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.

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
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Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

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

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.

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

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9SMT7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SRT Query on SRT Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth B] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth B] MOL2 format, chain F [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth B] mmCIF format, chain F [auth B]	C [auth A], D [auth A], E [auth B], F [auth B]	S,R MESO-TARTARIC ACID C₄ H₆ O₆ FEWJPZIEWOKRBE-XIXRPRMCSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth B]

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

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2016-12-07

Deposition Author(s):

Ran, M.R.

Li, M.

Chang, W.R.

Revision History (Full details and data files)

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