2Z12

Structure of the transformed monoclinic lysozyme by controlled dehydration


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.168 

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This is version 1.4 of the entry. See complete history


Literature

Effect of a sodium ion on the dehydration-induced phase transition of monoclinic lysozyme crystals.

Harata, K.Akiba, T.

(2007) Acta Crystallogr D Biol Crystallogr 63: 1016-1021

  • DOI: https://doi.org/10.1107/S0907444907031319
  • Primary Citation of Related Structures:  
    2Z12, 2Z18, 2Z19

  • PubMed Abstract: 

    A monoclinic lysozyme crystal grown in NaCl solution was transformed into a new monoclinic crystal form by controlled dehydration. This crystal-to-crystal phase transition was accompanied by 20-40% solvent loss and the transformed crystal diffracted to prominently high resolution. The structures of the native and transformed crystals were determined at 1.4 and 1.15 A resolution, respectively. In the native crystal a sodium ion was bound to the loop region Ser60-Asn74; however, it was released in the transformed crystal and a water molecule occupied this position. In the transformed crystal a sodium ion was bound to the carboxyl group of Asp52, a catalytic residue. The same structural change was observed in the phase transition of a crystal soaked in a saturated NaCl solution. In contrast, a crystal soaked in 10% NaCl solution was transformed in a shorter time with a smaller loss of solvent and the structure of the sodium-binding site was conserved in the transformed crystal. The high concentration of NaCl is likely to stabilize the crystal structure against dehydration by forming salt linkages between protein molecules. This suggests that the sodium ion in the crystal regulates not only the structural change of the loop region Ser60-Asn74 but also the molecular rearrangement caused by dehydration.


  • Organizational Affiliation

    Biological Information Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan. k-harata@aist.go.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
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.168 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 25.947α = 90
b = 58.021β = 110.4
c = 30.58γ = 90
Software Package:
Software NamePurpose
SHELXL-97model building
SHELXL-97refinement
SAINTdata reduction
SAINTdata scaling
SHELXL-97phasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-03-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-11
    Changes: Data collection, Refinement description
  • Version 1.3: 2018-01-24
    Changes: Experimental preparation
  • Version 1.4: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description