5ZSZ

Catechol 2,3-dioxygenase (C23O64) from Diaphorobacter sp DS2

• PDB DOI: https://doi.org/10.2210/pdb5ZSZ/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Diaphorobacter sp. DS2
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2018-04-30 Released: 2019-05-22 
• Deposition Author(s): Mishra, K., Arya, C.K., Subramanian, R., Ramanathan, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.241 
• R-Value Work: 0.200 
• R-Value Observed: 0.202 

Literature

Catechol 2,3-dioxygenase (C23O64) from Diaphorobacter sp DS2

Mishra, K., Arya, C.K., Subramanian, R., Ramanathan, G.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (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: 32.65 kDa 
• Atom Count: 2,312 
• Modelled Residue Count: 293 
• Deposited Residue Count: 293 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Catechol 2,3-dioxygenase, Extradiol ring cleavage protein	A	293	Diaphorobacter sp. DS2	Mutation(s): 0  EC: 1.13.11.2
UniProt
Find proteins for A0A509GUM5 (Diaphorobacter sp. DS2) Explore A0A509GUM5  Go to UniProtKB:  A0A509GUM5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FE	C [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N
CA	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.241 
• R-Value Work: 0.200 
• R-Value Observed: 0.202 
• Space Group: P 6₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.454	α = 90
b = 102.454	β = 90
c = 113.348	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-05-22 
Deposition Author(s): Mishra, K., Arya, C.K., Subramanian, R., Ramanathan, G.

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Funding Organization	Location	Grant Number
	India	BT/IN/SWEDEN/41/SR/2013
	India	BT/PR5081/INF/156/2012
	India	BT/PR12422/MED/31/287/214
	India	BT/INF/22/SP22660/2017
	India	09/092(0869)/2013-EMR-I

Revision History  

• Version 1.0: 2019-05-22
  Type: Initial release
  
• Version 1.1: 2024-03-27
  Changes: Data collection, Database references, Derived calculations