3UK7 | pdb_00003uk7

Crystal Structure of Arabidopsis thaliana DJ-1D

• PDB DOI: https://doi.org/10.2210/pdb3UK7/pdb

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


• Deposited: 2011-11-09 Released: 2011-11-23 
• Deposition Author(s): Seo, K.H., Zhuang, N.N., Son, D.Y., Lee, K.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 
  0.225 (Depositor), 0.228 (DCC) 
• R-Value Work: 
  0.174 (Depositor), 0.181 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Literature

Crystal Structure of Arabidopsis DJ-1D

Seo, K.H., Zhuang, N.N., Son, D.Y., Lee, K.H.

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: 128.45 kDa 
• Atom Count: 9,152 
• Modeled Residue Count: 1,168 
• Deposited Residue Count: 1,188 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Class I glutamine amidotransferase-like domain-containing protein	A, B, C	396	Arabidopsis thaliana	Mutation(s): 0  Gene Names: DJ-1D EC: 4.4.1.5
UniProt
Find proteins for Q9M8R4 (Arabidopsis thaliana) Explore Q9M8R4  Go to UniProtKB:  Q9M8R4

Small Molecules

Modified Residues  3 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSD	A, B, C	L-PEPTIDE LINKING	C3 H7 N O4 S		CYS
CSX	A, B, C	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS
MSE	A, B, C	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.225 (Depositor), 0.228 (DCC) 
• R-Value Work:  0.174 (Depositor), 0.181 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.778	α = 90
b = 75.214	β = 96.87
c = 141.673	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SOLVE	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-11-23 
Deposition Author(s): Seo, K.H., Zhuang, N.N., Son, D.Y., Lee, K.H.

Revision History  

• Version 1.0: 2011-11-23
  Type: Initial release
  
• Version 1.1: 2014-11-12
  Changes: Other
• Version 1.2: 2025-03-26
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary