6S7N

Crystal structure of orthorhombic lysozyme grown at pH 5.5 with a 26% of solvent content


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.160 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Major conformational changes in the structure of lysozyme obtained from a crystal with a very low solvent content.

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

(2019) Acta Crystallogr.,Sect.F 75: 687-696

  • DOI: 10.1107/S2053230X19013189

  • PubMed Abstract: 
  • A new crystal form of lysozyme with a very low solvent content (26.35%) has been obtained in the orthorhombic space group P2 <sub>1 </sub>2 <sub>1 </sub>2 <sub>1 </sub> (with unit-cell parameters a = 30.04, b = 51.68, c = 61.53 Å). The lysozyme struc ...

    A new crystal form of lysozyme with a very low solvent content (26.35%) has been obtained in the orthorhombic space group P2 1 2 1 2 1 (with unit-cell parameters a = 30.04, b = 51.68, c = 61.53 Å). The lysozyme structure obtained from these crystals does not show the typical overall fold. Instead, major conformational changes take place in some elements of the secondary structure and in the hydrophobic core of the protein. At the end of the central α-helix (α2), Glu35 is usually buried in the catalytic site and shows an abnormally high pK a value, which is key to the activity of the enzyme. The high pK a value of this glutamate residue is favoured by the hydrophobic environment, particularly by its neighbour Trp108, which is important for structural stability and saccharide binding. In this new structure, Trp108 shows a 90° rotation of its side chain, which results in the rearrangement of the hydrophobic core. Conformational changes also result in the exposure of Glu35 to the solvent, which impairs the catalytic site by increasing the distance between Glu35 and Asp52 and lowering the pK a value of the glutamate. Altogether, this new lysozyme structure reveals major conformational changes in the hydrophobic core and catalytic site that might play a role in the folding and bactericidal function of the protein.


    Organizational Affiliation

    Department of Chemistry and Physics, Agrifood Campus of International Excellence (ceiA3) and CIAMBITAL, University of Almería, Carretera de Sacramento s/n, 04120 Almería, 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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.160 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 30.037α = 90.00
b = 51.699β = 90.00
c = 61.531γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
PHASERphasing
XDSdata reduction
PDB_EXTRACTdata extraction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


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

Revision History 

  • Version 1.0: 2019-11-20
    Type: Initial release