Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 48.01 kDa 
• Atom Count: 4102 
• Modelled Residue Count: 456 
• Deposited Residue Count: 456 
• Unique protein chains: 1

2BOJ

crystal Structure of pseudomonas aeruginosa lectin (PA-IIL) complexed with methyl-B-D-Arabinopyranoside

• PDB DOI: 10.2210/pdb2BOJ/pdb

• Classification: LECTIN
• Organism(s): Pseudomonas aeruginosa PAO1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2005-04-12 Released: 2006-02-22 
• Deposition Author(s): Sabin, C.D., Mitchell, E.P., Wimmerova, M., Imberty, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.172 
• R-Value Work: 0.136 
• R-Value Observed: 0.137 

Literature

Binding of Different Monosaccharides by Lectin Pa-Iil from Pseudoman Aeruginosa: Thermodynamics Data Correlated with X-Ray Structures.

Sabin, C.D., Mitchell, E.P., Pokarna, M., Gautier, C., Utille, J.-P., Wimmerova, M., Imberty, A.

(2006) FEBS Lett 580: 982

• PubMed: 16438968 
• DOI: 10.1016/j.febslet.2006.01.030
• Primary Citation of Related Structures:  
  2BOJ, 2BP6


• PubMed Abstract: 
  

The lectin from Pseudomonas aeruginosa (PA-IIL) is involved in host recognition and biofilm formation. Lectin not only displays an unusually high affinity for fucose but also binds to L-fucose, L-galactose and D-arabinose that differ only by the group at position 5 of the sugar ring. Isothermal calorimetry experiments provided precise determination of affinity for the three methyl-glycosides and revealed a large enthalpy contribution. The crystal structures of the complexes of PA-IIL with L-galactose and Met-beta-D-arabinoside have been determined and compared with the PA-IIL/fucose complex described previously. A combination of the structures and thermodynamics provided clues for the role of the hydrophobic group in affinity.

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Related Citations: 

• High Affinity Fucose Binding of Pseudomonas Aeruginosa Lectin Pa-Iil: 1.0 A Resolution Crystal Structure of the Complex Combined with Thermodynamics and Computational Chemistry Approaches
  Mitchell, E., Sabin, C.D., Snajdrova, L., Pokorna, M., Perret, S., Gautier, C., Hofr, C., Gilboa-Garber, N., Koca, J., Wimmerova, M., Imberty, A.
  (2005) Proteins 58: 735

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Organizational Affiliation: 

CERMAV-CNRS (affiliated with Université Joseph Fourier), 601 rue de la Chimie, Grenoble BP53, F-38041 Grenoble cedex 09, France.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PSEUDOMONAS AERUGINOSA LECTIN II	A, B, C, D	114	Pseudomonas aeruginosa PAO1	Mutation(s): 0  Gene Names: lecB, PA3361
UniProt
Find proteins for Q9HYN5 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9HYN5  Go to UniProtKB:  Q9HYN5

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ARW	E [auth A], H [auth B], K [auth C], O [auth D]	methyl beta-D-arabinopyranoside C6 H12 O5 ZBDGHWFPLXXWRD-ARQDHWQXSA-N
SO4	N [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CA	F [auth A], G [auth A], I [auth B], J [auth B], L [auth C], M [auth C], P [auth D], Q [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
ARW	PDBBind:  2BOJ	Kd: 1700 (nM) from 1 assay(s)
	Binding MOAD:  2BOJ	Kd: 1700 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.172 
• R-Value Work: 0.136 
• R-Value Observed: 0.137 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.636	α = 90
b = 80.168	β = 109.92
c = 52.517	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALA	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-04-12 
• Released Date: 2006-02-22 
Deposition Author(s): Sabin, C.D., Mitchell, E.P., Wimmerova, M., Imberty, A.

Revision History  

• Version 1.0: 2006-02-22
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Other, Structure summary