Crystal structure of the Ralstonia pickettii toluene transporter TbuX

Experimental Data Snapshot

  • Resolution: 3.20 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.268 
  • R-Value Observed: 0.268 

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Ligand Structure Quality Assessment 

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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
441Ralstonia pickettiiMutation(s): 0 
Gene Names: tbuX
Membrane Entity: Yes 
Find proteins for Q9RBW8 (Ralstonia pickettii)
Explore Q9RBW8 
Go to UniProtKB:  Q9RBW8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9RBW8
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on C8E

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
C16 H34 O5
Experimental Data & Validation

Experimental Data

  • Resolution: 3.20 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.268 
  • R-Value Observed: 0.268 
  • Space Group: F 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 125.291α = 90
b = 125.244β = 90
c = 269.511γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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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: 2024-02-21
    Changes: Data collection, Database references, Derived calculations