6QNH

Liquid Application Method for time-resolved Analyses (LAMA) by serial synchrotron crystallography, Xylose Isomerase 0ms timepoint

• PDB DOI: https://doi.org/10.2210/pdb6QNH/pdb

• Classification: ISOMERASE
• Organism(s): Streptomyces rubiginosus
• Expression System: Streptomyces rubiginosus
• Mutation(s): No 


• Deposited: 2019-02-11 Released: 2019-10-02 
• Deposition Author(s): Mehrabi, P., Schulz, E.C., Miller, R.J.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.196 
• R-Value Work: 0.165 
• R-Value Observed: 0.166 

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

• PubMed: 31527838 
• DOI: https://doi.org/10.1038/s41592-019-0553-1
• Primary Citation of Related Structures:  
  6QND, 6QNH


• 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 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.

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Organizational Affiliation: 

Max-Planck-Institute for Structure and Dynamics of Matter, Department for Atomically Resolved Dynamics, Hamburg, Germany.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 43.37 kDa 
• Atom Count: 3,303 
• Modelled Residue Count: 387 
• Deposited Residue Count: 388 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Xylose isomerase	A	388	Streptomyces rubiginosus	Mutation(s): 0  Gene Names: xylA EC: 5.3.1.5
UniProt
Find proteins for P24300 (Streptomyces rubiginosus) Explore P24300  Go to UniProtKB:  P24300

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CO	C [auth A]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.196 
• R-Value Work: 0.165 
• R-Value Observed: 0.166 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.74	α = 90
b = 99.17	β = 90
c = 87.41	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-10-02 
Deposition Author(s): Mehrabi, P., Schulz, E.C., Miller, R.J.D.

Revision History  

• Version 1.0: 2019-10-02
  Type: Initial release
  
• Version 1.1: 2019-10-09
  Changes: Data collection, Database references
• Version 1.2: 2019-11-20
  Changes: Derived calculations, Refinement description