2GCU

X-Ray Structure of Gene Product from Arabidopsis Thaliana At1g53580


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.178 

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 D Biol Crystallogr 62: 964-970

  • DOI: 10.1107/S0907444906020592
  • Primary Citation of Related Structures:  
    2GCU

  • 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 nominal resolution of 1 ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Putative hydroxyacylglutathione hydrolase 3A, B, C, D245Arabidopsis thalianaMutation(s): 1 
Gene Names: At1g53580GLY3F22G10.9T3F20.11
EC: 3.1.2.6 (PDB Primary Data), 1.13.11.18 (UniProt)
UniProt
Find proteins for Q9C8L4 (Arabidopsis thaliana)
Explore Q9C8L4 
Go to UniProtKB:  Q9C8L4
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
F [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
G [auth A] , H [auth A] , I [auth A] , J [auth A] , K [auth A] , L [auth A] , N [auth B] , O [auth B] , 
G [auth A],  H [auth A],  I [auth A],  J [auth A],  K [auth A],  L [auth A],  N [auth B],  O [auth B],  Q [auth C],  R [auth C],  S [auth C],  T [auth C],  U [auth C],  W [auth D]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
FE2
Query on FE2

Download Ideal Coordinates CCD File 
E [auth A], M [auth B], P [auth C], V [auth D]FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSD
Query on CSD
A, B, C, DL-PEPTIDE LINKINGC3 H7 N O4 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.178 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.607α = 90
b = 64.469β = 97.83
c = 127.877γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
DMphasing
REFMACrefinement
PDB_EXTRACTdata extraction
PHENIXphasing
ARP/wARPmodel building

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

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