9G5X | pdb_00009g5x

Xylose Isomerase collected at 45C using serial fixed-target crystallography


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 
    0.182 (Depositor), 0.182 (DCC) 
  • R-Value Work: 
    0.145 (Depositor), 0.145 (DCC) 
  • R-Value Observed: 
    0.147 (Depositor) 

Starting Model: experimental
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This is version 1.0 of the entry. See complete history


Literature

Probing the modulation of enzyme kinetics by multi-temperature, time-resolved serial crystallography.

Schulz, E.C.Prester, A.von Stetten, D.Gore, G.Hatton, C.E.Bartels, K.Leimkohl, J.P.Schikora, H.Ginn, H.M.Tellkamp, F.Mehrabi, P.

(2025) Nat Commun 16: 6553-6553

  • DOI: https://doi.org/10.1038/s41467-025-61631-2
  • Primary Citation of Related Structures:  
    9G5S, 9G5W, 9G5X, 9G61, 9G6L, 9G6M, 9G6N, 9G6O, 9G6P, 9G7V, 9G7W, 9G7X, 9G7Y, 9G7Z, 9G80, 9G81, 9G82, 9I7L

  • PubMed Abstract: 

    The vast majority of protein structures are determined at cryogenic temperatures, which are far from physiological conditions. Nevertheless, it is well established that temperature is an essential thermodynamic parameter for understanding the conformational dynamics and functionality of proteins in their native environments. Time-resolved crystallography is a technique that aims to elucidate protein function by examining structural alterations during processes such as ligand binding, catalysis, or allostery. However, this approach is typically conducted under ambient conditions, which may obscure crucial conformational states, that are only visible at physiological temperatures. In this study, we directly address the interplay between protein structure and activity via a method that enables multi-temperature, time-resolved serial crystallography experiments in a temperature window from below 10 °C to above 70 °C. Via this 5D-SSX, time-resolved experiments can now be carried out at physiological temperatures and with long time delays, providing insights into protein function and enzyme catalysis. Our findings demonstrate the temperature-dependent modulation of turnover kinetics for the mesophilic β-lactamase CTX-M-14 and the thermophilic enzyme xylose isomerase, within the full protein structure.


  • Organizational Affiliation

    University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany. ec.schulz@uke.de.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Xylose isomerase388Streptomyces rubiginosusMutation(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: 1.70 Å
  • R-Value Free:  0.182 (Depositor), 0.182 (DCC) 
  • R-Value Work:  0.145 (Depositor), 0.145 (DCC) 
  • R-Value Observed: 0.147 (Depositor) 
Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.2α = 90
b = 103.05β = 90
c = 99.25γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)Germany451079909
German Research Foundation (DFG)Germany458246365
European Research Council (ERC)European Union101071843
German Research Foundation (DFG)Germany194651731
German Federal Ministry for Education and ResearchGermany05K16GU1
German Federal Ministry for Education and ResearchGermany05K19GU1
German Federal Ministry for Education and ResearchGermany05K22GU6

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-30
    Type: Initial release