4TVT

New ligand for thaumatin discovered using acoustic high throughput screening


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.163 
  • R-Value Work: 0.145 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

High throughput screening using acoustic droplet ejection to combine protein crystals and chemical libraries on crystallization plates at high density.

Teplitsky, E.Joshi, K.Ericson, D.L.Scalia, A.Mullen, J.D.Sweet, R.M.Soares, A.S.

(2015) J.Struct.Biol. 191: 49-58

  • DOI: 10.1016/j.jsb.2015.05.006
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • We describe a high throughput method for screening up to 1728 distinct chemicals with protein crystals on a single microplate. Acoustic droplet ejection (ADE) was used to co-position 2.5nL of protein, precipitant, and chemicals on a MiTeGen in situ-1 ...

    We describe a high throughput method for screening up to 1728 distinct chemicals with protein crystals on a single microplate. Acoustic droplet ejection (ADE) was used to co-position 2.5nL of protein, precipitant, and chemicals on a MiTeGen in situ-1 crystallization plateā„¢ for screening by co-crystallization or soaking. ADE-transferred droplets follow a precise trajectory which allows all components to be transferred through small apertures in the microplate lid. The apertures were large enough for 2.5nL droplets to pass through them, but small enough so that they did not disrupt the internal environment created by the mother liquor. Using this system, thermolysin and trypsin crystals were efficiently screened for binding to a heavy-metal mini-library. Fluorescence and X-ray diffraction were used to confirm that each chemical in the heavy-metal library was correctly paired with the intended protein crystal. A fragment mini-library was screened to observe two known lysozyme ligands using both co-crystallization and soaking. A similar approach was used to identify multiple, novel thaumatin binding sites for ascorbic acid. This technology pushes towards a faster, automated, and more flexible strategy for high throughput screening of chemical libraries (such as fragment libraries) using as little as 2.5nL of each component.


    Organizational Affiliation

    Office of Educational Programs, Brookhaven National Laboratory, Upton, NY 11973-5000, USA; Department of Electronics and Electrical Communication Engineering, PEC University of Technology, Chandigarh, India.,Office of Educational Programs, Brookhaven National Laboratory, Upton, NY 11973-5000, USA; Department of Biological Sciences, 4400 Vestal Parkway East, Binghamton University, NY 13902, USA.,Office of Educational Programs, Brookhaven National Laboratory, Upton, NY 11973-5000, USA; Department of Biochemistry and Cell Biology, Stony Brook University, NY 11794-5215, USA.,Office of Educational Programs, Brookhaven National Laboratory, Upton, NY 11973-5000, USA; Physics Department, University of Oregon, Eugene, OR 97403-1274, USA.,Office of Educational Programs, Brookhaven National Laboratory, Upton, NY 11973-5000, USA; Department of Biomedical Engineering, University at Buffalo, SUNY, 12 Capen Hall, Buffalo, NY 14260, USA.,Photon Sciences Directorate, Brookhaven National Laboratory, Upton, NY 11973-5000, USA. Electronic address: soares@bnl.gov.,Photon Sciences Directorate, Brookhaven National Laboratory, Upton, NY 11973-5000, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Thaumatin-1
A
207Thaumatococcus danielliiMutation(s): 0 
Find proteins for P02883 (Thaumatococcus daniellii)
Go to UniProtKB:  P02883
Small Molecules
Ligands 3 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
ASC
Query on ASC

Download SDF File 
Download CCD File 
A
ASCORBIC ACID
C6 H8 O6
CIWBSHSKHKDKBQ-JLAZNSOCSA-N
 Ligand Interaction
TLA
Query on TLA

Download SDF File 
Download CCD File 
A
L(+)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-JCYAYHJZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 57.837α = 90.00
b = 57.837β = 90.00
c = 149.584γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Energy (United States)United States11-008
Department of Energy (United States)United StatesP41RR012408
National Institutes of Health/National Institute of General Medical SciencesUnited StatesP41GM103473

Revision History 

  • Version 1.0: 2014-07-16
    Type: Initial release
  • Version 1.1: 2015-02-04
    Type: Database references
  • Version 1.2: 2015-07-15
    Type: Database references
  • Version 1.3: 2017-09-20
    Type: Advisory, Author supporting evidence, Database references, Derived calculations, Other, Source and taxonomy