
NA	A	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N
CL	A	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.17 Å
• R-Value Work: 0.161 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 56.690	α = 90.00
b = 60.790	β = 90.00
c = 33.680	γ = 90.00

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1999-01-11 
• Released Date: 1999-01-20 
• Deposition Author(s): Takano, K., Yamagata, Y., Kubota, M., Funahashi, J., Fujii, S., Yutani, K.

Revision History 

• Version 1.0: 1999-01-20
  Type: Initial release
• Version 1.1: 2008-04-27
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance