Racemic snakin-1 in P21/c

Experimental Data Snapshot

  • Resolution: 1.60 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.238 

wwPDB Validation   3D Report Full Report

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Radiation Damage and Racemic Protein Crystallography Reveal the Unique Structure of the GASA/Snakin Protein Superfamily.

Yeung, H.Squire, C.J.Yosaatmadja, Y.Panjikar, S.Lopez, G.Molina, A.Baker, E.N.Harris, P.W.Brimble, M.A.

(2016) Angew Chem Int Ed Engl 55: 7930-7933

  • DOI: https://doi.org/10.1002/anie.201602719
  • Primary Citation of Related Structures:  
    5E5Q, 5E5T, 5E5Y

  • PubMed Abstract: 

    Proteins from the GASA/snakin superfamily are common in plant proteomes and have diverse functions, including hormonal crosstalk, development, and defense. One 63-residue member of this family, snakin-1, an antimicrobial protein from potatoes, has previously been chemically synthesized in a fully active form. Herein the 1.5 Å structure of snakin-1, determined by a novel combination of racemic protein crystallization and radiation-damage-induced phasing (RIP), is reported. Racemic crystals of snakin-1 and quasi-racemic crystals incorporating an unnatural 4-iodophenylalanine residue were prepared from chemically synthesized d- and l-proteins. Breakage of the C-I bonds in the quasi-racemic crystals facilitated structure determination by RIP. The crystal structure reveals a unique protein fold with six disulfide crosslinks, presenting a distinct electrostatic surface that may target the protein to microbial cell surfaces.

  • Organizational Affiliation

    School of Biological Sciences, The University of Auckland, 3A Symonds St, Auckland Central, 1010, New Zealand.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
63Solanum tuberosumMutation(s): 0 
Find proteins for Q948Z4 (Solanum tuberosum)
Explore Q948Z4 
Go to UniProtKB:  Q948Z4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ948Z4
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.60 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.238 
  • Space Group: P 1 21/c 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.149α = 90
b = 27.744β = 100.19
c = 73.347γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Royal Society of New ZealandNew ZealandUOA1115

Revision History  (Full details and data files)

  • Version 1.0: 2016-05-18
    Type: Initial release
  • Version 1.1: 2016-07-20
    Changes: Database references