4ARR

Crystal structure of the N-terminal domain of Drosophila Toll receptor with the magic triangle I3C


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.224 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Liesegang-Like Patterns of Toll Crystals Grown in Gel.

Gangloff, M.Moreno, A.Gay, N.J.

(2013) J.Appl.Crystallogr. 46: 337

  • DOI: 10.1107/S0021889812051606
  • Also Cited By: 4ARN

  • PubMed Abstract: 
  • Generating high-quality crystals remains a bottleneck in biological and materials sciences. Here a counter-diffusion method was used to improve the X-ray diffraction quality of the N-terminal domain of Drosophila melanogaster Toll receptor crystals. ...

    Generating high-quality crystals remains a bottleneck in biological and materials sciences. Here a counter-diffusion method was used to improve the X-ray diffraction quality of the N-terminal domain of Drosophila melanogaster Toll receptor crystals. It was observed that crystallization occurred with a peculiar pattern along the capillary resembling Liesegang bands; this phenomenon is described at both macroscopic and atomic levels. It was found that bands appeared for native protein as well as for co-crystals of magic triangle (I3C)-bound protein even though they crystallize in different space groups. Crystallization occurred with a linear recurrence independent of the precipitant concentration and a protein-specific spacing coefficient. Bandwidth varied along the capillary, oscillating between large precipitation areas and single crystals. The reported data suggest that repetitive patterns can be generated with biological macromolecules in the presence of sodium malonate as a crystallization agent. A comparison with typical Liesegang patterns and the possible mechanism underlying this phenomenon are discussed.


    Organizational Affiliation

    Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TOLL RECEPTOR, VARIABLE LYMPHOCYTE RECEPTOR B.61 CHIMERA
A, B
279Drosophila melanogasterEptatretus burgeri
This entity is chimeric
Gene Names: Tl, VLRB
Find proteins for P08953 (Drosophila melanogaster)
Go to UniProtKB:  P08953
Find proteins for Q4G1L2 (Eptatretus burgeri)
Go to UniProtKB:  Q4G1L2
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
I3C
Query on I3C

Download SDF File 
Download CCD File 
A, B
5-amino-2,4,6-triiodobenzene-1,3-dicarboxylic acid
5-Amino-2,4,6-triiodoisophthalic acid
C8 H4 I3 N O4
JEZJSNULLBSYHV-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.224 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 87.643α = 90.00
b = 87.643β = 90.00
c = 220.741γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
XDSdata reduction
BUSTERrefinement
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-02-27
    Type: Initial release
  • Version 1.1: 2013-05-01
    Type: Database references
  • Version 1.2: 2017-03-15
    Type: Source and taxonomy