3QEF

The structure and function of an arabinan-specific alpha-1,2-arabinofuranosidase identified from screening the activities of bacterial GH43 glycoside hydrolases

• PDB DOI: https://doi.org/10.2210/pdb3QEF/pdb

• Classification: HYDROLASE
• Organism(s): Cellvibrio japonicus Ueda107
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2011-01-20 Released: 2011-02-16 
• Deposition Author(s): Cartmell, A., Mckee, L.S., Pena, M., Larsbrink, J., Brumer, H., Lewis, R.J., Viks-Nielsen, A., Gilbert, H.J., Marles-Wright, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free: 0.198 
• R-Value Work: 0.169 
• R-Value Observed: 0.171 

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)

Macromolecule Content

• Total Structure Weight: 70.33 kDa 
• Atom Count: 5,383 
• Modelled Residue Count: 593 
• Deposited Residue Count: 614 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-xylosidase/alpha-L-arabinfuranosidase, gly43N	A, B	307	Cellvibrio japonicus Ueda107	Mutation(s): 1  Gene Names: gly43N, CJA_3018 EC: 3.2.1
UniProt
Find proteins for B3PD60 (Cellvibrio japonicus (strain Ueda107)) Explore B3PD60  Go to UniProtKB:  B3PD60

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-arabinofuranose-(1-5)-alpha-L-arabinofuranose-(1-5)-alpha-L-arabinofuranose	C	3		N/A
Glycosylation Resources
GlyTouCan:  G56809YT GlyCosmos:  G56809YT

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-arabinofuranose-(1-3)-[alpha-L-arabinofuranose-(1-5)]alpha-L-arabinofuranose-(1-5)-alpha-L-arabinofuranose	D	4		N/A
Glycosylation Resources
GlyTouCan:  G45746QF GlyCosmos:  G45746QF

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	F [auth A], H [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA	E [auth A], G [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free: 0.198 
• R-Value Work: 0.169 
• R-Value Observed: 0.171 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.64	α = 90
b = 85.64	β = 90
c = 195.56	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MAR345dtb	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-02-16 
Deposition Author(s): Cartmell, A., Mckee, L.S., Pena, M., Larsbrink, J., Brumer, H., Lewis, R.J., Viks-Nielsen, A., Gilbert, H.J., Marles-Wright, J.

Revision History  

• Version 1.0: 2011-02-16
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2019-07-17
  Changes: Data collection, Derived calculations, Refinement description
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary
• Version 2.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
• Version 2.2: 2024-03-13
  Changes: Source and taxonomy