6F1O

Orthorhombic Lysozyme crystallized at 298 K and pH 4.5

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

  • Deposited: 2017-11-22 Released: 2018-05-09 
  • Deposition Author(s): Camara-Artigas, A.
  • Funding Organization(s): Spanish Ministry of Economy and Competitiveness 

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.96 Å
  • R-Value Free: 0.142 
  • R-Value Work: 0.131 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

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

  • DOI: 10.1107/S205979831800517X
  • Primary Citation of Related Structures:  

  • 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 <sub>1 </sub>2 <sub> ...

    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.


    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
MoleculeChainsSequence LengthOrganismDetails
Lysozyme C
A
129Gallus gallusMutation(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
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.96 Å
  • R-Value Free: 0.142 
  • R-Value Work: 0.131 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 30.062α = 90.00
b = 56.176β = 90.00
c = 73.289γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXrefinement
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-11-22 
  • Released Date: 2018-05-09 
  • Deposition Author(s): Camara-Artigas, A.

Funding OrganizationLocationGrant Number
Spanish Ministry of Economy and CompetitivenessSpainBIO2016-78020-R

Revision History 

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