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

1WQM

CONTRIBUTION OF HYDROGEN BONDS TO THE CONFORMATIONAL STABILITY OF HUMAN LYSOZYME

• DOI: 10.2210/pdb1WQM/pdb

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


• Deposited: 1998-02-09 Released: 1998-07-01 
• Deposition Author(s): Yamagata, Y., Kubota, M., Sumikawa, Y., Funahashi, J., Fujii, S., Yutani, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.8 Å
• R-Value Work: 0.164 

Literature

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

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

(1998) Biochemistry 37: 9355-9362

• PubMed: 9649316 
• DOI: 10.1021/bi980431i
• Primary Citation of Related Structures:  
  1WQR, 1WQQ, 1WQP, 1WQO, 1WQN


• PubMed Abstract: 
  

The contribution of hydrogen bonds to the conformational stability of human lysozyme was investigated by the combination of calorimetric and X-ray analyses of six Tyr --> Phe mutants. Unfolding Delta G and unfolding Delta H values of the Tyr --> Phe mutant proteins were changed by from +0.3 to -4.0 kJ/mol and from 0 to -16 kJ/mol, respectively, compared to those of the wild-type protein. The net contribution of a hydrogen bond at a specific site to stability (Delta Gwild/HB), considering factors affected by substitutions, was evaluated on the basis of X-ray structures of the mutant proteins. In the present study, one of six mutant proteins was suitable for evaluating the strength of the hydrogen bond. Delta Gwild/HB for the intramolecular hydrogen bond at Tyr124 was evaluated to be 7.5 kJ/mol. Results of the analysis of other mutants also suggest that hydrogen bonds of the hydroxyl group of Tyr, including the hydrogen bond with a water molecule, contribute to the stabilization of the human lysozyme.

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Related Citations: 

• 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
• 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




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Organizational Affiliation: 

Institute for Protein Research, Faculty of Pharmaceutical Sciences, 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 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: 1.8 Å
• R-Value Work: 0.164 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 56.720	α = 90.00
b = 61.120	β = 90.00
c = 33.740	γ = 90.00

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1998-02-09 
• Released Date: 1998-07-01 
• Deposition Author(s): Yamagata, Y., Kubota, M., Sumikawa, Y., Funahashi, J., Fujii, S., Yutani, K.

Revision History 

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