2BOJ

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

PDB DOI: https://doi.org/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.

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

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

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 Search on PubMed
DOI: https://doi.org/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.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 48.01 kDa
Atom Count: 4,102
Modelled Residue Count: 456
Deposited Residue Count: 456
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9HYN5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ARW Query on ARW Download Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain K [auth C] SDF format, chain O [auth D] SDF format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain K [auth C] MOL2 format, chain O [auth D] MOL2 format, chain E [auth A]	E [auth A], H [auth B], K [auth C], O [auth D]	methyl beta-D-arabinopyranoside C₆ H₁₂ O₅ ZBDGHWFPLXXWRD-ARQDHWQXSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain O [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain O [auth D]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain N [auth C] MOL2 format, chain N [auth C]	N [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain N [auth C] Interactions & Density Focus chain N [auth C]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain L [auth C] SDF format, chain P [auth D] SDF format, chain Q [auth D] SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain M [auth C] MOL2 format, chain G [auth A] MOL2 format, chain L [auth C] MOL2 format, chain P [auth D] MOL2 format, chain Q [auth D] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain M [auth C]	F [auth A] G [auth A] I [auth B] J [auth B] L [auth C] 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		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain P [auth D] Focus chain Q [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain P [auth D] Focus chain Q [auth D]

Binding Affinity Annotations
ID	Source	Binding Affinity
ARW	PDBBind: 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

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2006-02-22

Deposition Author(s):

Revision History (Full details and data files)

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
Version 1.4: 2023-12-13
Changes: Data collection, Database references, Refinement description, Structure summary