6STZ

Crystal structure of dimethylated RSLex - cucurbituril free form

• PDB DOI: https://doi.org/10.2210/pdb6STZ/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Ralstonia solanacearum
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2019-09-12 Released: 2020-02-19 
• Deposition Author(s): Guagnini, F., Engilberge, S., Crowley, P.B.
• Funding Organization(s): Science Foundation Ireland

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.14 Å
• R-Value Free: 0.198 
• R-Value Work: 0.173 
• R-Value Observed: 0.174 

Starting Model: experimental

Literature

Engineered assembly of a protein-cucurbituril biohybrid.

Guagnini, F., Engilberge, S., Ramberg, K.O., Perez, J., Crowley, P.B.

(2020) Chem Commun (Camb) 56: 360-363

• PubMed: 31825399 
• DOI: https://doi.org/10.1039/c9cc07198a
• Primary Citation of Related Structures:  
  6STZ, 6SU0


• PubMed Abstract: 
  

  A crystalline biohybrid with a 4 : 1 protein : cucurbituril mass ratio is presented. This result was achieved by engineering additional cucurbit[7]uril (Q7) binding sites into a β-propeller protein. In contrast to the parent protein, Q7-controlled assembly of the engineered variant occurred in solution, as evidenced by NMR and SAXS measurements.

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Organizational Affiliation: 

School of Chemistry, National University of Ireland Galway, University Road, Galway, H91 TK33, Ireland. [e-mail].

Biological Assembly 1  

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

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

Biological Assembly Evidence: SAXS, light scattering

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 61.25 kDa 
• Atom Count: 5,107 
• Modelled Residue Count: 529 
• Deposited Residue Count: 534 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fucose-binding lectin protein	A, B, C, D, E, F	89	Ralstonia solanacearum	Mutation(s): 1  Gene Names: rsl, RUN215_v1_180133
UniProt
Find proteins for Q8XXK6 (Ralstonia nicotianae (strain ATCC BAA-1114 / GMI1000)) Explore Q8XXK6  Go to UniProtKB:  Q8XXK6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BDF	G [auth A], H [auth A], I [auth B], J [auth B], K [auth C], L [auth C], M [auth D], N [auth D], O [auth E], P [auth E], Q [auth F], R [auth F]	beta-D-fructopyranose C6 H12 O6 LKDRXBCSQODPBY-ARQDHWQXSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MLY	A, B, C, D, E, F	L-PEPTIDE LINKING	C8 H18 N2 O2		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.14 Å
• R-Value Free: 0.198 
• R-Value Work: 0.173 
• R-Value Observed: 0.174 
• Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.948	α = 90
b = 43.948	β = 90
c = 207.273	γ = 120

Software Package:

Software Name	Purpose
BUSTER	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-02-19 
Deposition Author(s): Guagnini, F., Engilberge, S., Crowley, P.B.

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Funding Organization	Location	Grant Number
Science Foundation Ireland	Ireland	13/CDA/2168

Revision History  

• Version 1.0: 2020-02-19
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.2: 2024-01-24
  Changes: Data collection, Database references, Refinement description, Structure summary