4JP6

High resolution structure of a papaya barwin-like protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.00 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.153 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

High-resolution structure of a papaya plant-defence barwin-like protein solved by in-house sulfur-SAD phasing.

Huet, J.Teinkela Mbosso, E.J.Soror, S.Meyer, F.Looze, Y.Wintjens, R.Wohlkonig, A.

(2013) Acta Crystallogr D Biol Crystallogr 69: 2017-2026

  • DOI: 10.1107/S0907444913018015
  • Primary Citation of Related Structures:  
    4JP6, 4JP7

  • PubMed Abstract: 
  • The first crystal structure of a barwin-like protein, named carwin, has been determined at high resolution by single-wavelength anomalous diffraction (SAD) phasing using the six intrinsic S atoms present in the protein. The barwin-like protein was purified from Carica papaya latex and crystallized in the orthorhombic space group P212121 ...

    The first crystal structure of a barwin-like protein, named carwin, has been determined at high resolution by single-wavelength anomalous diffraction (SAD) phasing using the six intrinsic S atoms present in the protein. The barwin-like protein was purified from Carica papaya latex and crystallized in the orthorhombic space group P212121. Using in-house Cu Kα X-ray radiation, 16 cumulative diffraction data sets were acquired to increase the signal-to-noise level and thereby the anomalous scattering signal. A sequence-database search on the papaya genome identified two carwin isoforms of 122 residues in length, both containing six S atoms that yield an estimated Bijvoet ratio of 0.93% at 1.54 Å wavelength. A systematic analysis of data quality and redundancy was performed to assess the capacity to locate the S atoms and to phase the data. It was observed that the crystal decay was low during data collection and that successful S-SAD phasing could be obtained with a relatively low data multiplicity of about 7. Using a synchrotron source, high-resolution data (1 Å) were collected from two different crystal forms of the papaya latex carwin. The refined structures showed a central β-barrel of six strands surrounded by several α-helices and loops. The β-barrel of carwin appears to be a common structural module that is shared within several other unrelated proteins. Finally, the possible biological function of the protein is discussed.


    Organizational Affiliation

    Laboratoire des Biopolymères et des Nanomatériaux Supramoléculaires (CP206/04), Faculté de Pharmacie, Université Libre de Bruxelles, B-1050 Brussels, Belgium.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
papaya barwin-like proteinA122Carica papayaMutation(s): 0 
UniProt
Find proteins for U5HK42 (Carica papaya)
Explore U5HK42 
Go to UniProtKB:  U5HK42
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupU5HK42
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA
A L-PEPTIDE LINKINGC5 H7 N O3GLN
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.00 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.153 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 27.688α = 90
b = 54.971β = 90
c = 73.509γ = 90
Software Package:
Software NamePurpose
XDSdata scaling
SHELXSphasing
REFMACrefinement
XDSdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-10-02
    Type: Initial release
  • Version 1.1: 2014-01-15
    Changes: Database references
  • Version 2.0: 2019-12-25
    Changes: Derived calculations, Polymer sequence