4DJ0

Thaumatin I by Langmuir-Blodgett Hanging Drop Method at 1.98A resolution for Unique Water Distribution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.168 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Unique water distribution of Langmuir-Blodgett versus classical crystals.

Pechkova, E.Sivozhelezov, V.Belmonte, L.Nicolini, C.

(2012) J.Struct.Biol. 180: 57-64

  • DOI: 10.1016/j.jsb.2012.05.021
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Langmuir-Blodgett films when used as nanotemplates for crystallization often leads to marked changes in protein stability and structure. Earlier we found that stability of proteins is also correlated with aqueous surroundings in the crystals. Here we ...

    Langmuir-Blodgett films when used as nanotemplates for crystallization often leads to marked changes in protein stability and structure. Earlier we found that stability of proteins is also correlated with aqueous surroundings in the crystals. Here we study the direct relationships between presence of LB nanotemplates and unique patterns of water molecules surrounding the protein, for four model proteins for which 3D structures are available, and where crystallization conditions for each protein are the same except the presence of LB nanotemplate. Shape of frequency distribution of volumes occupied by water molecules were analyzed. They were found to be different between "classical" samples of different proteins, but surprisingly quite similar for LB samples. Volumes occupied by each water molecule as the function of the distance of the given molecule from the protein surface were studied. Introduction of LB film leads to appearance of water molecules close to protein surface but occupying large volumes. These findings confirm earlier experimental findings on the role of water molecules in determining protein stability and thereby pointing to water as a possible candidate for differences apparent in LB crystal stability against radiation.


    Organizational Affiliation

    Nanoworld Institute, Fondazione EL.B.A. Nicolini, Largo Redaelli 7, Pradalunga, Bergamo, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Thaumatin I
A
207Thaumatococcus danielliiMutation(s): 0 
Find proteins for P02883 (Thaumatococcus daniellii)
Go to UniProtKB:  P02883
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.168 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 57.840α = 90.00
b = 57.840β = 90.00
c = 150.070γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
MOSFLMdata reduction
REFMACrefinement
MOLREPphasing
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-07-18
    Type: Initial release
  • Version 1.1: 2012-10-31
    Type: Database references