1BHP

STRUCTURE OF BETA-PUROTHIONIN AT ROOM TEMPERATURE AND 1.7 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.281 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Refinement of purothionins reveals solute particles important for lattice formation and toxicity. Part 2: structure of beta-purothionin at 1.7 A resolution.

Stec, B.Rao, U.Teeter, M.M.

(1995) Acta Crystallogr.,Sect.D 51: 914-924

  • DOI: 10.1107/S0907444995002976

  • PubMed Abstract: 
  • The crystal structure of beta-purothionin (beta-PT) has been determined at 1.7 A resolution. beta-PT and previously solved alpha(l)-PT belong to a family of membrane-active plant toxins homologous to crambin. (beta-PT crystallizes in the same space g ...

    The crystal structure of beta-purothionin (beta-PT) has been determined at 1.7 A resolution. beta-PT and previously solved alpha(l)-PT belong to a family of membrane-active plant toxins homologous to crambin. (beta-PT crystallizes in the same space group as alpha(l)-PT (1422) but with the c axis 3 A longer than (alpha(l)-PT. The unit-cell dimensions of beta-PT crystals are a = b = 53.94 and c = 72.75 A. Two data sets were collected on a multiwire area detector, each with R(sym) around 6.0%, and were merged to get a single data set at 1.7 A, (R(merge) = 9.6%). The X-ray structure of alpha(l)-PT was used to build a starting model for beta-PT. The beta-PT model was refined using the program PROLSQ from 10 to 1.7 A resolution to an R-factor of 19.8% with very good geometry. The final structure contains 439 atoms including 337 protein atoms, 77 waters, two acetates, two glycerols and one phosphate. The high-resolution structure of the beta-PT agreed well with that of the lower resolution alpha(l)-PT structure only after the latter was extensively rerefined. Both refinements revealed phosphate and glycerol molecules which are important in lattice formation. The binding of phosphate and glycerol molecules to purothionins (PT) was confirmed by NMR and was implicated in the biological activity of toxins. Modeling of phospholipid binding to PT based on glycerol and phosphate-binding site could shed light on the lytic toxicity of this protein-toxin family. Although the structures of (alpha(l)-PT and beta-PT preserve the overall fold of crambin, they exhibit key differences that are directly relevant to the toxicity of thionins.


    Organizational Affiliation

    Department of Chemistry, Boston College, Chestnut Hill, MA 02167, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
BETA-PUROTHIONIN
A
45Triticum aestivumGene Names: THI1.3
Find proteins for P01543 (Triticum aestivum)
Go to UniProtKB:  P01543
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
ACT
Query on ACT

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Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.281 
  • Space Group: I 4 2 2
Unit Cell:
Length (Å)Angle (°)
a = 53.940α = 90.00
b = 53.940β = 90.00
c = 72.750γ = 90.00
Software Package:
Software NamePurpose
SDMSdata collection
SDMSdata reduction
PROLSQrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1996-03-15
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance