6QNJ

Liquid Application Method for time-resolved Analyses (LAMA) by serial synchrotron crystallography, Xylose Isomerase 4.5 s timepoint


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.851 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Liquid application method for time-resolved analyses by serial synchrotron crystallography.

Mehrabi, P.Schulz, E.C.Agthe, M.Horrell, S.Bourenkov, G.von Stetten, D.Leimkohl, J.P.Schikora, H.Schneider, T.R.Pearson, A.R.Tellkamp, F.Miller, R.J.D.

(2019) Nat.Methods 16: 979-982

  • DOI: 10.1038/s41592-019-0553-1
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • We introduce a liquid application method for time-resolved analyses (LAMA), an in situ mixing approach for serial crystallography. Picoliter-sized droplets are shot onto chip-mounted protein crystals, achieving near-full ligand occupancy within theor ...

    We introduce a liquid application method for time-resolved analyses (LAMA), an in situ mixing approach for serial crystallography. Picoliter-sized droplets are shot onto chip-mounted protein crystals, achieving near-full ligand occupancy within theoretical diffusion times. We demonstrate proof-of-principle binding of GlcNac to lysozyme, and resolve glucose binding and subsequent ring opening in a time-resolved study of xylose isomerase.


    Organizational Affiliation

    Max-Planck-Institute for Structure and Dynamics of Matter, Department for Atomically Resolved Dynamics, Hamburg, Germany. dwayne.miller@mpsd.mpg.de.,European Molecular Biology Laboratory, Hamburg Unit c/o Deutsches Elektronen Synchrotron, Hamburg, Germany.,Max-Planck-Institute for Structure and Dynamics of Matter, Department for Atomically Resolved Dynamics, Hamburg, Germany.,Max-Planck-Institute for Structure and Dynamics of Matter, Scientific Support Unit Machine Physics, Hamburg, Germany.,Centre for Ultrafast Imaging, Universität Hamburg, Hamburg, Germany. dwayne.miller@mpsd.mpg.de.,Institute for Nanostructure and Solid State Physics, Universität Hamburg, Hamburg, Germany.,Centre for Ultrafast Imaging, Universität Hamburg, Hamburg, Germany.,University of Toronto, Departments of Chemistry and Physics, Toronto, Ontario, Canada. dwayne.miller@mpsd.mpg.de.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Xylose isomerase
A
388Streptomyces rubiginosusMutation(s): 0 
Gene Names: xylA
EC: 5.3.1.5
Find proteins for P24300 (Streptomyces rubiginosus)
Go to UniProtKB:  P24300
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GLC
Query on GLC

Download SDF File 
Download CCD File 
A
ALPHA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
CO
Query on CO

Download SDF File 
Download CCD File 
A
COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.851 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.180 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 94.620α = 90.00
b = 99.380β = 90.00
c = 87.630γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-10-02
    Type: Initial release
  • Version 1.1: 2019-10-09
    Type: Data collection, Database references