9cfo

Human DJ-1, 10 sec mixing with methylglyoxal, pink beam time-resolved serial crystallography

Method: X-RAY DIFFRACTION Dmax: 51.2 Å Quality: GOOD

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

Parkinson disease protein 7

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 Non-standard monomer:Yes (specific site not provided by mmCIF) No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:BATCH MODE;pH 7.5;293 K;100 mM HEPES pH=7.5, 200 mM NaCl, and 15% PEG 3350 Resolution 1.77 Å R-free 0.231

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 4–192; 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 9cfo

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9cfo
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9cfo
Deposition date deposition_date2024-06-27
最后修订 last_revision2025-03-12
Structure title titleHuman DJ-1, 10 sec mixing with methylglyoxal, pink beam time-resolved serial crystallography
Keywords keywordsglutathione-independent glyoxalase, mix-and-inject serial crystallography, Laue diffraction, HYDROLASE; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier16.76
Radius of gyration Rg (electron density) rg_electron15.34
Forward intensity I(0) i07223040.00
Molecular weight molecular_weight19812.0 kDa
Excluded volume excluded_volume24995 ų
Envelope volume envelope_volume28253 ų
Hydration-shell volume shell_volume15243 ų
Envelope diameter envelope_diameter51.9
Shell Rg shell_rg21.54
Envelope Rg envelope_rg15.70
Shape Rg shape_rg15.29
Total Rg total_rg16.61
Total atoms total_atoms2827
Residues n_residues187
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 dmax51.2
Rg (real space) rg_real16.63
Rg uncertainty (real space) rg_real_error0.28
I(0) (real space) i0_real7.2230e+06
I(0) uncertainty (real space) i0_real_error9.5580e+04
Rg (reciprocal space) rg_reciprocal16.64
I(0) (reciprocal space) i0_reciprocal7223000.0000
Solution quality estimate total_estimate0.8945
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary22.6
Skewness Skewness skewness0.044
Kurtosis Kurtosis kurtosis-0.463
Angular range angular_range— – 0.4750 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1683000.0000
Real-space data points n_real_points78
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.883; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.979; Smooth: 0.997

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

8. Citations (1)

9. Files and Curves (10)