2GCU | pdb_00002gcu

X-Ray Structure of Gene Product from Arabidopsis Thaliana At1g53580

• PDB DOI: https://doi.org/10.2210/pdb2GCU/pdb

• Classification: HYDROLASE
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2006-03-14 Released: 2006-04-18 
• Deposition Author(s): McCoy, J.G., Wesenberg, G.E., Phillips Jr., G.N., Bitto, E., Bingman, C.A., Center for Eukaryotic Structural Genomics (CESG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.48 Å
• R-Value Free: 
  0.204 (Depositor), 0.204 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.175 (DCC) 
• R-Value Observed: 
  0.178 (Depositor) 

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

• PubMed: 16929096 
• DOI: https://doi.org/10.1107/S0907444906020592
• Primary Citation 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 1.48 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.

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 108.99 kDa 
• Atom Count: 8,619 
• Modeled Residue Count: 962 
• Deposited Residue Count: 980 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative hydroxyacylglutathione hydrolase 3	A, B, C, D	245	Arabidopsis thaliana	Mutation(s): 1  Gene Names: At1g53580 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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	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
FE2	E [auth A], M [auth B], P [auth C], V [auth D]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSD	A, B, C, D	L-PEPTIDE LINKING	C3 H7 N O4 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.48 Å
• R-Value Free:  0.204 (Depositor), 0.204 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.175 (DCC) 
• R-Value Observed: 0.178 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.607	α = 90
b = 64.469	β = 97.83
c = 127.877	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHARP	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
PHENIX	phasing
ARP/wARP	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-04-18 
Deposition Author(s): McCoy, J.G., Wesenberg, G.E., Phillips Jr., G.N., Bitto, E., Bingman, C.A., Center for Eukaryotic Structural Genomics (CESG)

Revision History  

• 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
• Version 1.5: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary