8IL8

Crystal structure of Pyruvic Oxime Dioxygenase (POD) from Alcaligenes faecalis

• PDB DOI: https://doi.org/10.2210/pdb8IL8/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Alcaligenes faecalis subsp. faecalis NBRC 13111
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-03-03 Released: 2024-03-06 
• Deposition Author(s): Tsujino, S., Yamada, Y., Fujiwara, T.
• Funding Organization(s): Ministry of Education, Culture, Sports, Science and Technology (Japan)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free: 0.212 
• R-Value Work: 0.182 
• R-Value Observed: 0.184 

Starting Model: experimental

Literature

Structural and functional analysis of pyruvic oxime dioxygenase, a key enzyme of heterotrophic nitrification

Tsujino, S., Yamada, Y., Senda, M., Senda, T., Fujiwara, T.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 116.78 kDa 
• Atom Count: 7,813 
• Modelled Residue Count: 920 
• Deposited Residue Count: 1,044 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aldolase	A, B, C, D	261	Alcaligenes faecalis subsp. faecalis NBRC 13111	Mutation(s): 0
UniProt
Find proteins for A0A0A2N3A3 (Alcaligenes faecalis) Explore A0A0A2N3A3  Go to UniProtKB:  A0A0A2N3A3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FE2 (Subject of Investigation/LOI)	E [auth A], F [auth B], G [auth C], H [auth D]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free: 0.212 
• R-Value Work: 0.182 
• R-Value Observed: 0.184 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 138.002	α = 90
b = 107.552	β = 128.07
c = 87.794	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
REFMAC	refinement
Coot	model building
autoPROC	data processing
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-03-06 
Deposition Author(s): Tsujino, S., Yamada, Y., Fujiwara, T.

---

Funding Organization	Location	Grant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	21K12220
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	17K00517

Revision History  

• Version 1.0: 2024-03-06
  Type: Initial release