5ZHQ

Crystal structure of Scylla paramamosain arginine kinase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.183 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structure determination of Scylla paramamosain arginine kinase, an allergen that may cause cross-reactivity among invertebrates.

Yang, Y.Liu, G.Y.Yang, H.Hu, M.J.Cao, M.J.Su, W.J.Jin, T.Liu, G.M.

(2019) Food Chem 271: 597-605

  • DOI: https://doi.org/10.1016/j.foodchem.2018.08.003
  • Primary Citation of Related Structures:  
    5ZHQ

  • PubMed Abstract: 

    Shellfish are one of the most common causes of food allergy. Arginine kinase (AK) is known as an important allergen in shellfish. In the present study, AK from crab (Scylla paramamosain) was purified and its crystal structure was determined. A comparison of AK from S. paramamosain to AKs of other species showed high amino acid sequence and secondary structure identity, while the superposition of crystal structures of AKs from different species revealed only slight differences. Similarity of the linear epitope regions among species was observed in the epitope alignment of AKs; conformational epitopes were located in the regions where secondary structure was conserved. The structure of S. paramamosain AK is an accurate template for the analysis of the IgE binding pattern, and the structure conservation and epitope similarity of AKs among species could help to inform our understanding of the cross-reactivity and contribute to the prediction of cross-reactivity related epitopes.


  • Organizational Affiliation

    College of Food and Biological Engineering, Xiamen Key Laboratory of Marine Functional Food, Fujian Provincial Engineering Technology Research Center of Marine Functional Food, Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Jimei University, Xiamen, Fujian, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Arginine kinase
A, B
357Scylla paramamosainMutation(s): 0 
UniProt
Find proteins for H6VGI3 (Scylla paramamosain)
Explore H6VGI3 
Go to UniProtKB:  H6VGI3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupH6VGI3
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.183 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 136.72α = 90
b = 136.72β = 90
c = 145.9γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-03-20
    Type: Initial release
  • Version 1.1: 2019-08-28
    Changes: Data collection
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description