3LDK

Crystal Structure of A. japonicus CB05

• PDB DOI: https://doi.org/10.2210/pdb3LDK/pdb

• Classification: HYDROLASE
• Organism(s): Aspergillus japonicus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-01-13 Released: 2010-05-12 
• Deposition Author(s): Chuankhayan, P., Chen, C.J., Chaing, C.M., Hsieh, C.Y., Chen, C.D., Hsieh, Y.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.264 
• R-Value Work: 0.224 
• R-Value Observed: 0.229 

Literature

Crystal structure of Aspergillus japonicus fructosyltransferase complex with donor/acceptor substrates reveal complete sbusites in the active site for catalysis

Chuankhayan, P., Hsieh, C.Y., Huang, Y.C., Hsieh, Y.Y., Guan, H.H., Hsieh, Y.C., Tien, Y.C., Chen, C.D., Chaing, C.M., Chen, C.J.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 69.28 kDa 
• Atom Count: 5,134 
• Modelled Residue Count: 634 
• Deposited Residue Count: 634 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fructosyltransferase	A	634	Aspergillus japonicus	Mutation(s): 0
UniProt
Find proteins for Q1W3Z7 (Aspergillus japonicus) Explore Q1W3Z7  Go to UniProtKB:  Q1W3Z7

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

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: 2.20 Å
• R-Value Free: 0.264 
• R-Value Work: 0.224 
• R-Value Observed: 0.229 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.35	α = 90
b = 110.967	β = 90
c = 66.129	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-05-12 
Deposition Author(s): Chuankhayan, P., Chen, C.J., Chaing, C.M., Hsieh, C.Y., Chen, C.D., Hsieh, Y.C.

Revision History  

• Version 1.0: 2010-05-12
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: 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: 2024-03-20
  Changes: Data collection, Database references, Structure summary