2Z19

Phase transition of monoclinic lysozyme crystal soaked in a saturated NaCl solution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 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

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

Harata, K.Akiba, T.

(2007) Acta Crystallogr.,Sect.D 63: 1016-1021

  • DOI: 10.1107/S0907444907031319
  • Primary Citation of Related Structures:  

  • 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 ...

    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: 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 Gene View: LYZ
Go to UniProtKB:  P00698
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.178 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 26.085α = 90.00
b = 59.055β = 110.63
c = 30.703γ = 90.00
Software Package:
Software NamePurpose
SHELXL-97phasing
SAINTdata scaling
SAINTdata reduction
SHELXL-97model building
SHELXL-97refinement

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2007-05-08 
  • Released Date: 2008-03-18 
  • Deposition Author(s): Harata, K., Akiba, T.

Revision History 

  • Version 1.0: 2008-03-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-10-11
    Type: Refinement description
  • Version 1.3: 2018-01-24
    Type: Experimental preparation