5IE0

Crystal structure of a plant enzyme

• PDB DOI: https://doi.org/10.2210/pdb5IE0/pdb

• Classification: LIGASE
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-02-24 Released: 2016-12-07 
• Deposition Author(s): Ran, M.R., Li, M., Chang, W.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.206 
• R-Value Work: 0.173 
• R-Value Observed: 0.174 

Starting Model: experimental

Literature

Crystal Structures of Arabidopsis thaliana Oxalyl-CoA Synthetase Essential for Oxalate Degradation

Fan, M., Xiao, Y., Li, M., Chang, W.

(2016) Mol Plant 9: 1349-1352

• PubMed: 27326693 
• DOI: https://doi.org/10.1016/j.molp.2016.06.002
• Primary Citation of Related Structures:  
  5IE0, 5IE2, 5IE3

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Organizational Affiliation: 

National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15th Datun Road, Chaoyang District, Beijing 100101, People's Republic of China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049, People's Republic of China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 111.83 kDa 
• Atom Count: 8,950 
• Modelled Residue Count: 1,006 
• Deposited Residue Count: 1,028 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Oxalate--CoA ligase	A, B	514	Arabidopsis thaliana	Mutation(s): 0  Gene Names: AAE3, 4CLL10, AMPBP3, At3g48990, T2J13.170 EC: 6.2.1.8
UniProt
Find proteins for Q9SMT7 (Arabidopsis thaliana) Explore Q9SMT7  Go to UniProtKB:  Q9SMT7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SRT	C [auth A], D [auth A], E [auth B], F [auth B]	S,R MESO-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-XIXRPRMCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.206 
• R-Value Work: 0.173 
• R-Value Observed: 0.174 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.164	α = 90
b = 117.763	β = 93.71
c = 72.16	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-12-07 
Deposition Author(s): Ran, M.R., Li, M., Chang, W.R.

Revision History  

• Version 1.0: 2016-12-07
  Type: Initial release
  
• Version 1.1: 2017-08-30
  Changes: Data collection
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Refinement description