9R47 | pdb_00009r47

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


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
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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

  • DOI: https://doi.org/10.1038/s42004-025-01784-9
  • Primary Citation of 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.


  • Organizational Affiliation
    • University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Xylose isomerase388Streptomyces pseudogriseolusMutation(s): 0 
Gene Names: xylA
EC: 5.3.1.5
UniProt
Find proteins for P24300 (Streptomyces rubiginosus)
Explore P24300 
Go to UniProtKB:  P24300
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP24300
Sequence Annotations
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  • Reference Sequence
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 = 85.643α = 90
b = 93.922β = 90
c = 98.322γ = 90
Software Package:
Software NamePurpose
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
PHENIXrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Max Planck SocietyGermany--
European Research Council (ERC)European Union--
German Research Foundation (DFG)Germany458246365
German Research Foundation (DFG)Germany451079909
German Federal Ministry for Education and ResearchGermany01KI2114

Revision History  (Full details and data files)

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