6S7G | pdb_00006s7g

Cfucosylated linker peptide SBL1 bound to Fucose binding Lectin LecB (PA-IIL) from Pseudomonas aeruginosa at 1.84 Angstrom resolution

• PDB DOI: https://doi.org/10.2210/pdb6S7G/pdb

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


• Deposited: 2019-07-04 Released: 2019-08-21 
• 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: 1.84 Å
• R-Value Free: 
  0.211 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Starting Model: experimental

Literature

X-Ray Crystal Structure of a Second Generation Peptide Dendrimer in Complex with Pseudomonas aeruginosa Lectin LecB

Baeriswyl, S., Javor, S., Stocker, A., Darbre, T., Reymond, J.-L.

(2019) Helvetica Chim Acta 

• DOI: https://doi.org/10.1002/hlca.201900178

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A4B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 6-mer - A4B1C1 

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

Biological Assembly Evidence: mass spectrometry

Macromolecule Content 

• Total Structure Weight: 50.16 kDa 
• Atom Count: 3,879 
• Modeled Residue Count: 471 
• Deposited Residue Count: 480 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fucose-binding lectin	A, B, D [auth C], F [auth D]	114	Pseudomonas aeruginosa	Mutation(s): 0  Gene Names:  lecB, C0043_24310, C0044_25260, C0046_23510, CAZ10_21840, CW299_25270, DI492_13230, DT376_00595, 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
SBL1	C [auth F], E [auth G], G [auth H], H [auth E]	6	synthetic construct	Mutation(s): 0

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free:  0.211 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 123.23	α = 90
b = 56.742	β = 90
c = 70.622	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-08-21 
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: 2019-08-21
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations
• Version 1.2: 2024-01-24
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-11-06
  Changes: Structure summary