9R47 | pdb_00009r47

Spitrobot-2 advances time-resolvedcryo-trapping crystallography to under 25 ms: Xylose isomerase bound with glucose (50 ms soaking)

• PDB DOI: https://doi.org/10.2210/pdb9R47/pdb

• Classification: ISOMERASE
• Organism(s): Streptomyces pseudogriseolus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-05-07 Released: 2025-12-03 
• Deposition Author(s): Hatton, C.E., Spiliopoulou, M., Schulz, E.C., Mehrabi, P.
• Funding Organization(s): Max Planck Society, European Research Council (ERC), German Research Foundation (DFG), German Federal Ministry for Education and Research

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.206 (Depositor), 0.208 (DCC) 
• R-Value Work: 
  0.169 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.171 (Depositor) 

Starting Model: experimental

Literature

Spitrobot-2 advances time-resolved cryo-trapping crystallography to under 25 ms.

Spiliopoulou, M., Hatton, C.E., Kollewe, M., Leimkohl, J.P., Schikora, H., Tellkamp, F., Mehrabi, P., Schulz, E.C.

(2025) Commun Chem 8: 363-363

• PubMed: 41266557 
• DOI: https://doi.org/10.1038/s42004-025-01784-9
• Primary Citation Related Structures: 
  9R45, 9R46, 9R47, 9R48, 9R49, 9R4A, 9R4B, 9R4C, 9R4E, 9R4F, 9R4G, 9R4H


• PubMed Abstract: 
  

  We previously introduced the spitrobot, a protein crystal plunging system that enables reaction quenching via cryo-trapping with a time resolution in the millisecond range. Here we present the next generation, spitrobot-2, as an integrated benchtop device. User-friendliness has been improved by semi-automatic sample exchange. Moreover, a fully automated shutter shields the liquid nitrogen from the humidified environment, improving sample integrity. Most importantly, the cryo-trapping delay time has been reduced to 23 ms, making spitrobot-2 twice as fast as the previous generation. This further expands the number of target systems that can be addressed by cryo-trapping time-resolved crystallography. Using 12 crystal structures of three independent model systems, we demonstrate successful cryo-trapping via observation of conformational changes and ligand binding within 25 ms. These improvements increase the convenient access to cryo-trapping, time-resolved X-ray crystallography empowering the MX community with efficient tools to advance research in structural biology.

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Organizational Affiliation: 
• University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany.
Institute for Nanostructure and Solid State Physics, Universität Hamburg, Hamburg, Germany.
Max-Planck-Institute for Structure and Dynamics of Matter, Hamburg, Germany.
Max-Planck-Institute for Structure and Dynamics of Matter, Hamburg, Germany. [e-mail].
Institute for Nanostructure and Solid State Physics, Universität Hamburg, Hamburg, Germany. [e-mail].
Max-Planck-Institute for Structure and Dynamics of Matter, Hamburg, Germany. [e-mail].
University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany. [e-mail].
Institute for Nanostructure and Solid State Physics, Universität Hamburg, Hamburg, Germany. [e-mail].
Max-Planck-Institute for Structure and Dynamics of Matter, Hamburg, Germany. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 43.54 kDa 
• Atom Count: 3,413 
• Modeled Residue Count: 386 
• Deposited Residue Count: 388 
• Unique protein chains: 1

Macromolecules

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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BGC (Subject of Investigation/LOI)	D [auth A]	beta-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-VFUOTHLCSA-N
MN	C [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.206 (Depositor), 0.208 (DCC) 
• R-Value Work:  0.169 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.171 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.643	α = 90
b = 93.922	β = 90
c = 98.322	γ = 90

Software Package:

Software Name	Purpose
autoPROC	data reduction
autoPROC	data scaling
PHASER	phasing
PHENIX	refinement

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-12-03 
Deposition Author(s): Hatton, C.E., Spiliopoulou, M., Schulz, E.C., Mehrabi, P.

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Funding Organization	Location	Grant Number
Max Planck Society	Germany	--
European Research Council (ERC)	European Union	--
German Research Foundation (DFG)	Germany	458246365
German Research Foundation (DFG)	Germany	451079909
German Federal Ministry for Education and Research	Germany	01KI2114

Revision History  

• Version 1.0: 2025-12-03
  Type: Initial release