9OET | pdb_00009oet

Hydrox with succinate and vanadium(IV)-oxo

• PDB DOI: https://doi.org/10.2210/pdb9OET/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Streptomyces roseifaciens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-04-29 Released: 2025-11-19 
• Deposition Author(s): Kissman, E.N., Yang, A.Y., Whitten, A.M., Chang, M.C.Y.
• Funding Organization(s): Department of Energy (DOE, United States), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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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

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.

(2026) Nat Chem Biol 22: 491-500

• PubMed: 41272319 
• DOI: https://doi.org/10.1038/s41589-025-02077-x
• Primary Citation 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.

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Organizational Affiliation: 
• Department of Chemistry, University of California, Berkeley, CA, USA.
Miller Institute for Basic Research in Science, University of California, Berkeley, CA, USA.
Department of Chemistry, The Pennsylvania State University, University Park, PA, USA.
Department of Chemistry and Biochemistry, Fairfield University, Fairfield, CT, USA.
Department of Chemistry, Stanford University, Stanford, CA, USA.
Department of Chemical & Biomolecular Engineering, University of California, Berkeley, CA, USA.
Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA.
Department of Chemistry, University of California, Berkeley, CA, USA. [e-mail].
Department of Chemical & Biomolecular Engineering, University of California, Berkeley, CA, USA. [e-mail].
Department of Chemistry, Princeton University, Princeton, NJ, USA. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 59.82 kDa 
• Atom Count: 3,851 
• Modeled Residue Count: 448 
• Deposited Residue Count: 520 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysine hydroxylase	A [auth D], B [auth A]	260	Streptomyces roseifaciens	Mutation(s): 0
UniProt
Find proteins for A0A8M0FGT0 (Streptomyces roseifaciens) Explore A0A8M0FGT0  Go to UniProtKB:  A0A8M0FGT0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SIN (Subject of Investigation/LOI)	D [auth A]	SUCCINIC ACID C4 H6 O4 KDYFGRWQOYBRFD-UHFFFAOYSA-N
VVO (Subject of Investigation/LOI)	C [auth D], E [auth A]	oxovanadium(2+) O V MHHDXUNFNAZUGB-UHFFFAOYSA-N

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 = 88.892	α = 90
b = 139.97	β = 90
c = 95.427	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-11-19 
Deposition Author(s): Kissman, E.N., Yang, A.Y., Whitten, A.M., Chang, M.C.Y.

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Funding Organization	Location	Grant Number
Department of Energy (DOE, United States)	United States	DOE/LBL DEAC02-05CH11231 FWP CH030201
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM134271

Revision History  

• Version 1.0: 2025-11-19
  Type: Initial release
  
• Version 1.1: 2025-12-03
  Changes: Database references
• Version 1.2: 2026-03-18
  Changes: Database references