Tetragonal Lysozyme crystallized at 298 K and pH 4.5 with phosphate bound: control experiment

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

  • 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

  • Resolution: 1.10 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.154 

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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: https://doi.org/10.1107/S205979831800517X
  • Primary Citation of Related Structures:  
    6F1L, 6F1M, 6F1O, 6F1P, 6F1R, 6F9X, 6F9Y, 6F9Z, 6FA0

  • 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.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lysozyme C129Gallus gallusMutation(s): 0 
Find proteins for P00698 (Gallus gallus)
Explore P00698 
Go to UniProtKB:  P00698
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00698
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.10 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.154 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.694α = 90
b = 78.694β = 90
c = 37.66γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Entry History & Funding Information

Deposition Data

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

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-09
    Type: Initial release
  • Version 2.0: 2024-01-17
    Changes: Atomic model, Data collection, Database references, Refinement description