9TK3 | pdb_00009tk3

Room temperature structure of urocanate reductase in complex with imidazole propionate and sulfate

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 
    0.176 (Depositor), 0.176 (DCC) 
  • R-Value Work: 
    0.146 (Depositor), 0.146 (DCC) 
  • R-Value Observed: 
    0.148 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Structural insights into urocanate reductase using room-temperature X-ray crystallography.

Aggarwal, S., Gurav, N., Oksanen, E., Lindkvist-Petersson, K., Venskutonyte, R.

(2026) Acta Crystallogr D Struct Biol 

  • DOI: https://doi.org/10.1107/S2059798326003360
  • Primary Citation Related Structures: 
    9TK1, 9TK3, 9TK5, 9TK6, 9TK7, 9TK8

  • PubMed Abstract: 

    Urocanate reductase (UrdA) is a bacterial enzyme that converts urocanic acid to imidazole propionate. Its catalytic residue Arg411 undergoes a large conformational change in the substrate-bound versus product-bound states. In contrast to previously studied cryo-conditions, the room-temperature X-ray data of UrdA presented here show that the occupancy distribution of Arg411 is affected by crystal cryocooling. We further provide evidence that a phosphate ion stabilizes the substrate complex and can bias the conformation of Arg411. Both room-temperature and cryogenic X-ray datasets were essential to elucidate the dynamic nature of the UrdA active site, highlighting the importance of collecting data at both temperatures, as each may reveal distinct conformational states.

    • Organizational Affiliation: 
    • European Spallation Source ERIC (ESS), 221 00 Lund, Sweden.

Macromolecule Content 

  • Total Structure Weight: 51.03 kDa 
  • Atom Count: 3,907 
  • Modeled Residue Count: 454 
  • Deposited Residue Count: 460 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Urocanate reductase460Shewanella oneidensis MR-1Mutation(s): 0 
Gene Names: urdA, SO_4620
EC: 1.3.99.33
UniProt
Find proteins for Q8CVD0 (Shewanella oneidensis (strain ATCC 700550 / JCM 31522 / CIP 106686 / LMG 19005 / NCIMB 14063 / MR-1))
Explore Q8CVD0 
Go to UniProtKB:  Q8CVD0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8CVD0
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free:  0.176 (Depositor), 0.176 (DCC) 
  • R-Value Work:  0.146 (Depositor), 0.146 (DCC) 
  • R-Value Observed: 0.148 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 126.265α = 90
b = 126.265β = 90
c = 66.782γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
AutoProcessdata reduction
AutoProcessdata scaling
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Swedish Research CouncilSweden2020-02028
Swedish Research CouncilSweden2024-02673
Other privateSwedenDIA2020-500
Other privateSwedenDIA2022-706

Revision History  (Full details and data files)

  • Version 1.0: 2026-05-20
    Type: Initial release