5DOM | pdb_00005dom

Crystal structure, maturation and flocculating properties of a 2S albumin from Moringa oleifera seeds


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 
    0.263 (Depositor), 0.281 (DCC) 
  • R-Value Work: 
    0.222 (Depositor), 0.237 (DCC) 
  • R-Value Observed: 
    0.224 (Depositor) 

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This is version 1.4 of the entry. See complete history

Literature

Crystal structure of mature 2S albumin from Moringa oleifera seeds.

Ullah, A.Mariutti, R.B.Masood, R.Caruso, I.P.Gravatim Costa, G.H.Millena de Freita, C.Santos, C.R.Zanphorlin, L.M.Rossini Mutton, M.J.Murakami, M.T.Arni, R.K.

(2015) Biochem Biophys Res Commun 468: 365-371

  • DOI: https://doi.org/10.1016/j.bbrc.2015.10.087
  • Primary Citation Related Structures: 
    5DOM

  • PubMed Abstract: 

    2S albumins, the seed storage proteins, are the primary sources of carbon and nitrogen and are involved in plant defense. The mature form of Moringa oleifera (M. oleifera), a chitin binding protein isoform 3-1 (mMo-CBP3-1) a thermostable antifungal, antibacterial, flocculating 2S albumin is widely used for the treatment of water and is potentially interesting for the development of both antifungal drugs and transgenic crops. The crystal structure of mMo-CBP3-1 determined at 1.7 Å resolution demonstrated that it is comprised of two proteolytically processed α-helical chains, stabilized by four disulfide bridges that is stable, resistant to pH changes and has a melting temperature (TM) of approximately 98 °C. The surface arginines and the polyglutamine motif are the key structural factors for the observed flocculating, antibacterial and antifungal activities. This represents the first crystal structure of a 2S albumin and the model of the pro-protein indicates the structural changes that occur upon formation of mMo-CBP3-1 and determines the structural motif and charge distribution patterns for the diverse observed activities.


  • Organizational Affiliation
    • Multiuser Center for Biomolecular Innovation, Department of Physics, IBILCE/UNESP, São Jose do Rio Preto, SP, Brazil. Electronic address: anwar.ms90@yahoo.com.

Macromolecule Content 

  • Total Structure Weight: 14.41 kDa 
  • Atom Count: 798 
  • Modeled Residue Count: 90 
  • Deposited Residue Count: 122 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
2S albumin122Moringa oleiferaMutation(s): 0 
UniProt
Find proteins for W5S2D2 (Moringa oleifera)
Explore W5S2D2 
Go to UniProtKB:  W5S2D2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupW5S2D2
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free:  0.263 (Depositor), 0.281 (DCC) 
  • R-Value Work:  0.222 (Depositor), 0.237 (DCC) 
  • R-Value Observed: 0.224 (Depositor) 
Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.867α = 90
b = 106.867β = 90
c = 43.16γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
HKL-2000data collection

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Sao Paulo Research Foundation (FAPESP)Brazil--
Brazilian National Council for Scientific and Technological Development (CNPq)Brazil--
CAPESBrazil--

Revision History  (Full details and data files)

  • Version 1.0: 2015-11-11
    Type: Initial release
  • Version 1.1: 2015-12-16
    Changes: Database references
  • Version 1.2: 2019-04-17
    Changes: Author supporting evidence, Data collection, Database references, Derived calculations
  • Version 1.3: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.4: 2024-10-23
    Changes: Data collection, Database references, Structure summary