4YM8 | pdb_00004ym8

Crystal structure of hen egg-white lysozyme

• PDB DOI: https://doi.org/10.2210/pdb4YM8/pdb

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


• Deposited: 2015-03-06 Released: 2015-12-23 
• Deposition Author(s): Sugahara, M., Nakane, T., Suzuki, M., Nango, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.179 (Depositor), 0.177 (DCC) 
• R-Value Work: 
  0.161 (Depositor), 0.168 (DCC) 
• R-Value Observed: 
  0.163 (Depositor) 

Literature

Crystal structure of hen egg-white lysozyme

Sugahara, M., Nakane, T., Suzuki, M., Nango, E.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 14.39 kDa 
• Atom Count: 1,041 
• Modeled Residue Count: 129 
• Deposited Residue Count: 129 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysozyme C	A	129	Gallus gallus	Mutation(s): 0  EC: 3.2.1.17
UniProt
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	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	B [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.179 (Depositor), 0.177 (DCC) 
• R-Value Work:  0.161 (Depositor), 0.168 (DCC) 
• R-Value Observed: 0.163 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.2	α = 90
b = 79.2	β = 90
c = 37.9	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SHELXDE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-12-23 
Deposition Author(s): Sugahara, M., Nakane, T., Suzuki, M., Nango, E.

Revision History  

• Version 1.0: 2015-12-23
  Type: Initial release
  
• Version 1.1: 2018-01-24
  Changes: Data collection, Derived calculations
• Version 1.2: 2024-10-16
  Changes: Data collection, Database references, Structure summary