3ZYH | pdb_00003zyh

CRYSTAL STRUCTURE OF PA-IL LECTIN COMPLEXED WITH GALBG0 AT 1.5 A RESOLUTION

• PDB DOI: https://doi.org/10.2210/pdb3ZYH/pdb

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


• Deposited: 2011-08-23 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: 1.50 Å
• R-Value Free: 
  0.202 (Depositor), 0.205 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.192 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Starting Model: experimental

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 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)

Macromolecule Content 

• Total Structure Weight: 26.42 kDa 
• Atom Count: 2,490 
• Modeled Residue Count: 242 
• Deposited Residue Count: 244 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PA-I galactophilic lectin	A, B	122	Pseudomonas aeruginosa PAO1	Mutation(s): 0  Gene Names: lecA, pa1L, PA2570
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
G0S	D [auth A], F [auth B]	3-(beta-D-galactopyranosylthio)propanoic acid C9 H16 O7 S XMQYQVUZHDCFEM-MRCFXUCSSA-N
CA	C [auth A], E [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.202 (Depositor), 0.205 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.192 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.559	α = 90
b = 72.865	β = 90
c = 133.723	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: 2011-09-28
  Changes: Database references
• Version 1.2: 2011-10-05
  Changes: Atomic model, Other
• Version 1.3: 2011-10-26
  Changes: Atomic model
• Version 1.4: 2011-11-16
  Changes: Database references
• Version 1.5: 2012-11-30
  Changes: Other
• Version 1.6: 2015-09-16
  Changes: Source and taxonomy
• Version 1.7: 2017-08-02
  Changes: Structure summary
• Version 1.8: 2019-10-02
  Changes: Data collection, Derived calculations, Experimental preparation, Other
• Version 1.9: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations
• Version 1.10: 2023-12-20
  Changes: Data collection, Database references, Refinement description, Structure summary