9L8R | pdb_00009l8r

Dihydroxyacid dehydratase (DHAD)

• PDB DOI: https://doi.org/10.2210/pdb9L8R/pdb

• Classification: LYASE
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli K-12
• Mutation(s): No 


• Deposited: 2024-12-28 Released: 2025-06-04 
• Deposition Author(s): Zhou, J., Liu, D.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.19 Å
• R-Value Free: 
  0.231 (Depositor), 0.234 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.185 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Starting Model: experimental

Literature

The mutant structure of DHAD

Zhou, J., Liu, D.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 61.4 kDa 
• Atom Count: 4,485 
• Modeled Residue Count: 569 
• Deposited Residue Count: 572 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydroxy-acid dehydratase, chloroplastic	A	572	Arabidopsis thaliana	Mutation(s): 0  Gene Names: DHAD, At3g23940, F14O13.13 EC: 4.2.1.9
UniProt
Find proteins for Q9LIR4 (Arabidopsis thaliana) Explore Q9LIR4  Go to UniProtKB:  Q9LIR4

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1L7A (Subject of Investigation/LOI)	C [auth A]	(2~{R})-7-fluoranyl-2-oxidanyl-3-oxidanylidene-4-prop-2-ynyl-1,4-benzoxazine-2-carboxylic acid C12 H8 F N O5 WTUVRXLEVFSMKU-GFCCVEGCSA-N
FES (Subject of Investigation/LOI)	B [auth A]	FE2/S2 (INORGANIC) CLUSTER Fe2 S2 NIXDOXVAJZFRNF-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.19 Å
• R-Value Free:  0.231 (Depositor), 0.234 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.185 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 136.04	α = 90
b = 136.04	β = 90
c = 66.829	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-06-04 
Deposition Author(s): Zhou, J., Liu, D.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2025-06-04
  Type: Initial release