7C62 | pdb_00007c62

The Crystal Structure of Parkinson disease protein 7 (DJ-1) from Biortus

• PDB DOI: https://doi.org/10.2210/pdb7C62/pdb

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


• Deposited: 2020-05-21 Released: 2020-07-08 
• Deposition Author(s): Wang, F., Lin, D., Lv, Z., Tan, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.03 Å
• R-Value Free: 
  0.174 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.152 (Depositor), 0.160 (DCC) 

Starting Model: experimental

Literature

The Crystal Structure of Parkinson disease protein 7 (DJ-1) from Biortus.

Wang, F., Lin, D., Lv, Z., Tan, J.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 22.02 kDa 
• Atom Count: 1,545 
• Modelled Residue Count: 187 
• Deposited Residue Count: 206 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein/nucleic acid deglycase DJ-1	A	206	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 (PDB Primary Data)
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
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.03 Å
• R-Value Free:  0.174 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.152 (Depositor), 0.160 (DCC) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.57	α = 90
b = 74.57	β = 90
c = 74.956	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-07-08 
Deposition Author(s): Wang, F., Lin, D., Lv, Z., Tan, J.

Revision History  

• Version 1.0: 2020-07-08
  Type: Initial release
  
• Version 1.1: 2022-02-09
  Changes: Database references, Structure summary
• Version 1.2: 2023-11-29
  Changes: Data collection, Derived calculations, Refinement description