4YOP

CRYSTAL STRUCTURE OF HEN EGG-WHITE LYSOZYME

• PDB DOI: https://doi.org/10.2210/pdb4YOP/pdb

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


• Deposited: 2015-03-12 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: 0.191 
• R-Value Work: 0.157 
• R-Value Observed: 0.161 

Literature

Native sulfur/chlorine SAD phasing for serial femtosecond crystallography

Nakane, T., Song, C., Suzuki, M., Nango, E., Kobayashi, J., Masuda, T., Inoue, S., Mizohata, E., Nakatsu, T., Tanaka, T., Tanaka, R., Shimamura, T., Tono, K., Joti, Y., Kameshima, T., Hatsui, T., Yabashi, M., Nureki, O., Iwata, S., Sugahara, M.

(2015) Acta Crystallogr D Biol Crystallogr 71: 2519-2525

• PubMed: 26627659 
• DOI: https://doi.org/10.1107/S139900471501857X
• Primary Citation of Related Structures:  
  4YOP


• PubMed Abstract: 
  

  Serial femtosecond crystallography (SFX) allows structures to be determined with minimal radiation damage. However, phasing native crystals in SFX is not very common. Here, the structure determination of native lysozyme from single-wavelength anomalous diffraction (SAD) by utilizing the anomalous signal of sulfur and chlorine at a wavelength of 1.77 Å is successfully demonstrated. This sulfur SAD method can be applied to a wide range of proteins, which will improve the determination of native crystal structures.

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Organizational Affiliation: 

Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.

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: 1,044 
• Modelled 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: 0.191 
• R-Value Work: 0.157 
• R-Value Observed: 0.161 
• Space Group: P 4₃ 2₁ 2
• Diffraction Data: https://doi.org/10.11577/1236754

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: 2023-09-06
  Changes: Data collection, Database references
• Version 1.3: 2024-10-09
  Changes: Structure summary