1XRI

X-ray structure of a putative phosphoprotein phosphatase from Arabidopsis thaliana gene AT1G05000


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Structural and functional characterization of a novel phosphatase from the Arabidopsis thaliana gene locus At1g05000.

Aceti, D.J.Bitto, E.Yakunin, A.F.Proudfoot, M.Bingman, C.A.Frederick, R.O.Sreenath, H.K.Vojtik, F.C.Wrobel, R.L.Fox, B.G.Markley, J.L.Phillips Jr., G.N.

(2008) Proteins 73: 241-253

  • DOI: 10.1002/prot.22041

  • PubMed Abstract: 
  • The crystal structure of the protein product of the gene locus At1g05000, a hypothetical protein from A. thaliana, was determined by the multiple-wavelength anomalous diffraction method and was refined to an R factor of 20.4% (R(free) = 24.9%) at 3.3 ...

    The crystal structure of the protein product of the gene locus At1g05000, a hypothetical protein from A. thaliana, was determined by the multiple-wavelength anomalous diffraction method and was refined to an R factor of 20.4% (R(free) = 24.9%) at 3.3 A. The protein adopts the alpha/beta fold found in cysteine phosphatases, a superfamily of phosphatases that possess a catalytic cysteine and form a covalent thiol-phosphate intermediate during the catalytic cycle. In At1g05000, the analogous cysteine (Cys(150)) is located at the bottom of a positively-charged pocket formed by residues that include the conserved arginine (Arg(156)) of the signature active site motif, HCxxGxxRT. Of 74 model phosphatase substrates tested, purified recombinant At1g05000 showed highest activity toward polyphosphate (poly-P(12-13)) and deoxyribo- and ribonucleoside triphosphates, and less activity toward phosphoenolpyruvate, phosphotyrosine, phosphotyrosine-containing peptides, and phosphatidyl inositols. Divalent metal cations were not required for activity and had little effect on the reaction.


    Organizational Affiliation

    Department of Biochemistry, The Center for Eukaryotic Structural Genomics, University of Wisconsin at Madison, Madison, Wisconsin 53706, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
At1g05000
A, B
151Arabidopsis thalianaEC: 3.1.3.48
Find proteins for Q9ZVN4 (Arabidopsis thaliana)
Go to UniProtKB:  Q9ZVN4
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.204 
  • Space Group: P 21 3
Unit Cell:
Length (Å)Angle (°)
a = 124.483α = 90.00
b = 124.483β = 90.00
c = 124.483γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
SOLVEphasing
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling
RESOLVEphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-10-26
    Type: Initial release
  • Version 1.1: 2008-02-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2013-02-06
    Type: Database references
  • Version 1.4: 2017-10-11
    Type: Refinement description