3ZYF

CRYSTAL STRUCTURE OF PA-IL LECTIN COMPLEXED WITH NPG AT 1.9 A RESOLUTION

• PDB DOI: https://doi.org/10.2210/pdb3ZYF/pdb

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


• Deposited: 2011-08-22 Released: 2011-09-21 
• Deposition Author(s): Kadam, R.U., Bergmann, M., Hurley, M., Garg, D., Cacciarini, M., Swiderska, M.A., Nativi, C., Sattler, M., Smyth, A.R., Williams, P., Camara, M., Stocker, A., Darbre, T., Reymond, J.-L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free: 0.210 
• R-Value Work: 0.185 
• R-Value Observed: 0.187 

Literature

A Glycopeptide Dendrimer Inhibitor of the Galactose-Specific Lectin Leca and of Pseudomonas Aeruginosa Biofilms.

Kadam, R.U., Bergmann, M., Hurley, M., Garg, D., Cacciarini, M., Swiderska, M.A., Nativi, C., Sattler, M., Smyth, A.R., Williams, P., Camara, M., Stocker, A., Darbre, T., Reymond, J.-L.

(2011) Angew Chem Int Ed Engl 50: 10631

• PubMed: 21919164 
• DOI: https://doi.org/10.1002/anie.201104342
• Primary Citation of Related Structures:  
  3ZYB, 3ZYF, 3ZYH

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Organizational Affiliation: 

Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, 3012 Berne, Switzerland.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 52.97 kDa 
• Atom Count: 4,083 
• Modelled Residue Count: 484 
• Deposited Residue Count: 488 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PA-I GALACTOPHILIC LECTIN	A, B, C, D	122	Pseudomonas aeruginosa PAO1	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
147	F [auth A], H [auth B], J [auth C], L [auth D]	4-nitrophenyl beta-D-galactopyranoside C12 H15 N O8 IFBHRQDFSNCLOZ-YBXAARCKSA-N
CA	E [auth A], G [auth B], I [auth C], K [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
147	Binding MOAD:  3ZYF	Kd: 1.41e+4 (nM) from 1 assay(s)
	PDBBind:  3ZYF	Kd: 1.41e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free: 0.210 
• R-Value Work: 0.185 
• R-Value Observed: 0.187 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.562	α = 90
b = 84.562	β = 90
c = 163.709	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-09-21 
Deposition Author(s): Kadam, R.U., Bergmann, M., Hurley, M., Garg, D., Cacciarini, M., Swiderska, M.A., Nativi, C., Sattler, M., Smyth, A.R., Williams, P., Camara, M., Stocker, A., Darbre, T., Reymond, J.-L.

Revision History  

• Version 1.0: 2011-09-21
  Type: Initial release
  
• Version 1.1: 2012-04-25
  Changes: Other
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary
• Version 2.1: 2023-12-20
  Changes: Data collection, Database references, Refinement description, Structure summary