2LYO

CROSS-LINKED CHICKEN LYSOZYME CRYSTAL IN 90% ACETONITRILE-WATER


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

X-ray studies on cross-linked lysozyme crystals in acetonitrile-water mixture.

Wang, Z.Zhu, G.Huang, Q.Qian, M.Shao, M.Jia, Y.Tang, Y.

(1998) Biochim.Biophys.Acta 1384: 335-344

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Tetragonal crystals of hen egg white lysozyme were cross-linked and subjected to X-ray diffraction study in acetonitrile-water media with different acetonitrile concentrations. Crystals in neat acetonitrile did not scatter X-ray well. Structures of c ...

    Tetragonal crystals of hen egg white lysozyme were cross-linked and subjected to X-ray diffraction study in acetonitrile-water media with different acetonitrile concentrations. Crystals in neat acetonitrile did not scatter X-ray well. Structures of crystals in neat water, in 90% and 95% acetonitrile, and crystal back-soaked from acetonitrile to water, were determined to about 2 A resolution. For crystals in both 90% acetonitrile, and crystal back-soaked from acetonitrile to water, were determined to about 2 A resolution. For crystals in both 90% and 95% acetonitrile, only one protein-bond acetonitrile molecule is found in the active site cleft, and its location and binding-protein mode is similar to the C subunit of polysaccharide. The alteration in conformation and hydrogen-bond pattern involving water as solvent causes the reduction of the protein's flexibility in organic media. The back-soaked crystal regained its ordinary three-dimensional structure in water.


    Organizational Affiliation

    Department of Chemistry, Peking University, Beijing, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LYSOZYME
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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CCN
Query on CCN

Download SDF File 
Download CCD File 
A
ACETONITRILE
C2 H3 N
WEVYAHXRMPXWCK-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.178 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 79.230α = 90.00
b = 79.230β = 90.00
c = 37.430γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
R-AXISdata reduction
R-AXISdata collection
R-AXISdata scaling
X-PLORphasing
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-05-27
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other