2APJ

X-Ray Structure of Protein from Arabidopsis Thaliana AT4G34215 at 1.6 Angstrom Resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.146 
  • R-Value Observed: 0.147 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The structure at 1.6 Angstroms resolution of the protein product of the At4g34215 gene from Arabidopsis thaliana.

Bitto, E.Bingman, C.A.McCoy, J.G.Allard, S.T.Wesenberg, G.E.Phillips, G.N.

(2005) Acta Crystallogr D Biol Crystallogr 61: 1655-1661

  • DOI: 10.1107/S0907444905034074
  • Primary Citation of Related Structures:  
    2APJ

  • PubMed Abstract: 
  • The crystal structure of the At4g34215 protein of Arabidopsis thaliana was determined by molecular replacement and refined to an R factor of 14.6% (R(free) = 18.3%) at 1.6 Angstroms resolution. The crystal structure confirms that At4g34215 belongs to the SGNH-hydrolase superfamily of enzymes ...

    The crystal structure of the At4g34215 protein of Arabidopsis thaliana was determined by molecular replacement and refined to an R factor of 14.6% (R(free) = 18.3%) at 1.6 Angstroms resolution. The crystal structure confirms that At4g34215 belongs to the SGNH-hydrolase superfamily of enzymes. The catalytic triad of the enzyme comprises residues Ser31, His238 and Asp235. In this structure the catalytic serine residue was found to be covalently modified, possibly by phenylmethylsulfonyl fluoride. The structure also reveals a previously undescribed variation within the active site. The conserved asparagine from block III, which provides a hydrogen bond for an oxyanion hole in the SGNH-hydrolase superfamily enzymes, is missing in At4g34215 and is functionally replaced by Gln30 from block I. This residue is positioned in a catalytically competent conformation by nearby residues, including Gln159, Gly160 and Glu161, which are fully conserved in the carbohydrate esterase family 6 enzymes.


    Organizational Affiliation

    Center for Eukaryotic Structural Genomics, Department of Biochemistry, University of Wisconsin-Madison, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Putative EsteraseA, B, C, D260Arabidopsis thalianaMutation(s): 1 
Gene Names: At4g34215F10M10.12F28A23_20
EC: 3.1
UniProt
Find proteins for Q8L9J9 (Arabidopsis thaliana)
Explore Q8L9J9 
Go to UniProtKB:  Q8L9J9
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SEB
Query on SEB
A, B, C, DL-PEPTIDE LINKINGC10 H13 N O5 SSER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.146 
  • R-Value Observed: 0.147 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.688α = 108.16
b = 71.918β = 93.25
c = 93.213γ = 90.4
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-08-30
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description