Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 14389.60 
• Atom Count: 1002 
• Residue Count: 129 
• Unique protein chains: 1

5WR9

Crystal structure of hen egg-white lysozyme

• DOI: 10.2210/pdb5WR9/pdb

• Classification: HYDROLASE
• Organism(s): Gallus gallus
• Expression System: Gallus gallus


• Deposited: 2016-12-01 Released: 2017-12-06 
• Deposition Author(s): Sugahara, M., Suzuki, M., Masuda, T., Inoue, S., Nango, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.8 Å
• R-Value Free: 0.184 
• R-Value Work: 0.175 

Literature

Hydroxyethyl cellulose matrix applied to serial crystallography

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

(2017) Sci Rep 7: 703-703

• PubMed: 28386083 
• DOI: 10.1038/s41598-017-00761-0
• Primary Citation of Related Structures:  
  5WRC, 5WRA, 5WR8, 5WRB


• PubMed Abstract: 
  

Serial femtosecond crystallography (SFX) allows structures of proteins to be determined at room temperature with minimal radiation damage. A highly viscous matrix acts as a crystal carrier for serial sample loading at a low flow rate that enables the determination of the structure, while requiring consumption of less than 1 mg of the sample. However, a reliable and versatile carrier matrix for a wide variety of protein samples is still elusive. Here we introduce a hydroxyethyl cellulose-matrix carrier, to determine the structure of three proteins. The de novo structure determination of proteinase K from single-wavelength anomalous diffraction (SAD) by utilizing the anomalous signal of the praseodymium atom was demonstrated using 3,000 diffraction images.

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Organizational Affiliation: 

RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan. [e-mail].

Macromolecules

Find similar proteins by: Sequence  |  Structure

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

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 Free: 0.184 
• R-Value Work: 0.175 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length (Å)	Angle (°)
a = 80.000	α = 90.00
b = 80.000	β = 90.00
c = 38.400	γ = 90.00

Software Package:

Software Name	Purpose
CrystFEL	data processing
Coot	model building
CrystFEL	data scaling
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2016-12-01 
• Released Date: 2017-12-06 
• Deposition Author(s): Sugahara, M., Suzuki, M., Masuda, T., Inoue, S., Nango, E.

Revision History 

• Version 1.0: 2017-12-06
  Type: Initial release
• Version 1.1: 2018-01-24
  Type: Data collection