7PRG

Joint X-ray/neutron room temperature structure of perdeuterated LecB lectin in complex with perdeuterated fucose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.142 
  • R-Value Work: 0.104 
  • R-Value Observed: 0.106 

  • Method: NEUTRON DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.194 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Neutron crystallography reveals mechanisms used by Pseudomonas aeruginosa for host-cell binding.

Gajdos, L.Blakeley, M.P.Haertlein, M.Forsyth, V.T.Devos, J.M.Imberty, A.

(2022) Nat Commun 13: 194-194

  • DOI: https://doi.org/10.1038/s41467-021-27871-8
  • Primary Citation of Related Structures:  
    7PRG, 7PSY

  • PubMed Abstract: 

    The opportunistic pathogen Pseudomonas aeruginosa, a major cause of nosocomial infections, uses carbohydrate-binding proteins (lectins) as part of its binding to host cells. The fucose-binding lectin, LecB, displays a unique carbohydrate-binding site that incorporates two closely located calcium ions bridging between the ligand and protein, providing specificity and unusually high affinity. Here, we investigate the mechanisms involved in binding based on neutron crystallography studies of a fully deuterated LecB/fucose/calcium complex. The neutron structure, which includes the positions of all the hydrogen atoms, reveals that the high affinity of binding may be related to the occurrence of a low-barrier hydrogen bond induced by the proximity of the two calcium ions, the presence of coordination rings between the sugar, calcium and LecB, and the dynamic behaviour of bridging water molecules at room temperature. These key structural details may assist in the design of anti-adhesive compounds to combat multi-resistance bacterial infections.


  • Organizational Affiliation

    Life Sciences Group, Institut Laue-Langevin, 71 Avenue des Martyrs, 38000, Grenoble, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fucose-binding lectin
A, B, C, D
115Pseudomonas aeruginosaMutation(s): 0 
Gene Names: 
UniProt
Find proteins for A0A069Q9V4 (Pseudomonas aeruginosa)
Explore A0A069Q9V4 
Go to UniProtKB:  A0A069Q9V4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A069Q9V4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FUC (Subject of Investigation/LOI)
Query on FUC

Download Ideal Coordinates CCD File 
G [auth A],
J [auth B],
N [auth C],
O [auth D]
alpha-L-fucopyranose
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
K [auth B]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
CA
Query on CA

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
H [auth B]
I [auth B]
L [auth C]
E [auth A],
F [auth A],
H [auth B],
I [auth B],
L [auth C],
M [auth C],
P [auth D],
Q [auth D]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.142 
  • R-Value Work: 0.104 
  • R-Value Observed: 0.106 
  • Space Group: P 1 21 1
  • Method: NEUTRON DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.194 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.9α = 90
b = 73.87β = 94.58
c = 55.003γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
iMOSFLMdata reduction
Cootmodel building
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Institut Laue-LangevinFrance--

Revision History  (Full details and data files)

  • Version 1.0: 2022-01-12
    Type: Initial release
  • Version 1.1: 2022-01-26
    Changes: Database references
  • Version 1.2: 2024-05-01
    Changes: Data collection, Experimental preparation, Refinement description