6I98 | pdb_00006i98

Structure of the ferrioxamine B transporter FoxA from Pseudomonas aeruginosa, apo state


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.260 (Depositor), 0.269 (DCC) 
  • R-Value Work: 
    0.213 (Depositor), 0.225 (DCC) 
  • R-Value Observed: 
    0.216 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 6I98

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Ternary structure of the outer membrane transporter FoxA with resolved signalling domain provides insights into TonB-mediated siderophore uptake.

Josts, I.Veith, K.Tidow, H.

(2019) Elife 8

  • DOI: https://doi.org/10.7554/eLife.48528
  • Primary Citation Related Structures: 
    6I96, 6I97, 6I98

  • PubMed Abstract: 

    Many microbes and fungi acquire the essential ion Fe 3+ through the synthesis and secretion of high-affinity chelators termed siderophores. In Gram-negative bacteria, these ferric-siderophore complexes are actively taken up using highly specific TonB-dependent transporters (TBDTs) located in the outer bacterial membrane (OM). However, the detailed mechanism of how the inner-membrane protein TonB connects to the transporters in the OM as well as the interplay between siderophore- and TonB-binding to the transporter is still poorly understood. Here, we present three crystal structures of the TBDT FoxA from Pseudomonas aeruginosa (containing a signalling domain) in complex with the siderophore ferrioxamine B and TonB and combine them with a detailed analysis of binding constants. The structures show that both siderophore and TonB-binding is required to form a translocation-competent state of the FoxA transporter in a two-step TonB-binding mechanism. The complex structure also indicates how TonB-binding influences the orientation of the signalling domain.


  • Organizational Affiliation
    • The Hamburg Centre for Ultrafast Imaging, University of Hamburg, Hamburg, Germany.

Macromolecule Content 

  • Total Structure Weight: 79.01 kDa 
  • Atom Count: 5,532 
  • Modeled Residue Count: 677 
  • Deposited Residue Count: 677 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Metal-pseudopaline receptor CntO677Pseudomonas aeruginosaMutation(s): 0 
Gene Names: foxAPA2466
Membrane Entity: Yes 
UniProt
Find proteins for Q9I116 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q9I116 
Go to UniProtKB:  Q9I116
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9I116
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
C8E

Query on C8E



Download:Ideal Coordinates CCD File
G [auth A],
H [auth A],
I [auth A],
J [auth A]
(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE
C16 H34 O5
FEOZZFHAVXYAMB-UHFFFAOYSA-N
FTT

Query on FTT



Download:Ideal Coordinates CCD File
K [auth A],
L [auth A],
M [auth A]
3-HYDROXY-TETRADECANOIC ACID
C14 H28 O3
ATRNZOYKSNPPBF-CYBMUJFWSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
N [auth A]
O [auth A]
P [auth A]
Q [auth A]
R [auth A]
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
T [auth A],
U [auth A],
V [auth A],
W [auth A],
X [auth A],
Y [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A],
E [auth A],
F [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
NI

Query on NI



Download:Ideal Coordinates CCD File
B [auth A]NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
NA

Query on NA



Download:Ideal Coordinates CCD File
AA [auth A],
Z [auth A]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.260 (Depositor), 0.269 (DCC) 
  • R-Value Work:  0.213 (Depositor), 0.225 (DCC) 
  • R-Value Observed: 0.216 (Depositor) 
Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 174.554α = 90
b = 174.554β = 90
c = 180.245γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2019-08-28
    Type: Initial release
  • Version 1.1: 2024-10-16
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 1.2: 2026-01-21
    Changes: Database references, Refinement description, Source and taxonomy, Structure summary