8Z53 | pdb_00008z53

Arabidopsis Dwarf14 (AtD14) co-crystallized in the presence of Zaxinone

• PDB DOI: https://doi.org/10.2210/pdb8Z53/pdb

• Classification: HYDROLASE
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2024-04-18 Released: 2025-04-23 
• Deposition Author(s): Arold, S.T., Hameed, U.F.S.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.226 (Depositor), 0.234 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.192 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Starting Model: experimental

Literature

Arabidopsis Dwarf14 (AtD14) co-crystallized in the presence of Zaxinone

Arold, S.T., Hameed, U.F.S.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 59.48 kDa 
• Atom Count: 4,238 
• Modeled Residue Count: 527 
• Deposited Residue Count: 530 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Strigolactone esterase D14	A, B	265	Arabidopsis thaliana	Mutation(s): 0  Gene Names: D14, At3g03990, T11I18.10 EC: 3.1
UniProt
Find proteins for Q9SQR3 (Arabidopsis thaliana) Explore Q9SQR3  Go to UniProtKB:  Q9SQR3

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1L1M (Subject of Investigation/LOI)	C [auth A], F [auth B]	(7E)-6-methyl-8-[(4S)-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octa-3,5,7-trien-2-one C18 H26 O2 JLNMEHQAHDSEEE-FRIDJMAZSA-N
PEG	D [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL (Subject of Investigation/LOI)	E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.226 (Depositor), 0.234 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.192 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.82	α = 90
b = 69.58	β = 92.85
c = 89.86	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-04-23 
Deposition Author(s): Arold, S.T., Hameed, U.F.S.

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Funding Organization	Location	Grant Number
Other private	Saudi Arabia	King Abdullah University of Science and Technology

Revision History  

• Version 1.0: 2025-04-23
  Type: Initial release
  
• Version 2.0: 2025-06-11
  Type: Coordinate replacement
  Reason: Ligand geometry
  Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Other, Polymer sequence, Refinement description, Source and taxonomy, Structure summary