5FLY

The FhuD protein from S.pseudintermedius


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

Crystal Structure of Fhud at 1.6 Angstrom Resolution: A Ferrichrome-Binding Protein from the Animal and Human Pathogen Staphylococcus Pseudintermedius

Abate, F.Cozzi, R.Maritan, M.Lo Surdo, P.Maione, D.Malito, E.Bottomley, M.J.

(2016) Acta Crystallogr Sect F Struct Biol Cryst Commun 72: 214

  • DOI: https://doi.org/10.1107/S2053230X16002272
  • Primary Citation of Related Structures:  
    5FLY

  • PubMed Abstract: 

    Staphylococcus pseudintermedius is a leading cause of disease in dogs, and zoonosis causes human infections. Methicillin-resistant S. pseudintermedius strains are emerging, resembling the global health threat of S. aureus. Therefore, it is increasingly important to characterize potential targets for intervention against S. pseudintermedius. Here, FhuD, an S. pseudintermedius surface lipoprotein implicated in iron uptake, was characterized. It was found that FhuD bound ferrichrome in an iron-dependent manner, which increased the thermostability of FhuD by >15 °C. The crystal structure of ferrichrome-free FhuD was determined via molecular replacement at 1.6 Å resolution. FhuD exhibits the class III solute-binding protein (SBP) fold, with a ligand-binding cavity between the N- and C-terminal lobes, which is here occupied by a PEG molecule. The two lobes of FhuD were oriented in a closed conformation. These results provide the first detailed structural characterization of FhuD, a potential therapeutic target of S. pseudintermedius.


  • Organizational Affiliation

    XBrane Biopharma, Stureplan 15, 111 45 Stockholm, Sweden.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ferrichrome ABC transporter substrate-binding protein
A, B
282Staphylococcus pseudintermediusMutation(s): 0 
Gene Names: DD902_02645
UniProt
Find proteins for A0A2P5JFB2 (Staphylococcus pseudintermedius)
Explore A0A2P5JFB2 
Go to UniProtKB:  A0A2P5JFB2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2P5JFB2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
7PG
Query on 7PG

Download Ideal Coordinates CCD File 
CA [auth B],
P [auth A]
2,5,8,11,14,17,20,23-OCTAOXAPENTACOSAN-25-OL
C17 H36 O9
SZGNWRSFHADOMY-UHFFFAOYSA-N
CD
Query on CD

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
Q [auth B],
R [auth B],
S [auth B],
T [auth B]
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
AA [auth B]
BA [auth B]
H [auth A]
I [auth A]
J [auth A]
AA [auth B],
BA [auth B],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
U [auth B],
V [auth B],
W [auth B],
X [auth B],
Y [auth B],
Z [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.582α = 90
b = 53.822β = 99.17
c = 120.248γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Released Date: 2015-12-02 
  • Deposition Author(s): Malito, E.

Revision History  (Full details and data files)

  • Version 1.0: 2015-12-02
    Type: Initial release
  • Version 1.1: 2016-03-09
    Changes: Database references
  • Version 2.0: 2019-09-25
    Changes: Atomic model, Data collection, Database references, Other, Source and taxonomy, Structure summary
  • Version 2.1: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Refinement description