Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 14.50 kDa 
• Atom Count: 1202 
• Residue Count: 129 
• Unique protein chains: 1

4WM5

High pressure protein crystallography of hen egg white lysozyme at 890 MPa

• DOI: 10.2210/pdb4WM5/pdb

• Classification: HYDROLASE
• Organism(s): Gallus gallus
• Mutation(s): No 


• Deposited: 2014-10-08 Released: 2015-04-08 
• Deposition Author(s): Yamada, H., Nagae, T., Watanabe, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.217 
• R-Value Work: 0.163 
• R-Value Observed: 0.166 

Literature

High-pressure protein crystallography of hen egg-white lysozyme

Yamada, H., Nagae, T., Watanabe, N.

(2015) Acta Crystallogr D Biol Crystallogr 71: 742-753

• PubMed: 25849385 
• DOI: 10.1107/S1399004715000292
• Primary Citation of Related Structures:  
  4WLD, 4WLY, 4WM2, 4WM3, 4WM4, 4WLT, 4WM5, 4WM6, 4WLX, 4WM1


• PubMed Abstract: 
  

Crystal structures of hen egg-white lysozyme (HEWL) determined under pressures ranging from ambient pressure to 950 MPa are presented. From 0.1 to 710 MPa, the molecular and internal cavity volumes are monotonically compressed. However, from 710 to 890 MPa the internal cavity volume remains almost constant. Moreover, as the pressure increases to 950 MPa, the tetragonal crystal of HEWL undergoes a phase transition from P43212 to P43. Under high pressure, the crystal structure of the enzyme undergoes several local and global changes accompanied by changes in hydration structure. For example, water molecules penetrate into an internal cavity neighbouring the active site and induce an alternate conformation of one of the catalytic residues, Glu35. These phenomena have not been detected by conventional X-ray crystal structure analysis and might play an important role in the catalytic activity of HEWL.

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Organizational Affiliation: 

Department of Biotechnology, Graduate School of Engineering, Nagoya University, Chikusa, Nagoya, Aichi 464-8603, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysozyme C	A	129	Gallus gallus	Mutation(s): 0  Gene Names: LYZ EC: 3.2.1.17
Find proteins for P00698 (Gallus gallus) Explore P00698  Go to UniProtKB:  P00698

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: 1.60 Å
• R-Value Free: 0.217 
• R-Value Work: 0.163 
• R-Value Observed: 0.166 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.203	α = 90
b = 76.203	β = 90
c = 37.643	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-10-08 
• Released Date: 2015-04-08 
Deposition Author(s): Yamada, H., Nagae, T., Watanabe, N.

Revision History 

• Version 1.0: 2015-04-08
  Type: Initial release
  
• Version 1.1: 2015-04-22
  Changes: Database references
• Version 1.2: 2020-02-05
  Changes: Data collection, Derived calculations, Other, Source and taxonomy