9OET | pdb_00009oet

Hydrox with succinate and vanadium(IV)-oxo


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.243 (Depositor), 0.243 (DCC) 
  • R-Value Work: 
    0.201 (Depositor), 0.201 (DCC) 
  • R-Value Observed: 
    0.203 (Depositor) 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history


Literature

Dynamic metal coordination controls chemoselectivity in a radical halogenase.

Kissman, E.N.Kipouros, I.Slater, J.W.Stone, E.A.Yang, A.Y.Braun, A.Ensberg, A.R.Whitten, A.M.Chatterjee, K.Bogacz, I.Yano, J.Martin Bollinger Jr., J.Chang, M.C.Y.

(2025) Nat Chem Biol 

  • DOI: https://doi.org/10.1038/s41589-025-02077-x
  • Primary Citation of Related Structures:  
    9OER, 9OES, 9OET, 9OEU, 9OEV, 9OEW

  • PubMed Abstract: 

    The activation of inert C(sp 3 )-H bonds by nonheme Fe enzymes provides a powerful biocatalytic platform for the chemical synthesis of molecules with increased sp 3 complexity. In this context, Fe II /α-ketoglutarate-dependent radical halogenases are uniquely capable of carrying out transfer of a diverse array of bound anions following C-H activation. Here, we provide experimental evidence that bifurcation of radical rebound after H-atom abstraction can be driven both by the ability of a dynamic metal coordination sphere to reorganize and by a second-sphere hydrogen-bonding network where only two residues are sufficient. In addition, we present crystallographic data supporting the existence of an early peroxyhemiketal intermediate in the O 2 activation pathway of Fe II /α-ketoglutarate-dependent enzymes. These data provide a paradigm for understanding the evolution of catalytic plasticity in these enzymes and yields insight into the design principles by which to expand their reaction scope.


  • Organizational Affiliation
    • Department of Chemistry, University of California, Berkeley, CA, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lysine hydroxylaseA [auth D],
B [auth A]
260Streptomyces roseifaciensMutation(s): 0 
UniProt
Find proteins for A0A8M0FGT0 (Streptomyces roseifaciens)
Explore A0A8M0FGT0 
Go to UniProtKB:  A0A8M0FGT0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A8M0FGT0
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.243 (Depositor), 0.243 (DCC) 
  • R-Value Work:  0.201 (Depositor), 0.201 (DCC) 
  • R-Value Observed: 0.203 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.892α = 90
b = 139.97β = 90
c = 95.427γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Energy (DOE, United States)United StatesDOE/LBL DEAC02-05CH11231 FWP CH030201
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM134271

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-19
    Type: Initial release
  • Version 1.1: 2025-12-03
    Changes: Database references