2XIB

CRYSTAL STRUCTURE OF AN ALPHA-L-FUCOSIDASE GH29 FROM BACTEROIDES THETAIOTAOMICRON IN COMPLEX WITH DEOXYFUCONOJIRIMYCIN

• PDB DOI: https://doi.org/10.2210/pdb2XIB/pdb

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


• Deposited: 2010-06-28 Released: 2010-07-21 
• Deposition Author(s): Lammerts van Bueren, A., Popat, S.D., Lin, C.H., Davies, G.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.235 
• R-Value Work: 0.185 
• R-Value Observed: 0.188 

Literature

Structural and Thermodynamic Analyses of Alpha-L-Fucosidase Inhibitors.

Lammerts Van Bueren, A., Popat, S.D., Lin, C.H., Davies, G.J.

(2010) Chembiochem 11: 1971

• PubMed: 20665773 
• DOI: https://doi.org/10.1002/cbic.201000339
• Primary Citation of Related Structures:  
  2XIB, 2XII

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Organizational Affiliation: 

Department of Chemistry, University of York, Heslington, York YO10 5DD, UK.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 211.29 kDa 
• Atom Count: 15,070 
• Modelled Residue Count: 1,748 
• Deposited Residue Count: 1,812 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ALPHA-L-FUCOSIDASE	A, B, C, D	453	Bacteroides thetaiotaomicron	Mutation(s): 0
UniProt
Find proteins for Q8A3I4 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50)) Explore Q8A3I4  Go to UniProtKB:  Q8A3I4

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DFU	E [auth A], I [auth B], M [auth C], P [auth D]	(2S,3R,4S,5R)-2-METHYLPIPERIDINE-3,4,5-TRIOL C6 H13 N O3 VYOCYWDJTQRZLC-KCDKBNATSA-N
TRS	R [auth D]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
SO4	F [auth A], G [auth A], J [auth B], N [auth C], Q [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	H [auth A], K [auth B], L [auth B], O [auth C], S [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
DFU	Binding MOAD:  2XIB	Kd: 55.1 (nM) from 1 assay(s)
	PDBBind:  2XIB	Kd: 55.1 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.235 
• R-Value Work: 0.185 
• R-Value Observed: 0.188 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.68	α = 90
b = 185.99	β = 94.75
c = 97.63	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-07-21 
Deposition Author(s): Lammerts van Bueren, A., Popat, S.D., Lin, C.H., Davies, G.J.

Revision History  

• Version 1.0: 2010-07-21
  Type: Initial release
  
• Version 1.1: 2012-04-25
  Changes: Database references, Non-polymer description, Other, Refinement description, Structure summary, Version format compliance
• Version 1.2: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description