5E5T

Quasi-racemic snakin-1 in P1 after radiation damage

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.57 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.206 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

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: 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 ...

    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: 

    Maurice Wilkins Centre for Molecular Biodiscovery, Thomas Building Level 2, 3A Symonds St, Auckland Central, 1010, New Zealand. m.brimble@auckland.ac.nz.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Snakin-1A, C63Solanum tuberosumMutation(s): 1 
Gene Names: SN1
UniProt
Find proteins for Q948Z4 (Solanum tuberosum)
Explore Q948Z4 
Go to UniProtKB:  Q948Z4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ948Z4
Protein Feature View
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
D- snakin-1B, D63Solanum tuberosumMutation(s): 0 
Gene Names: SN1
UniProt
Find proteins for Q948Z4 (Solanum tuberosum)
Explore Q948Z4 
Go to UniProtKB:  Q948Z4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ948Z4
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PHI
Query on PHI		A, C L-PEPTIDE LINKINGC9 H10 I N O2PHE
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.57 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.206 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 31.256α = 92.96
b = 37.442β = 90.55
c = 50.391γ = 102.58
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction
SHELXDEphasing

Structure Validation

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View more in-depth experimental data

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