2OXB

Crystal structure of a cell-wall invertase (E203Q) from Arabidopsis thaliana in complex with sucrose

• PDB DOI: https://doi.org/10.2210/pdb2OXB/pdb

• Classification: HYDROLASE
• Organism(s): Arabidopsis thaliana
• Expression System: Komagataella pastoris
• Mutation(s): Yes 


• Deposited: 2007-02-20 Released: 2008-01-22 
• Deposition Author(s): Lammens, W., Le Roy, K., Van Laere, A., Van den Ende, W., Rabijns, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.268 
• R-Value Work: 0.205 
• R-Value Observed: 0.205 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 62.11 kDa 
• Atom Count: 4,414 
• Modelled Residue Count: 537 
• Deposited Residue Count: 537 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-fructofuranosidase	A	537	Arabidopsis thaliana	Mutation(s): 1  Gene Names: ATBFRUCT1 EC: 3.2.1.26
UniProt
Find proteins for Q43866 (Arabidopsis thaliana) Explore Q43866  Go to UniProtKB:  Q43866

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose	B	2		N/A
Glycosylation Resources
GlyTouCan:  G05551OP GlyCosmos:  G05551OP

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	C [auth A], D [auth A], E [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900003	B	sucrose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.268 
• R-Value Work: 0.205 
• R-Value Observed: 0.205 
• Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.454	α = 90
b = 106.454	β = 90
c = 50.548	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
MAR345dtb	data collection
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-01-22 
Deposition Author(s): Lammens, W., Le Roy, K., Van Laere, A., Van den Ende, W., Rabijns, A.

Revision History  

• Version 1.0: 2008-01-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2021-10-20
  Changes: Database references, Structure summary
• Version 2.2: 2023-08-30
  Changes: Data collection, Refinement description