2D43

Crystal structure of arabinofuranosidase complexed with arabinotriose

• PDB DOI: https://doi.org/10.2210/pdb2D43/pdb

• Classification: HYDROLASE
• Organism(s): Aspergillus luchuensis
• Expression System: Komagataella pastoris
• Mutation(s): Yes 


• Deposited: 2005-10-07 Released: 2006-09-19 
• Deposition Author(s): Miyanaga, A., Koseki, T., Miwa, Y., Matsuzawa, H., Wakagi, T., Shoun, H., Fushinobu, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.248 
• R-Value Work: 0.199 
• R-Value Observed: 0.199 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 51.81 kDa 
• Atom Count: 3,700 
• Modelled Residue Count: 482 
• Deposited Residue Count: 482 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
alpha-L-arabinofuranosidase B	A	482	Aspergillus luchuensis	Mutation(s): 1  EC: 3.2.1.55
UniProt
Find proteins for Q8NK89 (Aspergillus kawachii (strain NBRC 4308)) Explore Q8NK89  Go to UniProtKB:  Q8NK89

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-arabinofuranose-(1-5)-alpha-L-arabinofuranose	C, D	2		N/A
Glycosylation Resources
GlyTouCan:  G41001SE GlyCosmos:  G41001SE

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.248 
• R-Value Work: 0.199 
• R-Value Observed: 0.199 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.482	α = 90
b = 98.75	β = 90
c = 144.473	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-09-19 
Deposition Author(s): Miyanaga, A., Koseki, T., Miwa, Y., Matsuzawa, H., Wakagi, T., Shoun, H., Fushinobu, S.

Revision History  

• Version 1.0: 2006-09-19
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
• Version 2.1: 2021-11-10
  Changes: Database references, Derived calculations, Structure summary