2UZ2

Crystal structure of Xenavidin

• PDB DOI: https://doi.org/10.2210/pdb2UZ2/pdb

• Classification: GLYCOPROTEIN
• Organism(s): Xenopus tropicalis
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2007-04-24 Released: 2008-06-03 
• Deposition Author(s): Helppolainen, S.H., Maatta, J.A.E., Airenne, T.T., Johnson, M.S., Kulomaa, M.S., Nordlund, H.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.216 
• R-Value Work: 0.181 
• R-Value Observed: 0.183 

Literature

Structural and Functional Characteristics of Xenavidin, the First Frog Avidin from Xenopus Tropicalis.

Maatta, J.A.E., Helppolainen, S.H., Hytonen, V.P., Johnson, M.S., Kulomaa, M.S., Airenne, T.T., Nordlund, H.R.

(2009) BMC Struct Biol 9: 63

• PubMed: 19788720 
• DOI: https://doi.org/10.1186/1472-6807-9-63
• Primary Citation of Related Structures:  
  2UYW, 2UZ2


• PubMed Abstract: 
  

  Avidins are proteins with extraordinarily high ligand-binding affinity, a property which is used in a wide array of life science applications. Even though useful for biotechnology and nanotechnology, the biological function of avidins is not fully understood. Here we structurally and functionally characterise a novel avidin named xenavidin, which is to our knowledge the first reported avidin from a frog.

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Organizational Affiliation: 

Institute of Medical Technology, Biokatu 6, FI-33014 University of Tampere and Tampere University Hospital, Tampere, Finland. [e-mail]

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 30.08 kDa 
• Atom Count: 2,225 
• Modelled Residue Count: 234 
• Deposited Residue Count: 260 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
XENAVIDIN	A, B [auth D]	130	Xenopus tropicalis	Mutation(s): 0
UniProt
Find proteins for A7YYL1 (Xenopus tropicalis) Explore A7YYL1  Go to UniProtKB:  A7YYL1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BTN	D	BIOTIN C10 H16 N2 O3 S YBJHBAHKTGYVGT-ZKWXMUAHSA-N
ACT	C [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.216 
• R-Value Work: 0.181 
• R-Value Observed: 0.183 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.817	α = 90
b = 110.817	β = 90
c = 142.339	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
ARP/wARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-06-03 
Deposition Author(s): Helppolainen, S.H., Maatta, J.A.E., Airenne, T.T., Johnson, M.S., Kulomaa, M.S., Nordlund, H.R.

Revision History  

• Version 1.0: 2008-06-03
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Refinement description, Version format compliance
• Version 1.2: 2017-06-28
  Changes: Refinement description