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.

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)

wwPDB Validation 3D Report Full Report

Validation slider image for 3UK7

This is version 1.2 of the entry. See complete history.

Literature

Crystal Structure of Arabidopsis DJ-1D

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

To be published.

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

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9M8R4
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

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Entry History

Deposition Data

Released Date: 2011-11-23

Deposition Author(s):

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.