2EI1 | pdb_00002ei1

Anaerobic Crystal Structure Analysis of the 1,2-dihydroxynaphthalene dioxygeanse of Pseudomonas sp. strain C18 complexes to 1,2-dihydroxynaphthalene

• PDB DOI: https://doi.org/10.2210/pdb2EI1/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: 1.52 Å
• R-Value Free: 
  0.180 (Depositor), 0.218 (DCC) 
• R-Value Work: 
  0.171 (Depositor) 
• R-Value Observed: 
  0.172 (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: 34.32 kDa 
• Atom Count: 2,632 
• Modeled Residue Count: 293 
• 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
D1N	D [auth A]	NAPHTHALENE-1,2-DIOL C10 H8 O2 NXPPAOGUKPJVDI-UHFFFAOYSA-N
GOL	E [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: 1.52 Å
• R-Value Free:  0.180 (Depositor), 0.218 (DCC) 
• R-Value Work:  0.171 (Depositor) 
• R-Value Observed: 0.172 (Depositor) 

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.848	α = 90
b = 117.848	β = 90
c = 120.965	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: 2020-09-09
  Changes: Advisory, Derived calculations, Structure summary
• Version 1.3: 2023-10-25
  Changes: Advisory, Data collection, Database references, Refinement description