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 
  • R-Value Observed: 0.178 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.5 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

  • DOI: https://doi.org/10.1016/s0167-4838(98)00027-2
  • Primary Citation of Related Structures:  
    1LYO, 2LYO, 3LYO, 4LYO

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
LYSOZYME129Gallus 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
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CCN
Query on CCN

Download Ideal Coordinates CCD File 
B [auth A]ACETONITRILE
C2 H3 N
WEVYAHXRMPXWCK-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.178 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.23α = 90
b = 79.23β = 90
c = 37.43γ = 90
Software Package:
Software NamePurpose
R-AXISdata collection
R-AXISdata reduction
X-PLORmodel building
X-PLORrefinement
R-AXISdata scaling
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-05-27
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-11-29
    Changes: Derived calculations, Other
  • Version 1.4: 2023-08-09
    Changes: Database references, Derived calculations, Refinement description
  • Version 1.5: 2024-10-30
    Changes: Data collection, Structure summary