2EI0 | pdb_00002ei0

Anaerobic Crystal Structure Analysis of 1,2-dihydroxynaphthalene dioxygenase from Pseudomonas sp. strain C18 complexed with 3,4-dihydroxybiphenyl

• PDB DOI: https://doi.org/10.2210/pdb2EI0/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: 1.60 Å
• R-Value Free: 
  0.176 (Depositor), 0.177 (DCC) 
• R-Value Work: 
  0.160 (Depositor), 0.162 (DCC) 
• R-Value Observed: 
  0.161 (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: 34.72 kDa 
• Atom Count: 2,673 
• Modeled Residue Count: 286 
• 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
BP7	D [auth A], E [auth A], F [auth A]	1,1'-BIPHENYL-3,4-DIOL C12 H10 O2 QDNPCYCBQFHNJC-UHFFFAOYSA-N
GOL	G [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-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: 1.60 Å
• R-Value Free:  0.176 (Depositor), 0.177 (DCC) 
• R-Value Work:  0.160 (Depositor), 0.162 (DCC) 
• R-Value Observed: 0.161 (Depositor) 

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.87	α = 90
b = 117.87	β = 90
c = 121.594	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