6ABZ

Crystal Structure of HEWL in deionized water


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.171 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The role of Cinnamaldehyde and Phenyl ethyl alcohol as two types of precipitants affecting protein hydration levels.

Seraj, Z.Seyedarabi, A.

(2019) Int.J.Biol.Macromol. 146: 705-715

  • DOI: 10.1016/j.ijbiomac.2019.12.204
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Release of water is the main force which drives proteins towards crystallisation (giving rise to protein crystals for crystallography) and aggregation (main cause of neurodegenerative diseases), and as such it is possible to make changes in the cryst ...

    Release of water is the main force which drives proteins towards crystallisation (giving rise to protein crystals for crystallography) and aggregation (main cause of neurodegenerative diseases), and as such it is possible to make changes in the crystallisation/aggregation process by using compounds which are able to reduce the amount of water molecules around proteins. Cinnamaldehyde and Phenyl ethyl alcohol are the active constituents of cinnamon and rose flower, respectively. Traditional Iranian Medicine (TIM) suggests the use of cinnamon and rose flower for the reduction of excess coldness and wetness from the brain of patients suffering from Dementia. Using crystallisation as a model system and X-ray crystallography, we tested whether Cinnamaldehyde or Phenyl ethyl alcohol can mimic the role of precipitants resulting in the formation of crystals of HEWL (as a model protein) by releasing water from the surrounding protein environment. Results have revealed that both Cinnamaldehyde and Phenyl ethyl alcohol, in particular, were capable to adequately act as 'precipitants' but in the presence of NaCl (as a salt), resulting in better crystals of HEWL by changing the amount of charge and/or making water molecules unavailable in the symmetry related position, in line with the role suggested for these compounds by TIM.


    Organizational Affiliation

    Department of Biochemistry, Institute of Biochemistry and Biophysics, University of Tehran, Tehran 1417614411, Iran. Electronic address: a.seyedarabi@ut.ac.ir.,Department of Biochemistry, Institute of Biochemistry and Biophysics, University of Tehran, Tehran 1417614411, Iran.




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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

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

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
PGO
Query on PGO

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Download CCD File 
A
S-1,2-PROPANEDIOL
C3 H8 O2
DNIAPMSPPWPWGF-VKHMYHEASA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.171 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 78.139α = 90.00
b = 78.139β = 90.00
c = 37.140γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
iMOSFLMdata reduction
SCALAdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-07-31
    Type: Initial release
  • Version 1.1: 2020-01-29
    Type: Database references
  • Version 1.2: 2020-02-05
    Type: Database references