2EAD

Crystal structure of 1,2-a-L-fucosidase from Bifidobacterium bifidum in complex with substrate

• PDB DOI: https://doi.org/10.2210/pdb2EAD/pdb

• Classification: HYDROLASE
• Organism(s): Bifidobacterium bifidum
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2007-01-31 Released: 2007-04-24 
• Deposition Author(s): Nagae, M., Tsuchiya, A., Katayama, T., Yamamoto, K., Wakatsuki, S., Kato, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free: 0.210 
• R-Value Work: 0.159 
• R-Value Observed: 0.162 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 194.67 kDa 
• Atom Count: 15,308 
• Modelled Residue Count: 1,770 
• Deposited Residue Count: 1,798 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-fucosidase	A, B	899	Bifidobacterium bifidum	Mutation(s): 1  EC: 3.2.1.63
UniProt
Find proteins for Q6JV24 (Bifidobacterium bifidum) Explore Q6JV24  Go to UniProtKB:  Q6JV24

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose	C	3		N/A
Glycosylation Resources
GlyTouCan:  G61399NC GlyCosmos:  G61399NC GlyGen:  G61399NC

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MES	H [auth B]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
CA	D [auth A], E [auth A], F [auth B], G [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900070	C	2'-fucosyllactose	Oligosaccharide / Glycan component

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free: 0.210 
• R-Value Work: 0.159 
• R-Value Observed: 0.162 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.448	α = 90
b = 72.743	β = 96.68
c = 129.207	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-04-24 
Deposition Author(s): Nagae, M., Tsuchiya, A., Katayama, T., Yamamoto, K., Wakatsuki, S., Kato, R.

Revision History  

• Version 1.0: 2007-04-24
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
• Version 2.1: 2021-11-10
  Changes: Database references, Structure summary