1XKW | pdb_00001xkw

Pyochelin outer membrane receptor FptA from Pseudomonas aeruginosa


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.242 (Depositor), 0.233 (DCC) 
  • R-Value Work: 
    0.222 (Depositor), 0.212 (DCC) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Crystal structure at high resolution of ferric-pyochelin and its membrane receptor FptA from Pseudomonas aeruginosa

Cobessi, D.Celia, H.Pattus, F.

(2005) J Mol Biology 352: 893-904

  • DOI: https://doi.org/10.1016/j.jmb.2005.08.004
  • Primary Citation Related Structures: 
    1XKW

  • PubMed Abstract: 

    Pyochelin is a siderophore and virulence factor common to Burkholderia cepacia and several Pseudomonas strains. We describe at 2.0 A resolution the crystal structure of the pyochelin outer membrane receptor FptA bound to the iron-pyochelin isolated from Pseudomonas aeruginosa. One pyochelin molecule bound to iron is found in the protein structure, providing the first three-dimensional structure at the atomic level of this siderophore. The pyochelin molecule provides a tetra-dentate coordination of iron, while the remaining bi-dentate coordination is ensured by another molecule not specifically recognized by the protein. The overall structure of the pyochelin receptor is typical of the TonB-dependent transporter superfamily, which uses the proton motive force from the cytoplasmic membrane through the TonB-ExbB-ExbD energy transducing complex to transport ferric ions across the bacterial outer membrane: a transmembrane 22 beta-stranded barrel occluded by a N-terminal domain that contains a mixed four-stranded beta-sheet. The N-terminal TonB box is disordered in two crystal forms, and loop L8 is found to point towards the iron-pyochelin complex, suggesting that the receptor is in a transport-competent conformation.


  • Organizational Affiliation
    • Département Récepteurs et Protéines Membranaires, UMR7100 CNRS, Ecole Supérieure de Biotechnologie de Strasbourg, Boulevard Sébastien Brant, 67412 Illkirch, France. cobessi@esbs.u.strasbg.fr

Macromolecule Content 

  • Total Structure Weight: 76.23 kDa 
  • Atom Count: 5,655 
  • Modeled Residue Count: 655 
  • Deposited Residue Count: 665 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Fe(III)-pyochelin receptor665Pseudomonas aeruginosaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P42512 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore P42512 
Go to UniProtKB:  P42512
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP42512
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
188

Query on 188



Download:Ideal Coordinates CCD File
K [auth A]PYOCHELIN FE(III)
C14 H14 Fe N2 O3 S2
ZSCWPMBACNZOHT-CLNWDJMDSA-L
LDA

Query on LDA



Download:Ideal Coordinates CCD File
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A]
LAURYL DIMETHYLAMINE-N-OXIDE
C14 H31 N O
SYELZBGXAIXKHU-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
B [auth A],
C [auth A],
D [auth A],
E [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO

Query on EDO



Download:Ideal Coordinates CCD File
L [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.242 (Depositor), 0.233 (DCC) 
  • R-Value Work:  0.222 (Depositor), 0.212 (DCC) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.91α = 90
b = 84.54β = 90
c = 162.16γ = 90
Software Package:
Software NamePurpose
XDSdata scaling
XDSdata reduction
AMoREphasing
CNSrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-10-04
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-23
    Changes: Data collection, Database references, Derived calculations, Refinement description