2PLH

STRUCTURE OF ALPHA-1-PUROTHIONIN AT ROOM TEMPERATURE AND 2.8 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Refinement of purothionins reveals solute particles important for lattice formation and toxicity. Part 1: alpha1-purothionin revisited.

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

(1995) Acta Crystallogr.,Sect.D 51: 904-913

  • DOI: 10.1107/S0907444995002964

  • PubMed Abstract: 
  • The three-dimensional structure of alpha(1)-purothionin (alpha(1)-PT), a wheat-germ protein and a basic lytic toxin, was previously solved by molecular-replacement methods using an energy-minimized predicted model and refined to an R-factor of 21.6% ...

    The three-dimensional structure of alpha(1)-purothionin (alpha(1)-PT), a wheat-germ protein and a basic lytic toxin, was previously solved by molecular-replacement methods using an energy-minimized predicted model and refined to an R-factor of 21.6% [Teeter, Ma, Rao & Whitlow (1990). Proteins Struct. Funct. Genet. 8, 118-1321. Some deficiencies of the model motivated us to revisit the structure and to continue the refinement. Here we report a significantly improved structure refined to an R-factor of 15.5% with excellent geometry. The refinement of this relatively low resolution structure ( approximately 2.8 A) is well suited to test the limitations of classical methods of refinement and to address the problem of overfitting, The final structure contains 434 atoms including 330 protein atoms, 70 waters, three acetates, two glycerols, one sec-butanol and one phosphate. The key solute molecules (acetate ion and phosphate ion) play a crucial role in the lattice formation. Phosphate and glycerol found in the structure may be important for biological activity of the toxins.


    Related Citations: 
    • Crystal Structure of a Protein-Toxin Alpha1-Purothionin at 2.5 Angstroms and a Comparison with Predicted Models
      Teeter, M.M.,Ma, X.-Q.,Rao, U.,Whitlow, M.
      (1990) Proteins 8: 118


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ALPHA-1-PUROTHIONIN
A
45Triticum aestivumMutation(s): 0 
Gene Names: THI1.1 (PUR-D1)
Find proteins for P01544 (Triticum aestivum)
Go to UniProtKB:  P01544
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SBT
Query on SBT

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Download CCD File 
A
2-BUTANOL
C4 H10 O
BTANRVKWQNVYAZ-BYPYZUCNSA-N
 Ligand Interaction
PO4
Query on PO4

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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

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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: 2.5 Å
  • Space Group: I 4 2 2
Unit Cell:
Length (Å)Angle (°)
a = 53.590α = 90.00
b = 53.590β = 90.00
c = 69.790γ = 90.00
Software Package:
Software NamePurpose
DTPdata collection
DTPdata reduction
PROLSQrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1996-04-03
    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
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other