8W8H | pdb_00008w8h

2-Ketoglutarate-Dependent Dioxygenase

• PDB DOI: https://doi.org/10.2210/pdb8W8H/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Bacillus licheniformis
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2023-09-02 Released: 2024-09-04 
• Deposition Author(s): Zheng, C.N., Wei, W.Q.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 
  0.267 (Depositor), 0.261 (DCC) 
• R-Value Work: 
  0.216 (Depositor), 0.219 (DCC) 
• R-Value Observed: 
  0.219 (Depositor) 

Starting Model: experimental

Literature

Rational Design of the Spatial Effect in a Fe(II)/ alpha-Ketoglutarate-Dependent Dioxygenase Reverses the Regioselectivity of C(sp3)-H Bond Hydroxylation in Aliphatic Amino Acids

Zheng, C., Wei, W., Wen, J., Song, W., Wu, J., Wang, R., Yin, D., Chen, X., Gao, C., Liu, J., Liu, L.

(2024) Angew Chem Int Ed Engl 63

• DOI: https://doi.org/10.1002/anie.202406060

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 119.74 kDa 
• Atom Count: 7,608 
• Modeled Residue Count: 939 
• Deposited Residue Count: 1,052 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2OG-Fe dioxygenase family protein	A, B, C, D	263	Bacillus licheniformis	Mutation(s): 2  Gene Names: CJ481_05930

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ILE (Subject of Investigation/LOI)	E [auth A], F [auth A], G [auth B], H [auth B], I [auth C], J [auth C], K [auth D], L [auth D]	ISOLEUCINE C6 H13 N O2 AGPKZVBTJJNPAG-WHFBIAKZSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free:  0.267 (Depositor), 0.261 (DCC) 
• R-Value Work:  0.216 (Depositor), 0.219 (DCC) 
• R-Value Observed: 0.219 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.145	α = 90
b = 129.628	β = 90
c = 153.684	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-09-04 
Deposition Author(s): Zheng, C.N., Wei, W.Q.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-09-04
  Type: Initial release
  
• Version 1.1: 2025-09-17
  Changes: Database references, Structure summary