8S2X

SSX structure of Arabidopsis thaliana Pdx1.3 grown in microfluidic droplets


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.158 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Droplet microfluidics for time-resolved serial crystallography.

Stubbs, J.Hornsey, T.Hanrahan, N.Esteban, L.B.Bolton, R.Maly, M.Basu, S.Orlans, J.de Sanctis, D.Shim, J.U.Shaw Stewart, P.D.Orville, A.M.Tews, I.West, J.

(2024) IUCrJ 11: 237-248

  • DOI: https://doi.org/10.1107/S2052252524001799
  • Primary Citation of Related Structures:  
    8S2U, 8S2V, 8S2W, 8S2X

  • PubMed Abstract: 

    Serial crystallography requires large numbers of microcrystals and robust strategies to rapidly apply substrates to initiate reactions in time-resolved studies. Here, we report the use of droplet miniaturization for the controlled production of uniform crystals, providing an avenue for controlled substrate addition and synchronous reaction initiation. The approach was evaluated using two enzymatic systems, yielding 3 µm crystals of lysozyme and 2 µm crystals of Pdx1, an Arabidopsis enzyme involved in vitamin B6 biosynthesis. A seeding strategy was used to overcome the improbability of Pdx1 nucleation occurring with diminishing droplet volumes. Convection within droplets was exploited for rapid crystal mixing with ligands. Mixing times of <2 ms were achieved. Droplet microfluidics for crystal size engineering and rapid micromixing can be utilized to advance time-resolved serial crystallography.


  • Organizational Affiliation

    Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pyridoxal 5'-phosphate synthase subunit PDX1.3
A, B, C, D
291Arabidopsis thalianaMutation(s): 0 
Gene Names: PDX13GIP2PDX1L3RSR4At5g01410T10O8.120
EC: 4.3.3.6
UniProt
Find proteins for Q8L940 (Arabidopsis thaliana)
Explore Q8L940 
Go to UniProtKB:  Q8L940
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8L940
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CIT
Query on CIT

Download Ideal Coordinates CCD File 
E [auth A],
G [auth B],
I [auth C],
K [auth D]
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
F [auth A],
H [auth B],
J [auth C],
L [auth D]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.158 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 180.3α = 90
b = 180.3β = 90
c = 119.2γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
CrystFELdata reduction
CrystFELdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/S008470/1
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/T008768/1

Revision History  (Full details and data files)

  • Version 1.0: 2024-02-28
    Type: Initial release
  • Version 1.1: 2024-03-20
    Changes: Database references