2EHZ | pdb_00002ehz

Anaerobic Crystal Structure Analysis of 1,2-dihydroxynaphthalene dioxygenase from Pseudomonas sp. strain C18 complexed with 4-methylcatechol

• PDB DOI: https://doi.org/10.2210/pdb2EHZ/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Pseudomonas sp. C18
• Expression System: Pseudomonas putida
• Mutation(s): No 


• Deposited: 2007-03-10 Released: 2008-02-19 
• Deposition Author(s): Neau, D.B., Kelker, M.S., Colbert, C.L., Bolin, J.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 
  0.178 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.165 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.166 (Depositor) 

Starting Model: experimental

Literature

Structural explanation for success and failure in the enzymatic ring-cleavage of 3,4 dihydroxybiphenyl and related PCB metabolites

Neau, D.B., Kelker, M.S., Maaroufi, H., Colbert, C.L., Eltis, L.D., Bolin, J.T.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D4  (Explore in 3D)
Global Stoichiometry: Homo 8-mer - A8 

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

Macromolecule Content 

• Total Structure Weight: 34.87 kDa 
• Atom Count: 2,748 
• Modeled Residue Count: 299 
• Deposited Residue Count: 302 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
1,2-dihydroxynaphthalene dioxygenase	A	302	Pseudomonas sp. C18	Mutation(s): 0  Gene Names: doxG EC: 1.13.11 (PDB Primary Data), 1.13.11.56 (UniProt)
UniProt
Find proteins for P0A108 (Pseudomonas sp. (strain C18)) Explore P0A108  Go to UniProtKB:  P0A108

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MCT	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	4-METHYLCATECHOL C7 H8 O2 ZBCATMYQYDCTIZ-UHFFFAOYSA-N
EDO	J [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
FE2	B [auth A]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free:  0.178 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.165 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.166 (Depositor) 

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.82	α = 90
b = 117.82	β = 90
c = 121.16	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-02-19 
Deposition Author(s): Neau, D.B., Kelker, M.S., Colbert, C.L., Bolin, J.T.

Revision History  

• Version 1.0: 2008-02-19
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Derived calculations, Source and taxonomy, Version format compliance
• Version 1.2: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description