4CQ7 | pdb_00004cq7

The crystal structure of the allene oxide cyclase 2 from Arabidopsis thaliana with bound product - OPDA

• PDB DOI: https://doi.org/10.2210/pdb4CQ7/pdb

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


• Deposited: 2014-02-11 Released: 2015-03-04 
• Deposition Author(s): Terlecka, B.A., Pollmann, S., Hofmann, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.190 (Depositor), 0.199 (DCC) 
• R-Value Work: 
  0.165 (Depositor), 0.173 (DCC) 
• R-Value Observed: 
  0.167 (Depositor) 

Starting Model: experimental

Literature

The Ligand-Bound Structures of the Aoc2 from A. Thaliana and the Implications for the Catalytic Mechanism

Terlecka, B.A., Pollmann, S., Hofmann, E.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Macromolecule Content 

• Total Structure Weight: 63.28 kDa 
• Atom Count: 4,902 
• Modeled Residue Count: 519 
• Deposited Residue Count: 564 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ALLENE OXIDE CYCLASE 2, CHLOROPLASTIC	A, B, C	188	Arabidopsis thaliana	Mutation(s): 0  EC: 5.3.99.6
UniProt
Find proteins for Q9LS02 (Arabidopsis thaliana) Explore Q9LS02  Go to UniProtKB:  Q9LS02

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
WHW	D [auth A], E [auth B]	9S,13R-12-OXOPHYTODIENOIC ACID C18 H28 O3 PMTMAFAPLCGXGK-TTXFDSJOSA-N
MRD	F [auth C]	(4R)-2-METHYLPENTANE-2,4-DIOL C6 H14 O2 SVTBMSDMJJWYQN-RXMQYKEDSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.190 (Depositor), 0.199 (DCC) 
• R-Value Work:  0.165 (Depositor), 0.173 (DCC) 
• R-Value Observed: 0.167 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.5	α = 90
b = 100.4	β = 90
c = 105.6	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-03-04 
Deposition Author(s): Terlecka, B.A., Pollmann, S., Hofmann, E.

Revision History  

• Version 1.0: 2015-03-04
  Type: Initial release
  
• Version 2.0: 2019-10-23
  Changes: Atomic model, Data collection, Other
• Version 2.1: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Refinement description