4ZGG | pdb_00004zgg

Crystal structure of a DJ-1 (PARK7) from Homo sapiens at 1.23 A resolution

• PDB DOI: https://doi.org/10.2210/pdb4ZGG/pdb

• Classification: CHAPERONE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-04-22 Released: 2015-05-20 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG), Partnership for Nuclear Receptor Signaling Code Biology (NHRS), Partnership for T-Cell Biology (TCELL)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.23 Å
• R-Value Free: 
  0.134 (Depositor), 0.170 (DCC) 
• R-Value Work: 
  0.116 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.117 (Depositor) 

Literature

Crystal structure of a DJ-1 (PARK7) from Homo sapiens at 1.23 A resolution

Joint Center for Structural Genomics (JCSG), Partnership for Nuclear Receptor Signaling Code Biology (NHRs), Partnership for T-Cell Biology (TCELL)

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 20.83 kDa 
• Atom Count: 1,735 
• Modelled Residue Count: 190 
• Deposited Residue Count: 190 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein deglycase DJ-1	A	190	Homo sapiens	Mutation(s): 0  Gene Names: PARK7 EC: 3.1.2 (PDB Primary Data), 3.5.1 (PDB Primary Data), 3.5.1.124 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q99497 (Homo sapiens) Explore Q99497  Go to UniProtKB:  Q99497
PHAROS:  Q99497 GTEx:  ENSG00000116288

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.23 Å
• R-Value Free:  0.134 (Depositor), 0.170 (DCC) 
• R-Value Work:  0.116 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.117 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M38W24

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.002	α = 90
b = 75.002	β = 90
c = 74.897	γ = 120

Software Package:

Software Name	Purpose
PDB_EXTRACT	data extraction
SOLVE	phasing
SCALA	data scaling
REFMAC	refinement
MOSFLM	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-05-20 
Deposition Author(s): Joint Center for Structural Genomics (JCSG), Partnership for Nuclear Receptor Signaling Code Biology (NHRS), Partnership for T-Cell Biology (TCELL)

Revision History  

• Version 1.0: 2015-05-20
  Type: Initial release
  
• Version 1.1: 2015-05-27
  Changes: Database references, Structure summary
• Version 1.2: 2017-11-22
  Changes: Derived calculations, Refinement description, Source and taxonomy, Structure summary
• Version 1.3: 2023-02-01
  Changes: Data collection, Database references
• Version 1.4: 2024-10-23
  Changes: Data collection, Structure summary