4RDS | pdb_00004rds

Lysozyme crystallized with red food coloring dye

• PDB DOI: https://doi.org/10.2210/pdb4RDS/pdb

• Classification: HYDROLASE
• Organism(s): Gallus gallus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-09-19 Released: 2015-01-14 
• Deposition Author(s): Irimpan, E.M., Mathews, I.I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.23 Å
• R-Value Free: 
  0.173 (Depositor), 0.188 (DCC) 
• R-Value Work: 
  0.153 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.154 (Depositor) 

Starting Model: experimental

Literature

Lysozyme crystallized with red food coloring dye.

Irimpan, E.M., Mathews, I.I.

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: 14.63 kDa 
• Atom Count: 1,142 
• 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  Gene Names: LYZ EC: 3.2.1.17
UniProt
Find proteins for P00698 (Gallus gallus) Explore P00698  Go to UniProtKB:  P00698

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	B [auth A], C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	G [auth A], H [auth A], I [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	D [auth A], E [auth A], F [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.23 Å
• R-Value Free:  0.173 (Depositor), 0.188 (DCC) 
• R-Value Work:  0.153 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.154 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.89	α = 90
b = 78.89	β = 90
c = 36.84	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
MOLREP	phasing
REFMAC	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-01-14 
Deposition Author(s): Irimpan, E.M., Mathews, I.I.

Revision History  

• Version 1.0: 2015-01-14
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-11-06
  Changes: Structure summary