6T96 | pdb_00006t96

Photorhabdus laumondii subsp. laumondii lectin PLL3

• PDB DOI: https://doi.org/10.2210/pdb6T96/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Photorhabdus laumondii subsp. laumondii TTO1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-10-26 Released: 2019-12-25 
• Deposition Author(s): Melicher, F., Houser, J., Fujdiarova, E., Faltinek, L., Wimmerova, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.196 (Depositor), 0.205 (DCC) 
• R-Value Work: 
  0.169 (Depositor), 0.182 (DCC) 
• R-Value Observed: 
  0.171 (Depositor) 

Starting Model: experimental

Literature

Lectin PLL3, a Novel Monomeric Member of the Seven-Bladed beta-Propeller Lectin Family.

Faltinek, L., Fujdiarova, E., Melicher, F., Houser, J., Kasakova, M., Kondakov, N., Kononov, L., Parkan, K., Vidal, S., Wimmerova, M.

(2019) Molecules 24

• PubMed: 31835851 
• DOI: https://doi.org/10.3390/molecules24244540
• Primary Citation Related Structures: 
  6T96


• PubMed Abstract: 
  

  The Photorhabdus species is a Gram-negative bacteria of the family Morganellaceae that is known for its mutualistic relationship with Heterorhabditis nematodes and pathogenicity toward insects. This study is focused on the characterization of the recombinant lectin PLL3 with an origin in P. laumondii subsp. laumondii . PLL3 belongs to the PLL family of lectins with a seven-bladed β-propeller fold. The binding properties of PLL3 were tested by hemagglutination assay, glycan array, isothermal titration calorimetry, and surface plasmon resonance, and its structure was determined by X-ray crystallography. Obtained data revealed that PLL3 binds similar carbohydrates to those that the other PLL family members bind, with some differences in the binding properties. PLL3 exhibited the highest affinity toward l-fucose and its derivatives but was also able to interact with O -methylated glycans and other ligands. Unlike the other members of this family, PLL3 was discovered to be a monomer, which might correspond to a weaker avidity effect compared to homologous lectins. Based on the similarity to the related lectins and their proposed biological function, PLL3 might accompany them during the interaction of P. laumondii with both the nematode partner and the insect host.

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Organizational Affiliation: 
• Department of Biochemistry, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic.
Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic.
National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic.
Department of Chemistry of Natural Compounds, University of Chemistry and Technology, Prague (UCTP), Technická 5, 166 28 Prague, Czech Republic.
N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospect 47, Moscow 119 415, Russia.
Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, CO2-Glyco, UMR 5246, CNRS, Université Claude Bernard Lyon 1, 43 Boulevard du 11 Novembre 1918, 6922 Villeurbanne, France.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: equilibrium centrifugation

Macromolecule Content 

• Total Structure Weight: 40.55 kDa 
• Atom Count: 3,114 
• Modeled Residue Count: 348 
• Deposited Residue Count: 371 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lectin PLL3	A	371	Photorhabdus laumondii subsp. laumondii TTO1	Mutation(s): 0  Gene Names: plu0735
UniProt
Find proteins for Q7N8I7 (Photorhabdus laumondii subsp. laumondii (strain DSM 15139 / CIP 105565 / TT01)) Explore Q7N8I7  Go to UniProtKB:  Q7N8I7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA	B [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO	A	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.196 (Depositor), 0.205 (DCC) 
• R-Value Work:  0.169 (Depositor), 0.182 (DCC) 
• R-Value Observed: 0.171 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.582	α = 90
b = 69.416	β = 90
c = 76.706	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-12-25 
Deposition Author(s): Melicher, F., Houser, J., Fujdiarova, E., Faltinek, L., Wimmerova, M.

Revision History  

• Version 1.0: 2019-12-25
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-11-20
  Changes: Structure summary