5ZSZ | pdb_00005zsz

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.241 (Depositor), 0.241 (DCC)
R-Value Work:
0.200 (Depositor), 0.204 (DCC)
R-Value Observed:
0.202 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 5ZSZ

This is version 1.1 of the entry. See complete history.

Literature

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

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

To be published.

Macromolecule Content

Total Structure Weight: 32.65 kDa
Atom Count: 2,312
Modeled Residue Count: 293
Deposited Residue Count: 293
Unique protein chains: 1

Macromolecules

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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 A0ACD6BAU1 (Diaphorobacter sp. DS2) Explore A0ACD6BAU1 Go to UniProtKB: A0ACD6BAU1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0ACD6BAU1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FE Query on FE Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.241 (Depositor), 0.241 (DCC)
R-Value Work: 0.200 (Depositor), 0.204 (DCC)
R-Value Observed: 0.202 (Depositor)

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

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2019-05-22

Deposition Author(s):

Subramanian, R.

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 (Full details and data files)

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

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