6TVK

Alpha-L-fucosidase isoenzyme 2 from Paenibacillus thiaminolyticus

• PDB DOI: https://doi.org/10.2210/pdb6TVK/pdb

• Classification: HYDROLASE
• Organism(s): Paenibacillus thiaminolyticus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-01-09 Released: 2021-07-21 
• Deposition Author(s): Kovalova, T., Koval, T., Lipovova, P., Dohnalek, J.
• Funding Organization(s): Czech Academy of Sciences, European Regional Development Fund, Ministry of Education, Youth and Sports of the Czech Republic

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.225 
• R-Value Work: 0.189 

Literature

The first structure-function study of GH151 alpha-l-fucosidase uncovers new oligomerization pattern, active site complementation, and selective substrate specificity

Koval'ova, T., Koval, T., Stransky, J., Kolenko, P., Duskova, J., Svecova, L., Vodickova, P., Spiwok, V., Benesova, E., Lipovova, P., Dohnalek, J.

(2022) FEBS J 

• DOI: https://doi.org/10.1111/febs.16387

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)

Biological Assembly Evidence: gel filtration, light scattering, SAXS

Macromolecule Content

• Total Structure Weight: 80.33 kDa 
• Atom Count: 5,648 
• Modelled Residue Count: 660 
• Deposited Residue Count: 689 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-L-fucosidase	A [auth AAA]	689	Paenibacillus thiaminolyticus	Mutation(s): 0  Gene Names: aLfuk2, NCTC11027_00201
UniProt
Find proteins for K0JCW6 (Paenibacillus thiaminolyticus) Explore K0JCW6  Go to UniProtKB:  K0JCW6

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TBR	B [auth AAA]	HEXATANTALUM DODECABROMIDE Br12 Ta6 YWYIQTPPCOBSGN-UHFFFAOYSA-M
SO4	G [auth AAA]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	D [auth AAA], E [auth AAA], F [auth AAA]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	C [auth AAA]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO	A [auth AAA]	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.225 
• R-Value Work: 0.189 
• Space Group: P 6₄ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 125.118	α = 90
b = 125.118	β = 90
c = 231.905	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
AutoSol	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-07-21 
Deposition Author(s): Kovalova, T., Koval, T., Lipovova, P., Dohnalek, J.

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Funding Organization	Location	Grant Number
Czech Academy of Sciences	Czech Republic	86652036
European Regional Development Fund	Czech Republic	CZ.02.1.01/0.0/0.0/15_003/0000447
European Regional Development Fund	Czech Republic	CZ.02.1.01/0.0/0.0/16_013/0001776
Ministry of Education, Youth and Sports of the Czech Republic	Czech Republic	LM2015043
European Regional Development Fund	Czech Republic	CZ.1.05/1.1.00/02.0109

Revision History  

• Version 1.0: 2021-07-21
  Type: Initial release
  
• Version 1.1: 2022-05-18
  Changes: Database references