4NGO

Previously de-ionized HEW lysozyme batch crystallized in 1.0 M CoCl2

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.149 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

Weak protein-cationic co-ion interactions addressed by X-ray crystallography and mass spectrometry.

Benas, P., Auzeil, N., Legrand, L., Brachet, F., Regazzetti, A., Ries-Kautt, M.

(2014) Acta Crystallogr.,Sect.D 70: 2217-2231

  • DOI: 10.1107/S1399004714011304
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • The adsorption of Rb(+), Cs(+), Mn(2+), Co(2+) and Yb(3+) onto the positively charged hen egg-white lysozyme (HEWL) has been investigated by solving 13 X-ray structures of HEWL crystallized with their chlorides and by applying electrospray ionization ...

    The adsorption of Rb(+), Cs(+), Mn(2+), Co(2+) and Yb(3+) onto the positively charged hen egg-white lysozyme (HEWL) has been investigated by solving 13 X-ray structures of HEWL crystallized with their chlorides and by applying electrospray ionization mass spectrometry (ESI-MS) first to dissolved protein crystals and then to the protein in buffered salt solutions. The number of bound cations follows the order Cs(+) < Mn(2+) ≃ Co(2+) < Yb(3+) at 293 K. HEWL binds less Rb(+) (qtot = 0.7) than Cs(+) (qtot = 3.9) at 100 K. Crystal flash-cooling drastically increases the binding of Cs(+), but poorly affects that of Yb(3+), suggesting different interactions. The addition of glycerol increases the number of bound Yb(3+) cations, but only slightly increases that of Rb(+). HEWL titrations with the same chlorides, followed by ESI-MS analysis, show that only about 10% of HEWL binds Cs(+) and about 40% binds 1-2 Yb(3+) cations, while the highest binding reaches 60-70% for protein binding 1-3 Mn(2+) or Co(2+) cations. The binding sites identified by X-ray crystallography show that the monovalent Rb(+) and Cs(+) preferentially bind to carbonyl groups, whereas the multivalent Mn(2+), Co(2+) and Yb(3+) interact with carboxylic groups. This work elucidates the basis of the effect of the Hofmeister cation series on protein solubility.

    Related Citations: 
    • Strong and specific effects of cations on lysozyme chloride solubility.
      Benas, P.,Legrand, L.,Ries-Kautt, M.
      (2002) Acta Crystallogr.,Sect.D 58: 1582

    Organizational Affiliation: 

    Laboratoire de Cristallographie et RMN Biologiques, Faculté des Sciences Pharmaceutiques et Biologiques, Université Paris Descartes, UMR 8015 CNRS, 4 Avenue de l'Observatoire, 75270 Paris CEDEX 06, France.




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
CL
Query on CL
Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
CO
Query on CO
Download SDF File 
Download CCD File 
A
COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.149 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 79.299α = 90.00
b = 79.299β = 90.00
c = 37.543γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
HKL-2000data collection
REFMACrefinement
CNSrefinement
TRUNCATEdata scaling

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-05-28
    Type: Initial release
  • Version 1.1: 2014-08-13
    Type: Database references
  • Version 1.2: 2017-11-15
    Type: Refinement description