4B4E

1.00 A Structure of Lysozyme Crystallized with (R)-2-methyl-2,4- pentanediol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.00 Å
  • R-Value Free: 0.144 
  • R-Value Work: 0.124 
  • R-Value Observed: 0.125 

wwPDB Validation 3D Report Full Report


This is version 1.6 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: 10.1107/S1399004714025061
  • Structures With Same Primary Citation

  • 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 ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LYSOZYME C
A
129Gallus gallusMutation(s): 0 
Gene Names: LYZ
EC: 3.2.1.17
Find proteins for P00698 (Gallus gallus)
Go to UniProtKB:  P00698
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MRD
Query on MRD

Download CCD File 
A
(4R)-2-METHYLPENTANE-2,4-DIOL
C6 H14 O2
SVTBMSDMJJWYQN-RXMQYKEDSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.00 Å
  • R-Value Free: 0.144 
  • R-Value Work: 0.124 
  • R-Value Observed: 0.125 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.53α = 90
b = 77.53β = 90
c = 37.895γ = 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 

  • Version 1.0: 2012-08-22
    Type: Initial release
  • Version 1.1: 2013-03-27
    Changes: Atomic model, Other
  • Version 1.2: 2015-03-11
    Changes: Database references
  • Version 1.3: 2015-03-25
    Changes: Database references
  • Version 1.4: 2019-05-08
    Changes: Data collection, Experimental preparation, Other
  • Version 1.5: 2019-05-15
    Changes: Data collection, Experimental preparation
  • Version 1.6: 2019-07-17
    Changes: Data collection, Derived calculations