3eay

Crystal structure of the human SENP7 catalytic domain

Method: X-RAY DIFFRACTION Dmax: 63.6 Å Quality: GOOD

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

Sentrin-specific protease 7

Homo sapiens

UniProt Q9BQF6

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 662–984 Fragment:Catalytic domain: Residues 662-984 SO4 SULFATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.5;291 K;The reservoir solution contained 1.6 M ammonium sulfate and 100 mM sodium citrate pH 6.5. Single crystals appeared after 2 days from equal volumes of protein solution (10 mg/ml in 5 mM Tris-HCl pH 8.0, 25 mM NaCl) and reservoir solution, VAPOR DIFFUSION, SITTING DROP, temperature 291K Resolution 2.40 Å R-free 0.256

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.

1 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SENP7_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–323; UniProt 662–984

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 3eay

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id3eay
Deposition date deposition_date2008-08-26
Structure title titleCrystal structure of the human SENP7 catalytic domain
Keywords keywords;protease, sentrin-specific protease, ULP, SENP, SUMO, ubiquitin, crystal, Alternative splicing, Hydrolase, Phosphoprotein, Polymorphism, Thiol protease, Ubl conjugation pathway ;; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier20.00
Radius of gyration Rg (electron density) rg_electron18.65
Forward intensity I(0) i014074900.00
Molecular weight molecular_weight29254.0 kDa
Excluded volume excluded_volume37154 ų
Envelope volume envelope_volume43365 ų
Hydration-shell volume shell_volume19368 ų
Envelope diameter envelope_diameter65.9
Shell Rg shell_rg25.04
Envelope Rg envelope_rg19.12
Shape Rg shape_rg18.61
Total Rg total_rg19.76
Total atoms total_atoms2063
Residues n_residues247
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 dmax63.6
Rg (real space) rg_real19.91
Rg uncertainty (real space) rg_real_error0.36
I(0) (real space) i0_real1.4070e+07
I(0) uncertainty (real space) i0_real_error1.7210e+05
Rg (reciprocal space) rg_reciprocal19.93
I(0) (reciprocal space) i0_reciprocal14080000.0000
Solution quality estimate total_estimate0.8996
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary25.4
Skewness Skewness skewness0.193
Kurtosis Kurtosis kurtosis-0.403
Angular range angular_range— – 0.3950 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha2454000.0000
Real-space data points n_real_points71
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.899; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.998

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id3eayA01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology418 — Actin-binding Protein, T-fimbrin; domain 1
Homologous superfamily homologous superfamily20
Domain ID domain_id3eayA02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology310 — TATA-Binding Protein
Homologous superfamily homologous superfamily130 — Ubiquitin-related

8. Citations (1)

9. Files and Curves (10)