5ZNH

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


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 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Catechol 2,3-dioxygenase, extradiol proteinA314Diaphorobacter sp. DS2Mutation(s): 0 
EC: 1.13.11.2
UniProt
Find proteins for A0A4V8GZK8 (Diaphorobacter sp. DS2)
Explore A0A4V8GZK8 
Go to UniProtKB:  A0A4V8GZK8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A4V8GZK8
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MCT
Query on MCT

Download Ideal Coordinates CCD File 
C [auth A]4-METHYLCATECHOL
C7 H8 O2
ZBCATMYQYDCTIZ-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

Download Ideal Coordinates CCD File 
D [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
E [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
FE
Query on FE

Download Ideal Coordinates CCD File 
B [auth A]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
F [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
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 = 101.894α = 90
b = 101.894β = 90
c = 114.369γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
IndiaBT/IN/SWEDEN/41/SR/2013
IndiaBT/PR5081/INF/156/2012
IndiaBT/PR12422/MED/31/287/214
IndiaBT/INF/22/SP22660/2017
India09/092(0869)/2013-EMR-I

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-17
    Type: Initial release