2GCU

X-Ray Structure of Gene Product from Arabidopsis Thaliana At1g53580


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.477 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Structure of an ETHE1-like protein from Arabidopsis thaliana.

McCoy, J.G.Bingman, C.A.Bitto, E.Holdorf, M.M.Makaroff, C.A.Phillips, G.N.

(2006) ACTA CRYSTALLOGR.,SECT.D 62: 964-970

  • DOI: 10.1107/S0907444906020592

  • PubMed Abstract: 
  • The protein product of gene At1g53580 from Arabidopsis thaliana possesses 54% sequence identity to a human enzyme that has been implicated in the rare disorder ethylmalonic encephalopathy. The structure of the At1g53580 protein has been solved to a n ...

    The protein product of gene At1g53580 from Arabidopsis thaliana possesses 54% sequence identity to a human enzyme that has been implicated in the rare disorder ethylmalonic encephalopathy. The structure of the At1g53580 protein has been solved to a nominal resolution of 1.48 Angstrom. This structure reveals tertiary structure differences between the ETHE1-like enzyme and glyoxalase II enzymes that are likely to account for differences in reaction chemistry and multimeric state between the two types of enzymes. In addition, the Arabidopsis ETHE1 protein is used as a model to explain the significance of several mutations in the human enzyme that have been observed in patients with ethylmalonic encephalopathy.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Putative hydroxyacylglutathione hydrolase 3
A, B, C, D
245Arabidopsis thalianaGene Names: GLY3
EC: 1.13.11.18
Find proteins for Q9C8L4 (Arabidopsis thaliana)
Go to UniProtKB:  Q9C8L4
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B, C, D
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
FE2
Query on FE2

Download SDF File 
Download CCD File 
A, B, C, D
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSD
Query on CSD
A, B, C, D
L-PEPTIDE LINKINGC3 H7 N O4 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.477 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.176 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 66.607α = 90.00
b = 64.469β = 97.83
c = 127.877γ = 90.00
Software Package:
Software NamePurpose
DMphasing
REFMACrefinement
SHARPphasing
PHENIXphasing
DENZOdata reduction
ARP/wARPmodel building
PDB_EXTRACTdata extraction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-04-18
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2014-11-12
    Type: Non-polymer description
  • Version 1.4: 2017-10-18
    Type: Refinement description