2YFT

Crystal structure of inulosucrase from Lactobacillus johnsonii NCC533 in complex with 1-kestose

• PDB DOI: https://doi.org/10.2210/pdb2YFT/pdb

• Classification: TRANSFERASE
• Organism(s): Lactobacillus johnsonii
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-04-07 Released: 2011-08-03 
• Deposition Author(s): Pijning, T., Anwar, M.A., Leemhuis, H., Kralj, S., Dijkhuizen, L., Dijkstra, B.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.178 
• R-Value Work: 0.156 
• R-Value Observed: 0.157 

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: 64.8 kDa 
• Atom Count: 4,704 
• Modelled Residue Count: 519 
• Deposited Residue Count: 571 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LEVANSUCRASE	A	571	Lactobacillus johnsonii	Mutation(s): 0  EC: 2.4.1.9
UniProt
Find proteins for Q74K42 (Lactobacillus johnsonii (strain CNCM I-12250 / La1 / NCC 533)) Explore Q74K42  Go to UniProtKB:  Q74K42

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-fructofuranose-(2-1)-beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose	B	3		N/A
Glycosylation Resources
GlyTouCan:  G11260CN GlyCosmos:  G11260CN

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A], E [auth A], F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ACT	G [auth A], H [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA	C [auth A]	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_900029	B	1-kestose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.178 
• R-Value Work: 0.156 
• R-Value Observed: 0.157 
• Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 171.204	α = 90
b = 171.204	β = 90
c = 115.003	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-08-03 
Deposition Author(s): Pijning, T., Anwar, M.A., Leemhuis, H., Kralj, S., Dijkhuizen, L., Dijkstra, B.W.

Revision History  

• Version 1.0: 2011-08-03
  Type: Initial release
  
• Version 1.1: 2011-08-17
  Changes: Non-polymer description
• Version 1.2: 2011-08-31
  Changes: Database references
• Version 1.3: 2014-06-11
  Changes: Refinement description
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Other, Structure summary
• Version 2.1: 2023-12-20
  Changes: Data collection, Database references, Refinement description, Structure summary