5B07

Lysozyme (denatured by DCl and refolded)

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

  • Deposited: 2015-10-28 Released: 2016-01-13 
  • Deposition Author(s): Kita, A., Morimoto, Y.
  • Funding Organization(s): Ministry of Education, Culture, Sports, Science and Technology, Japan 

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.150 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

An Effective Deuterium Exchange Method for Neutron Crystal Structure Analysis with Unfolding-Refolding Processes

Kita, A.Morimoto, Y.

(2016) Mol Biotechnol. 58: 130-136

  • DOI: 10.1007/s12033-015-9908-8
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • A method of hydrogen/deuterium (H/D) exchange with an unfolding-refolding process has been applied to hen egg-white lysozyme (HWL), and accurate evaluation of its deuteration was carried out by time-of-flight mass spectroscopy. Neutron crystallograph ...

    A method of hydrogen/deuterium (H/D) exchange with an unfolding-refolding process has been applied to hen egg-white lysozyme (HWL), and accurate evaluation of its deuteration was carried out by time-of-flight mass spectroscopy. Neutron crystallography requires a suitable crystal with enough deuterium exchanged in the protein to decrease incoherent scattering from hydrogens. It is very expensive to prepare a fully deuterated protein, and therefore a simple H/D exchange technique is desirable for this purpose. Acid or base addition to protein solutions with heating effectively increased the number of deuterium up to more than 20 % of that of all hydrogen atoms, and refolded structures were determined by X-ray structure analysis at 1.8 Å resolution. Refolded HWL had increased deuterium content in its protein core and its native structure, determined at atomic resolution, was fully preserved.


    Organizational Affiliation

    Division of the Quantum Beam Material Science, Research Reactor Institute, Kyoto University, Kumatori, Osaka, 590-0494, Japan. kita@rri.kyoto-u.ac.jp.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lysozyme C
A
129Gallus gallusGene 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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
ethane-1,2-diol
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.150 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 78.816α = 90.00
b = 78.816β = 90.00
c = 36.800γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
HKL-2000data reduction
HKL-2000data scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2015-10-28 
  • Released Date: 2016-01-13 
  • Deposition Author(s): Kita, A., Morimoto, Y.

Funding OrganizationCountryGrant Number
Ministry of Education, Culture, Sports, Science and Technology, JapanJapan--

Revision History 

  • Version 1.0: 2016-01-13
    Type: Initial release
  • Version 1.1: 2016-02-10
    Type: Database references