7y4e

Crystal structure of DUSP10 mutant_N130A

Method: X-RAY DIFFRACTION Dmax: 68.5 Å Quality: EXCELLENT

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

Dual specificity protein phosphatase 10

Homo sapiens

UniProt Q9Y6W6

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 monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 320–467 Mutation:N130A No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;283 K;27.5% (w/v) PEG 3000, 100 mM Tris base /Hydrochloric acid, 175mM Calcium acetate Resolution 1.93 Å R-free 0.233
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 320–467 Mutation:N130A No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;283 K;27.5% (w/v) PEG 3000, 100 mM Tris base /Hydrochloric acid, 175mM Calcium acetate Resolution 1.93 Å R-free 0.233

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.

22 other PDB entries and 100 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name DUS10_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 2–149; UniProt 320–467 Author chain B; PDBConstruct 2–149; UniProt 320–467

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 7y4e

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7y4e
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7y4e
Deposition date deposition_date2022-06-14
Structure title titleCrystal structure of DUSP10 mutant_N130A
Keywords keywordsDual specificity protein phosphatase 10, MAP kinase phosphatase 5, HYDROLASE; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier21.74
Radius of gyration Rg (electron density) rg_electron20.56
Forward intensity I(0) i019355500.00
Molecular weight molecular_weight34117.0 kDa
Excluded volume excluded_volume42943 ų
Envelope volume envelope_volume49214 ų
Hydration-shell volume shell_volume20312 ų
Envelope diameter envelope_diameter70.7
Shell Rg shell_rg26.53
Envelope Rg envelope_rg20.66
Shape Rg shape_rg20.58
Total Rg total_rg21.30
Total atoms total_atoms4784
Residues n_residues298
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 dmax68.5
Rg (real space) rg_real21.68
Rg uncertainty (real space) rg_real_error0.36
I(0) (real space) i0_real1.9360e+07
I(0) uncertainty (real space) i0_real_error2.5010e+05
Rg (reciprocal space) rg_reciprocal21.70
I(0) (reciprocal space) i0_reciprocal19360000.0000
Solution quality estimate total_estimate0.9070
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary24.5
Skewness Skewness skewness0.236
Kurtosis Kurtosis kurtosis-0.532
Angular range angular_range— – 0.3650 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha2955000.0000
Real-space data points n_real_points68
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.933; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.993

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

8. Citations (1)

9. Files and Curves (10)