8ZYB | pdb_00008zyb

a-KG dependent oxygenase

• PDB DOI: https://doi.org/10.2210/pdb8ZYB/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Penicillium
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-06-17 Released: 2025-06-18 
• Deposition Author(s): Fan, A., Fan, S., Wu, M., Sun, Z.
• Funding Organization(s): Ministry of Science and Technology (MoST, China), National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.58 Å
• R-Value Free: 
  0.257 (Depositor), 0.254 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.203 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Starting Model: in silico

Literature

a-KG dependent oxygenase

Fan, A., Fan, S., Wu, M., Sun, Z.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 8-mer - A8 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: native gel electrophoresis

Macromolecule Content 

• Total Structure Weight: 249.73 kDa 
• Atom Count: 17,100 
• Modeled Residue Count: 2,169 
• Deposited Residue Count: 2,256 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DhiD	A [auth E], B [auth A], C [auth B], D [auth C], E [auth D], F, G, H	282	Penicillium	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FE (Subject of Investigation/LOI)	I [auth E], J [auth A], K [auth B], L [auth C], M [auth D], N [auth F], O [auth G], P [auth H]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.58 Å
• R-Value Free:  0.257 (Depositor), 0.254 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.203 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 368.944	α = 90
b = 78.254	β = 98.02
c = 81.912	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-06-18 
Deposition Author(s): Fan, A., Fan, S., Wu, M., Sun, Z.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	2022YFC2804900
National Natural Science Foundation of China (NSFC)	China	82173733

Revision History  

• Version 1.0: 2025-06-18
  Type: Initial release