Biological Assembly 1  

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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: 14192.32 
• Atom Count: 1019 
• Residue Count: 127 
• Unique protein chains: 1

6FA0

Lysozyme crystallized in presence of 100 mM ammonium sulphate at pH 4.5

• DOI: 10.2210/pdb6FA0/pdb

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


• Deposited: 2017-12-15 Released: 2018-05-09 
• Deposition Author(s): Camara-Artigas, A.
• Funding Organization(s): Spanish Ministry of Economy and Competitiveness 

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.3 Å
• R-Value Free: 0.188 
• R-Value Work: 0.151 

Literature

Orthorhombic lysozyme crystallization at acidic pH values driven by phosphate binding.

Plaza-Garrido, M., Salinas-Garcia, M.C., Camara-Artigas, A.

(2018) Acta Crystallogr D Struct Biol 74: 480-489

• PubMed: 29717719 
• DOI: 10.1107/S205979831800517X
• Primary Citation of Related Structures:  
  6F9Z, 6F9Y, 6F9X, 6F1R, 6F1P, 6F1O, 6F1M, 6F1L


• PubMed Abstract: 
  

The structure of orthorhombic lysozyme has been obtained at 298 K and pH 4.5 using sodium chloride as the precipitant and in the presence of sodium phosphate at a concentration as low as 5 mM. Crystals belonging to space group P2 ₁ 2 ₁ 2 ₁ (unit-cell parameters a = 30, b = 56, c = 73 Å, α = β = γ = 90.00°) diffracted to a resolution higher than 1 Å, and the high quality of these crystals permitted the identification of a phosphate ion bound to Arg14 and His15. The binding of this ion produces long-range conformational changes affecting the loop containing Ser60-Asn74. The negatively charged phosphate ion shields the electrostatic repulsion of the positively charged arginine and histidine residues, resulting in higher stability of the phosphate-bound lysozyme. Additionally, a low-humidity orthorhombic variant was obtained at pH 4.5, and comparison with those previously obtained at pH 6.5 and 9.5 shows a 1.5 Å displacement of the fifth α-helix towards the active-site cavity, which might be relevant to protein function. Since lysozyme is broadly used as a model protein in studies related to protein crystallization and amyloid formation, these results indicate that the interaction of some anions must be considered when analysing experiments performed at acidic pH values.

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Organizational Affiliation: 

Department of Chemistry and Physics, Agrifood Campus of International Excellence (ceiA3) and CIAMBITAL, University of Almería, Carretera de Sacramento, 04120 Almeria, Spain.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Lysozyme C	A	127	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
SO4	A	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	A	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.3 Å
• R-Value Free: 0.188 
• R-Value Work: 0.151 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 30.088	α = 90.00
b = 56.282	β = 90.00
c = 73.208	γ = 90.00

Software Package:

Software Name	Purpose
XDS	data reduction
PHENIX	refinement
PDB_EXTRACT	data extraction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2017-12-15 
• Released Date: 2018-05-09 
• Deposition Author(s): Camara-Artigas, A.

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Funding Organization	Location	Grant Number
Spanish Ministry of Economy and Competitiveness	Spain	BIO2016-78020-R

Revision History 

• Version 1.0: 2018-05-09
  Type: Initial release