8P1S

Bifidobacterium asteroides alpha-L-fucosidase (TT1819) in complex with fucose.

• PDB DOI: https://doi.org/10.2210/pdb8P1S/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Bifidobacterium asteroides
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-05-12 Released: 2024-05-22 
• Deposition Author(s): Owen, C.D., Penner, M., Gascuena, A.N., Wu, H., Hernando, P.J., Monaco, S., Le Gall, G., Gardner, R., Ndeh, D., Urbanowicz, P.A., Spencer, D.I.R., Walsh, M.A., Angulo, J., Juge, N.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC), Spanish Ministry of Science, Innovation, and Universities, H2020 Marie Curie Actions of the European Commission, UK Research and Innovation (UKRI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.207 
• R-Value Work: 0.169 

Starting Model: experimental

Literature

Exploring sequence, structure and function of microbial fucosidases from glycoside hydrolase GH29 family

Owen, C.D., Penner, M., Gascuena, A.N., Wu, H., Hernando, P.J., Monaco, S., Le Gall, G., Gardner, R., Ndeh, D., Urbanowicz, P.A., Spencer, D.I.R., Walsh, M.A., Angulo, J., Juge, N.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 234.97 kDa 
• Atom Count: 17,134 
• Modelled Residue Count: 2,010 
• Deposited Residue Count: 2,052 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bifidobacterium asteroides alpha-L-fucosidase (TT1819)	A, B, C, D, E, F	342	Bifidobacterium asteroides	Mutation(s): 0
UniProt
Find proteins for A0A0F4KU40 (Bifidobacterium asteroides) Explore A0A0F4KU40  Go to UniProtKB:  A0A0F4KU40

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FUC (Subject of Investigation/LOI)	I [auth A], L [auth B], N [auth C], Q [auth D], T [auth E], V [auth F]	alpha-L-fucopyranose C6 H12 O5 SHZGCJCMOBCMKK-SXUWKVJYSA-N
TRS	J [auth A], O [auth D]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
GOL	R [auth E]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
IMD	P [auth D], U [auth F]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O
EDO	G [auth A], H [auth A], K [auth B], M [auth C], S [auth E]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.207 
• R-Value Work: 0.169 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.058	α = 90
b = 142.765	β = 90
c = 167.202	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
REFMAC	refinement
xia2	data reduction
DIALS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-05-22 
Deposition Author(s): Owen, C.D., Penner, M., Gascuena, A.N., Wu, H., Hernando, P.J., Monaco, S., Le Gall, G., Gardner, R., Ndeh, D., Urbanowicz, P.A., Spencer, D.I.R., Walsh, M.A., Angulo, J., Juge, N.

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Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/P010660/1
Spanish Ministry of Science, Innovation, and Universities	Spain	PID2019-109395GB-I00
H2020 Marie Curie Actions of the European Commission	European Union	814102
UK Research and Innovation (UKRI)	United Kingdom	BB/M029042/

Revision History  

• Version 1.0: 2024-05-22
  Type: Initial release