3f71

Crystal structure of E18D DJ-1 with oxidized C106

Method: X-RAY DIFFRACTION Dmax: 49.3 Å Quality: GOOD

1. Protein Identity and Related Structures Protein Identity & Related Structures

Protein DJ-1

Homo sapiens

UniProt Q99497

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 1–189 Mutation:E18D Non-standard monomer:Yes (specific site not provided by mmCIF) No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;298 K;1.5 M sodium citrate, 25 mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 1.20 Å R-free 0.155

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

87 other PDB entries and 97 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PARK7_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–189; UniProt 1–189

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 3f71

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3f71
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3f71
Deposition date deposition_date2008-11-07
Structure title titleCrystal structure of E18D DJ-1 with oxidized C106
Keywords keywords;cysteine oxidation, Parkinson disease, Chaperone, Cytoplasm, Disease mutation, Nucleus, Oncogene, Oxidation, Phosphoprotein, Polymorphism, Ubl conjugation ;; CHAPERONE
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier16.56
Radius of gyration Rg (electron density) rg_electron15.17
Forward intensity I(0) i07157220.00
Molecular weight molecular_weight19631.0 kDa
Excluded volume excluded_volume24742 ų
Envelope volume envelope_volume27718 ų
Hydration-shell volume shell_volume15079 ų
Envelope diameter envelope_diameter48.5
Shell Rg shell_rg21.39
Envelope Rg envelope_rg15.56
Shape Rg shape_rg15.16
Total Rg total_rg16.34
Total atoms total_atoms1375
Residues n_residues186
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax49.3
Rg (real space) rg_real16.41
Rg uncertainty (real space) rg_real_error0.24
I(0) (real space) i0_real7.1570e+06
I(0) uncertainty (real space) i0_real_error8.1580e+04
Rg (reciprocal space) rg_reciprocal16.42
I(0) (reciprocal space) i0_reciprocal7157000.0000
Solution quality estimate total_estimate0.8986
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary22.4
Skewness Skewness skewness0.036
Kurtosis Kurtosis kurtosis-0.473
Angular range angular_range— – 0.4800 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1601000.0000
Real-space data points n_real_points78
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.919; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.975; Smooth: 0.944

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd3f71a_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.23 — Flavodoxin-like
Superfamily Superfamily superfamilyc.23.16 — Class I glutamine amidotransferase-like
Family Family familyc.23.16.2 — DJ-1/PfpI

CATH v4.4 (1 domains)

Domain ID domain_id3f71A00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily880 — Class I glutamine amidotransferase (GATase) domain

8. Citations (1)

9. Files and Curves (10)