5B07

Lysozyme (denatured by DCl and refolded)

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

  • 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: 1.80 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.152 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.2 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: https://doi.org/10.1007/s12033-015-9908-8
  • Primary Citation of Related Structures:  
    5B05, 5B06, 5B07

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lysozyme C129Gallus gallusMutation(s): 0 
EC: 3.2.1.17
UniProt
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
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A],
E [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
N [auth A],
O [auth A],
P [auth A],
Q [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA
Query on NA

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth A]
I [auth A]
J [auth A]
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.152 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.816α = 90
b = 78.816β = 90
c = 36.8γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japan--

Revision History  (Full details and data files)

  • Version 1.0: 2016-01-13
    Type: Initial release
  • Version 1.1: 2016-02-10
    Changes: Database references
  • Version 1.2: 2023-11-08
    Changes: Author supporting evidence, Data collection, Database references, Derived calculations, Refinement description