1OKO

Crystal structure of Pseudomonas Aeruginosa Lectin 1 complexed with galactose at 1.6 A resolution

• PDB DOI: https://doi.org/10.2210/pdb1OKO/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Pseudomonas aeruginosa
• Mutation(s): No 


• Deposited: 2003-07-28 Released: 2003-12-04 
• Deposition Author(s): Cioci, G., Mitchell, E., Gautier, C., Wimmerova, M., Perez, S., Gilboa-Garber, N., Imberty, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.187 
• R-Value Work: 0.154 
• R-Value Observed: 0.156 

Starting Model: other

Literature

Structural Basis of Calcium and Galactose Recognition by the Lectin Pa-Il of Pseudomonas Aeruginosa

Cioci, G., Mitchell, E., Gautier, C., Wimmerova, M., Sudakevitz, D., Perez, S., Gilboa-Garber, N., Imberty, A.

(2003) FEBS Lett 555: 297

• PubMed: 14644431 
• DOI: https://doi.org/10.1016/s0014-5793(03)01249-3
• Primary Citation of Related Structures:  
  1OKO, 1UOJ


• PubMed Abstract: 
  

  The structure of the tetrameric Pseudomonas aeruginosa lectin I (PA-IL) in complex with galactose and calcium was determined at 1.6 A resolution, and the native protein was solved at 2.4 A resolution. Each monomer adopts a beta-sandwich fold with ligand binding site at the apex. All galactose hydroxyl groups, except O1, are involved in a hydrogen bond network with the protein and O3 and O4 also participate in the co-ordination of the calcium ion. The stereochemistry of calcium galactose binding is reminiscent of that observed in some animal C-type lectins. The structure of the complex provides a framework for future design of anti-bacterial compounds.

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Organizational Affiliation: 

CERMAV-CNRS (affiliated with Université Joseph Fourier), PO Box 53, F-38041 Grenoble Cedex 09, France.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 52.91 kDa 
• Atom Count: 4,272 
• Modelled Residue Count: 484 
• Deposited Residue Count: 484 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PA-I GALACTOPHILIC LECTIN	A, B, C, D	121	Pseudomonas aeruginosa	Mutation(s): 0
UniProt
Find proteins for Q05097 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q05097  Go to UniProtKB:  Q05097

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GLA	K [auth B], O [auth C], R [auth D]	alpha-D-galactopyranose C6 H12 O6 WQZGKKKJIJFFOK-PHYPRBDBSA-N
GAL	F [auth A], L [auth B], P [auth C], S [auth D]	beta-D-galactopyranose C6 H12 O6 WQZGKKKJIJFFOK-FPRJBGLDSA-N
MPD	I [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
SO4	G [auth A], H [auth A], M [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CA	E [auth A], J [auth B], N [auth C], Q [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
GLA	BindingDB:  1OKO	Kd: min: 8.75e+4, max: 8.80e+4 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.187 
• R-Value Work: 0.154 
• R-Value Observed: 0.156 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.057	α = 90
b = 53.275	β = 90
c = 160.675	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-12-04 
Deposition Author(s): Cioci, G., Mitchell, E., Gautier, C., Wimmerova, M., Perez, S., Gilboa-Garber, N., Imberty, A.

Revision History  

• Version 1.0: 2003-12-04
  Type: Initial release
  
• Version 1.1: 2015-08-12
  Changes: Atomic model, Derived calculations, Other, Version format compliance
• Version 1.2: 2019-05-08
  Changes: Data collection, Experimental preparation, Other
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Other, Structure summary
• Version 1.4: 2024-05-01
  Changes: Data collection, Database references, Refinement description, Structure summary