9IOY | pdb_00009ioy

Isophthalate dioxygenase in complex with isophthalate

• PDB DOI: https://doi.org/10.2210/pdb9IOY/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Comamonas testosteroni KF-1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-07-10 Released: 2025-07-16 
• Deposition Author(s): Jangid, K., Mahto, J.K., Kumar, P.
• Funding Organization(s): Department of Biotechnology (DBT, India)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free: 
  0.218 (Depositor), 0.226 (DCC) 
• R-Value Work: 
  0.175 (Depositor), 0.181 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Starting Model: in silico

Literature

Isophthalate dioxygenase in complex with isophthalate

Jangid, K., Mahto, J.K., Kumar, P.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 51.12 kDa 
• Atom Count: 3,484 
• Modeled Residue Count: 435 
• Deposited Residue Count: 447 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Rieske (2Fe-2S) domain protein	A	447	Comamonas testosteroni KF-1	Mutation(s): 0  Gene Names: CtesDRAFT_PD2139
UniProt
Find proteins for B7WRK8 (Comamonas testosteroni (strain DSM 14576 / KF-1)) Explore B7WRK8  Go to UniProtKB:  B7WRK8

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FES (Subject of Investigation/LOI)	B [auth A]	FE2/S2 (INORGANIC) CLUSTER Fe2 S2 NIXDOXVAJZFRNF-UHFFFAOYSA-N
8G0 (Subject of Investigation/LOI)	D [auth A]	benzene-1,3-dicarboxylic acid C8 H6 O4 QQVIHTHCMHWDBS-UHFFFAOYSA-N
FE2 (Subject of Investigation/LOI)	C [auth A]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free:  0.218 (Depositor), 0.226 (DCC) 
• R-Value Work:  0.175 (Depositor), 0.181 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: P 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 146.956	α = 90
b = 146.956	β = 90
c = 146.956	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CrysalisPro	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-07-16 
Deposition Author(s): Jangid, K., Mahto, J.K., Kumar, P.

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Funding Organization	Location	Grant Number
Department of Biotechnology (DBT, India)	India	--

Revision History  

• Version 1.0: 2025-07-16
  Type: Initial release