Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 14.80 kDa 
• Atom Count: 1232 
• 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): Yes 


• 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: 1.80 Å
• R-Value Work: 0.164 
• R-Value Observed: 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
• Structures With Same Primary Citation


• 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 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 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 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

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 UniProtKB:  P61626
NIH Common Fund Data Resources
PHAROS  P61626 GTEx  ENSG00000090382

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Work: 0.164 
• R-Value Observed: 0.164 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.72	α = 90
b = 61.12	β = 90
c = 33.74	γ = 90

Software Package:

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

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
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance