4CE8 | pdb_00004ce8

Perdeuterated Pseudomonas aeruginosa Lectin II complex with hydrogenated L-Fucose and Calcium

• PDB DOI: https://doi.org/10.2210/pdb4CE8/pdb

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


• Deposited: 2013-11-10 Released: 2014-11-12 
• Deposition Author(s): Cuypers, M.G., Mitchell, E.P., Mossou, E., Pokorna, M., Wimmerova, M., Imberty, A., Moulin, M., Haertlein, M., Forsyth, V.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.90 Å
• R-Value Free: 
  0.141 (Depositor), 0.127 (DCC) 
• R-Value Work: 
  0.125 (Depositor), 0.113 (DCC) 
• R-Value Observed: 
  0.126 (Depositor) 

Starting Model: experimental

Literature

Perdeuterated Pseudomonas Aeruginosa Lectin II Complex with Hydrogenated L Fucose and Calcium

Cuypers, M.G., Mossou, E., Mitchell, E.P., Russi, S., Pokorna, M., Wimmerova, M., Imberty, A., Mcsweeney, S., Haertlein, M., Forsyth, V.T.

To be published.

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: 48.84 kDa 
• Atom Count: 4,775 
• Modeled Residue Count: 456 
• Deposited Residue Count: 456 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FUCOSE-BINDING LECTIN PA-IIL	A, B, C, D	114	Pseudomonas aeruginosa	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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FUC	G [auth A], L [auth B], Q [auth C], V [auth D]	alpha-L-fucopyranose C6 H12 O5 SHZGCJCMOBCMKK-SXUWKVJYSA-N
SO4	H [auth A], I [auth A], M [auth B], N [auth B], R [auth C], S [auth C], W [auth D], X [auth D], Y [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
URE	Z [auth D]	UREA C H4 N2 O XSQUKJJJFZCRTK-UHFFFAOYSA-N
CA	E [auth A], F [auth A], J [auth B], K [auth B], O [auth C], P [auth C], T [auth D], U [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.90 Å
• R-Value Free:  0.141 (Depositor), 0.127 (DCC) 
• R-Value Work:  0.125 (Depositor), 0.113 (DCC) 
• R-Value Observed: 0.126 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.48	α = 90
b = 72.49	β = 94.1
c = 54.61	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
ACORN	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-11-12 
Deposition Author(s): Cuypers, M.G., Mitchell, E.P., Mossou, E., Pokorna, M., Wimmerova, M., Imberty, A., Moulin, M., Haertlein, M., Forsyth, V.T.

Revision History  

• Version 1.0: 2014-11-12
  Type: Initial release
  
• Version 1.1: 2016-09-28
  Changes: Database references
• Version 1.2: 2019-05-08
  Changes: Advisory, Data collection, Experimental preparation, Other
• Version 2.0: 2019-10-23
  Changes: Atomic model, Data collection, Other
• Version 2.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 2.2: 2023-12-20
  Changes: Advisory, Data collection, Database references, Refinement description, Structure summary