6Y0X

Fucosylated antimicrobial peptide SB6 in complex with the lectin LecRSL from Ralstonia solanacearum at 2.4 Angstrom resolution

• PDB DOI: https://doi.org/10.2210/pdb6Y0X/pdb

• Classification: ANTIBIOTIC
• Organism(s): Ralstonia solanacearum, 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: 2.42 Å
• R-Value Free: 0.280 
• R-Value Work: 0.243 
• R-Value Observed: 0.245 

Starting Model: experimental

Literature

Fucosylated antimicrobial peptide SB6 in complex with the lectin LecRSL from Ralstonia solanacearum at 2.4 Angstrom resolution

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

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: mass spectrometry

Biological Assembly 2  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 73.25 kDa 
• Atom Count: 4,927 
• Modelled Residue Count: 621 
• Deposited Residue Count: 647 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fucose-binding lectin protein	A, B, E [auth C], H [auth D], J [auth E], L [auth F]	91	Ralstonia solanacearum	Mutation(s): 0  Gene Names: E7Z57_08365, RSP795_21825, RSP822_19650, RUN39_v1_50103
UniProt
Find proteins for A0A0S4TLR1 (Ralstonia solanacearum) Explore A0A0S4TLR1  Go to UniProtKB:  A0A0S4TLR1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
SB6	C [auth I], F [auth K], N [auth R]	12	synthetic construct	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
SB6	D [auth J], G [auth L], I [auth M], K [auth O], M [auth Q]	13	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZDC (Subject of Investigation/LOI)	AA [auth R], O [auth A], Q [auth A], R [auth I], S [auth J], T [auth K], U [auth L], V [auth D], W [auth M], X [auth E], Y [auth O], Z [auth Q]	3,7-anhydro-2,8-dideoxy-L-glycero-D-gluco-octonic acid C8 H14 O6 YTZUDUWVQZSKNN-OASCRQMUSA-N
DLY (Subject of Investigation/LOI)	P [auth A]	D-LYSINE C6 H14 N2 O2 KDXKERNSBIXSRK-RXMQYKEDSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.42 Å
• R-Value Free: 0.280 
• R-Value Work: 0.243 
• R-Value Observed: 0.245 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.51	α = 90
b = 100.51	β = 90
c = 271.653	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
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: 2024-01-24
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-10-16
  Changes: Structure summary