4B49

1.15 A Structure of Lysozyme Crystallized without 2-methyl-2,4- pentanediol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 0.151 
  • R-Value Work: 0.127 
  • R-Value Observed: 0.128 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Crystallization of Lysozyme with (R)-, (S)- and (Rs)-2-Methyl-2,4-Pentanediol

Stauber, M.Jakoncic, J.Berger, J.Karp, J.M.Axelbaum, A.Sastow, D.Buldyrev, S.V.Hrnjez, B.J.Asherie, N.

(2015) Acta Crystallogr D Biol Crystallogr 71: 427

  • DOI: https://doi.org/10.1107/S1399004714025061
  • Primary Citation of Related Structures:  
    4B49, 4B4E, 4B4I, 4B4J

  • PubMed Abstract: 

    Chiral control of crystallization has ample precedent in the small-molecule world, but relatively little is known about the role of chirality in protein crystallization. In this study, lysozyme was crystallized in the presence of the chiral additive 2-methyl-2,4-pentanediol (MPD) separately using the R and S enantiomers as well as with a racemic RS mixture. Crystals grown with (R)-MPD had the most order and produced the highest resolution protein structures. This result is consistent with the observation that in the crystals grown with (R)-MPD and (RS)-MPD the crystal contacts are made by (R)-MPD, demonstrating that there is preferential interaction between lysozyme and this enantiomer. These findings suggest that chiral interactions are important in protein crystallization.


  • Organizational Affiliation

    Department of Physics, Yeshiva University, 2495 Amsterdam Avenue, New York, NY 10033-3312, USA.


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
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 0.151 
  • R-Value Work: 0.127 
  • R-Value Observed: 0.128 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.841α = 90
b = 76.841β = 90
c = 38.691γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-08-22
    Type: Initial release
  • Version 1.1: 2015-03-11
    Changes: Database references
  • Version 1.2: 2015-03-25
    Changes: Database references
  • Version 1.3: 2019-05-08
    Changes: Data collection, Experimental preparation, Other
  • Version 1.4: 2019-05-15
    Changes: Data collection, Experimental preparation