Crystal structure of Acinetobacter baumannii OccAB3

Experimental Data Snapshot

  • Resolution: 1.75 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.169 

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Structural Insights into Outer Membrane Permeability of Acinetobacter baumannii.

Zahn, M.Bhamidimarri, S.P.Basle, A.Winterhalter, M.van den Berg, B.

(2016) Structure 24: 221-231

  • DOI: https://doi.org/10.1016/j.str.2015.12.009
  • Primary Citation of Related Structures:  
    5DL5, 5DL6, 5DL7, 5DL8

  • PubMed Abstract: 

    Bacterial resistance against antibiotics is an increasing global health problem. In Gram-negative bacteria the low permeability of the outer membrane (OM) is a major factor contributing to resistance, making it important to understand channel-mediated small-molecule passage of the OM. Acinetobacter baumannii has five Occ (OM carboxylate channel) proteins, which collectively are of major importance for the entry of small molecules. To improve our understanding of the OM permeability of A. baumannii, we present here the X-ray crystal structures of four Occ proteins, renamed OccAB1 to OccAB4. In addition we have carried out a biochemical and biophysical characterization using electrophysiology and liposome swelling experiments, providing information on substrate specificities. We identify OccAB1 as having the largest pore of the Occ proteins with corresponding high rates of small-molecule uptake, and we suggest that the future design of efficient antibiotics should focus on scaffolds that can permeate efficiently through the OccAB1 channel.

  • Organizational Affiliation

    Institute for Cellular and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Porin419Acinetobacter baumannii AB307-0294Mutation(s): 0 
Gene Names: ABUW_2771
Membrane Entity: Yes 
Find proteins for A0A0D5YKR4 (Acinetobacter baumannii)
Explore A0A0D5YKR4 
Go to UniProtKB:  A0A0D5YKR4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0D5YKR4
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on C8E

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth A]
I [auth A]
J [auth A]
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A]
C16 H34 O5
Query on CA

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

Experimental Data

  • Resolution: 1.75 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.169 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.563α = 90
b = 125.717β = 90
c = 137.459γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata 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: 2016-02-03
    Type: Initial release
  • Version 1.1: 2016-02-10
    Changes: Database references
  • Version 1.2: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Refinement description