Crystal structure of the P. putida toluene transporter TodX

Experimental Data Snapshot

  • Resolution: 2.60 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.253 
  • R-Value Observed: 0.253 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


Outer-membrane transport of aromatic hydrocarbons as a first step in biodegradation.

Hearn, E.M.Patel, D.R.van den Berg, B.

(2008) Proc Natl Acad Sci U S A 105: 8601-8606

  • DOI: https://doi.org/10.1073/pnas.0801264105
  • Primary Citation of Related Structures:  
    3BRY, 3BRZ, 3BS0

  • PubMed Abstract: 

    Bacterial biodegradation of hydrocarbons, an important process for environmental remediation, requires the passage of hydrophobic substrates across the cell membrane. Here, we report crystal structures of two outer membrane proteins, Pseudomonas putida TodX and Ralstonia pickettii TbuX, which have been implicated in hydrocarbon transport and are part of a subfamily of the FadL fatty acid transporter family. The structures of TodX and TbuX show significant differences with those previously determined for Escherichia coli FadL, which may provide an explanation for the substrate-specific transport of TodX and TbuX observed with in vivo transport assays. The TodX and TbuX structures revealed 14-stranded beta-barrels with an N-terminal hatch domain blocking the barrel interior. A hydrophobic channel with bound detergent molecules extends from the extracellular surface and is contiguous with a passageway through the hatch domain, lined by both hydrophobic and polar or charged residues. The TodX and TbuX structures support a mechanism for transport of hydrophobic substrates from the extracellular environment to the periplasm via a channel through the hatch domain.

  • Organizational Affiliation

    Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation Street, Worcester, MA 01605, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
439Pseudomonas putidaMutation(s): 2 
Gene Names: todX
Membrane Entity: Yes 
Find proteins for A5W4F4 (Pseudomonas putida (strain ATCC 700007 / DSM 6899 / BCRC 17059 / F1))
Explore A5W4F4 
Go to UniProtKB:  A5W4F4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA5W4F4
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.60 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.253 
  • R-Value Observed: 0.253 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.098α = 98.39
b = 41.415β = 90.01
c = 141.064γ = 90.06
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-06-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description