5ZNH

Catechol 2,3-dioxygenase with 4-methyl catechol from Diaphorobacter sp DS2

• PDB DOI: https://doi.org/10.2210/pdb5ZNH/pdb

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


• Deposited: 2018-04-09 Released: 2019-04-17 
• Deposition Author(s): Mishra, K., Arya, C.K., Subramaniyan, R., Ramanathan, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.239 
• R-Value Work: 0.199 
• R-Value Observed: 0.201 

Starting Model: experimental

Literature

catechol 2,3-dioxygenase with 4-methyl catechol from Diaphorobacter sp DS2

Mishra, K., Arya, C.K., Subramaniyan, 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: 35.31 kDa 
• Atom Count: 2,509 
• Modelled Residue Count: 314 
• Deposited Residue Count: 314 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Catechol 2,3-dioxygenase, extradiol protein	A	314	Diaphorobacter sp. DS2	Mutation(s): 0  EC: 1.13.11.2
UniProt
Find proteins for A0A4V8GZK8 (Diaphorobacter sp. DS2) Explore A0A4V8GZK8  Go to UniProtKB:  A0A4V8GZK8

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MCT	C [auth A]	4-METHYLCATECHOL C7 H8 O2 ZBCATMYQYDCTIZ-UHFFFAOYSA-N
PEG	D [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO	E [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
FE	B [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N
CA	F [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.239 
• R-Value Work: 0.199 
• R-Value Observed: 0.201 
• Space Group: P 6₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.894	α = 90
b = 101.894	β = 90
c = 114.369	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: 2019-04-17 
Deposition Author(s): Mishra, K., Arya, C.K., Subramaniyan, 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: 2019-04-17
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description