4ZGG | pdb_00004zgg

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


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) 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein deglycase DJ-1190Homo sapiensMutation(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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99497
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download Ideal Coordinates CCD File 
B [auth A]
C [auth A]
D [auth A]
E [auth A]
F [auth A]
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
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
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) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.002α = 90
b = 75.002β = 90
c = 74.897γ = 120
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
SOLVEphasing
SCALAdata scaling
REFMACrefinement
MOSFLMdata reduction

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • 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