6Y0W | pdb_00006y0w

Fucosylated antimicrobial linear peptide cFucRH46D in complex with the fucose binding lectin LecB from Pseudomonas aeruginosa at 2.1 Angstrom resolution

• PDB DOI: https://doi.org/10.2210/pdb6Y0W/pdb

• Classification: ANTIBIOTIC
• Organism(s): Pseudomonas aeruginosa, synthetic construct
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2020-02-10 Released: 2021-02-17 
• Deposition Author(s): Baeriswyl, S., Stocker, A., Reymond, J.-L.
• Funding Organization(s): Swiss National Science Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.06 Å
• R-Value Free: 
  0.222 (Depositor), 0.193 (DCC) 
• R-Value Work: 
  0.175 (Depositor), 0.189 (DCC) 
• R-Value Observed: 
  0.178 (Depositor) 

Starting Model: experimental

Literature

Fucosylated antimicrobial linear peptide cFucRH46D in complex with the fucose binding lectin LecB from Pseudomonas aeruginosa at 2.1 Angstrom resolution

Baeriswyl, S., Stocker, A., Reymond, J.-L.

To be published.

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 Evidence: mass spectrometry

Macromolecule Content 

• Total Structure Weight: 27.69 kDa 
• Atom Count: 2,017 
• Modeled Residue Count: 256 
• Deposited Residue Count: 258 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fucose-binding lectin	A, C [auth B]	115	Pseudomonas aeruginosa	Mutation(s): 0  Gene Names:  lecB, C0044_25260, CAZ10_21840, DT376_00595, DY979_15445, ECC04_10105, EFK27_13700, EGV95_09240, EGY23_15550, IPC669_23070, PA5486_01888, PAERUG_E15_London_28_01_14_00983, PAMH19_1713, RW109_RW109_02453
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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
cFucRH46D	B [auth C], D	14	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZDC (Subject of Investigation/LOI)	G [auth C], J [auth D]	3,7-anhydro-2,8-dideoxy-L-glycero-D-gluco-octonic acid C8 H14 O6 YTZUDUWVQZSKNN-OASCRQMUSA-N
CA	E [auth A], F [auth A], H [auth B], I [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.06 Å
• R-Value Free:  0.222 (Depositor), 0.193 (DCC) 
• R-Value Work:  0.175 (Depositor), 0.189 (DCC) 
• R-Value Observed: 0.178 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.999	α = 90
b = 68.999	β = 90
c = 271.453	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-02-17 
Deposition Author(s): Baeriswyl, S., Stocker, A., Reymond, J.-L.

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Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	--

Revision History  

• Version 1.0: 2021-02-17
  Type: Initial release
  
• Version 1.1: 2022-12-07
  Changes: Database references
• Version 1.2: 2024-01-31
  Changes: Data collection, Refinement description
• Version 1.3: 2024-11-20
  Changes: Structure summary