5YM0 | pdb_00005ym0

The crystal structure of DHAD

• PDB DOI: https://doi.org/10.2210/pdb5YM0/pdb

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


• Deposited: 2017-10-20 Released: 2018-10-24 
• Deposition Author(s): Zang, X., Huang, W.X., Cheng, R., Wu, L., Zhou, J.H., Tang, Y., Yan, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free: 
  0.197 (Depositor), 0.170 (DCC) 
• R-Value Work: 
  0.170 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.171 (Depositor) 

Literature

The crystal structure of DHAD

Zang, X., Huang, W.X., Cheng, R., Wu, L., Zhou, J.H.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 68.26 kDa 
• Atom Count: 4,285 
• Modeled Residue Count: 520 
• Deposited Residue Count: 633 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydroxy-acid dehydratase, chloroplastic	A	633	Arabidopsis thaliana	Mutation(s): 0  Gene Names: DHAD, ILVD, At3g23940, F14O13.13 EC: 4.2.1.9
UniProt
Find proteins for Q9LIR4 (Arabidopsis thaliana) Explore Q9LIR4  Go to UniProtKB:  Q9LIR4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free:  0.197 (Depositor), 0.170 (DCC) 
• R-Value Work:  0.170 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.171 (Depositor) 

Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 135.472	α = 90
b = 135.472	β = 90
c = 67.963	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: 2018-10-24 
Deposition Author(s): Zang, X., Huang, W.X., Cheng, R., Wu, L., Zhou, J.H., Tang, Y., Yan, Y.

Revision History  

• Version 1.0: 2018-10-24
  Type: Initial release
  
• Version 1.1: 2024-10-09
  Changes: Data collection, Database references, Structure summary