7BBC | pdb_00007bbc

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 
    0.140 (Depositor), 0.141 (DCC) 
  • R-Value Work: 
    0.121 (Depositor), 0.122 (DCC) 
  • R-Value Observed: 
    0.122 (Depositor) 

  • Method: NEUTRON DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.221 (Depositor) 
  • R-Value Work: 
    0.191 (Depositor) 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history

Literature

Visualization of hydrogen atoms in a perdeuterated lectin-fucose complex reveals key details of protein-carbohydrate interactions.

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

(2021) Structure 29: 1003-1013.e4

  • DOI: https://doi.org/10.1016/j.str.2021.03.003
  • Primary Citation Related Structures: 
    7B7C, 7B7E, 7B7F, 7BB4, 7BBC, 7BBI

  • PubMed Abstract: 

    Carbohydrate-binding proteins from pathogenic bacteria and fungi have been shown to be implicated in various pathological processes, where they interact with glycans present on the surface of the host cells. These interactions are part of the initial processes of infection of the host and are very important to study at the atomic level. Here, we report the room temperature neutron structures of PLL lectin from Photorhabdus laumondii in its apo form and in complex with deuterated L-fucose, which is, to our knowledge, the first neutron structure of a carbohydrate-binding protein in complex with a fully deuterated carbohydrate ligand. A detailed structural analysis of the lectin-carbohydrate interactions provides information on the hydrogen bond network, the role of water molecules, and the extent of the CH-π stacking interactions between fucose and the aromatic amino acids in the binding site.


  • Organizational Affiliation
    • Life Sciences Group, Institut Laue-Langevin, 38000 Grenoble, France; Partnership for Structural Biology (PSB), 38000 Grenoble, France; Université Grenoble Alpes, CNRS, CERMAV, 38000 Grenoble, France.

Macromolecule Content 

  • Total Structure Weight: 42.93 kDa 
  • Atom Count: 3,339 
  • Modeled Residue Count: 354 
  • Deposited Residue Count: 381 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
PLL lectin381Photorhabdus laumondiiMutation(s): 0 
Gene Names: CKY10_20885
UniProt
Find proteins for Q7N8J0 (Photorhabdus laumondii subsp. laumondii (strain DSM 15139 / CIP 105565 / TT01))
Explore Q7N8J0 
Go to UniProtKB:  Q7N8J0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7N8J0
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free:  0.140 (Depositor), 0.141 (DCC) 
  • R-Value Work:  0.121 (Depositor), 0.122 (DCC) 
  • R-Value Observed: 0.122 (Depositor) 
  • Method: NEUTRON DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.221 (Depositor) 
  • R-Value Work:  0.191 (Depositor) 
Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.665α = 90
b = 89.21β = 90
c = 159.235γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
iMOSFLMdata processing
Aimlessdata scaling
SCALAdata scaling
PHENIXphasing
LAUEGENdata processing
LAUEGENdata reduction
LSCALEdata scaling

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Institut Laue-LangevinFrance--

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-24
    Type: Initial release
  • Version 1.1: 2021-04-14
    Changes: Database references
  • Version 1.2: 2021-09-15
    Changes: Database references
  • Version 1.3: 2024-05-01
    Changes: Data collection, Refinement description
  • Version 1.4: 2024-10-09
    Changes: Structure summary