5C9P

Crystal structure of recombinant PLL lectin complexed with L-fucose from Photorhabdus luminescens at 1.75 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 
    0.181 (Depositor), 0.200 (DCC) 
  • R-Value Work: 
    0.142 (Depositor), 0.160 (DCC) 
  • R-Value Observed: 
    0.144 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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This is version 1.5 of the entry. See complete history


Literature

A Novel Fucose-binding Lectin from Photorhabdus luminescens (PLL) with an Unusual Heptabladed beta-Propeller Tetrameric Structure.

Kumar, A.Sykorova, P.Demo, G.Dobes, P.Hyrsl, P.Wimmerova, M.

(2016) J Biological Chem 291: 25032-25049

  • DOI: https://doi.org/10.1074/jbc.M115.693473
  • Primary Citation of Related Structures:  
    5C9L, 5C9O, 5C9P

  • PubMed Abstract: 

    Photorhabdus luminescens is known for its symbiosis with the entomopathogenic nematode Heterorhabditis bacteriophora and its pathogenicity toward insect larvae. A hypothetical protein from P. luminescens was identified, purified from the native source, and characterized as an l-fucose-binding lectin, named P. luminescens lectin (PLL). Glycan array and biochemical characterization data revealed PLL to be specific toward l-fucose and the disaccharide glycan 3,6-O-Me 2 -Glcβ1-4(2,3-O-Me 2 )Rhaα-O-(p-C 6 H 4 )-OCH 2 CH 2 NH 2 PLL was discovered to be a homotetramer with an intersubunit disulfide bridge. The crystal structures of native and recombinant PLL revealed a seven-bladed β-propeller fold creating seven putative fucose-binding sites per monomer. The crystal structure of the recombinant PLL·l-fucose complex confirmed that at least three sites were fucose-binding. Moreover, the crystal structures indicated that some of the other sites are masked either by the tetrameric nature of the lectin or by incorporation of the C terminus of the lectin into one of these sites. PLL exhibited an ability to bind to insect hemocytes and the cuticular surface of a nematode, H. bacteriophora.


  • Organizational Affiliation

    From the Central European Institute of Technology (CEITEC).


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PLL lectin381Photorhabdus luminescensMutation(s): 0 
Gene Names: plu0732
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
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FUC
Query on FUC

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

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free:  0.181 (Depositor), 0.200 (DCC) 
  • R-Value Work:  0.142 (Depositor), 0.160 (DCC) 
  • R-Value Observed: 0.144 (Depositor) 
Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.783α = 90
b = 87.717β = 90
c = 158.194γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted FUCClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Czech Science FoundationCzech Republic13-25401S
European Regional Development FundCzech RepublicCZ.1.05/1.1.00/02.0068
SYLICACzech RepublicCZ.1.05/1.1.00/02.0068

Revision History  (Full details and data files)

  • Version 1.0: 2016-10-19
    Type: Initial release
  • Version 1.1: 2016-11-02
    Changes: Database references
  • Version 1.2: 2016-12-07
    Changes: Database references
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.4: 2024-01-10
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 1.5: 2024-10-23
    Changes: Structure summary