7b7x

Notum-Fragment063

Method: X-RAY DIFFRACTION Dmax: 69.4 Å Quality: GOOD

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

Palmitoleoyl-protein carboxylesterase NOTUM

Homo sapiens

UniProt Q6P988

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 81–451 Not recorded SO4 SULFATE ION × 3 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 EDO 1,2-ETHANEDIOL × 5 WKA N-(2,1,3-benzoxadiazol-4-yl)acetamide × 1 X-RAY DIFFRACTION X-ray crystallization conditions:EVAPORATION;296 K;1.5 M Ammonium Sulphate 0.1 M Sodium Citrate, pH4.2 Resolution 2.41 Å R-free 0.245

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.

140 other PDB entries and 149 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NOTUM_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 4–374; UniProt 81–451

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 7b7x

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7b7x
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7b7x
Deposition date deposition_date2020-12-11
Structure title titleNotum-Fragment063
Keywords keywordsNotum Fragment, HYDROLASE; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier21.50
Radius of gyration Rg (electron density) rg_electron20.10
Forward intensity I(0) i030349200.00
Molecular weight molecular_weight40988.0 kDa
Excluded volume excluded_volume50720 ų
Envelope volume envelope_volume59807 ų
Hydration-shell volume shell_volume24003 ų
Envelope diameter envelope_diameter71.7
Shell Rg shell_rg27.47
Envelope Rg envelope_rg20.48
Shape Rg shape_rg20.06
Total Rg total_rg21.15
Total atoms total_atoms2880
Residues n_residues353
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 dmax69.4
Rg (real space) rg_real21.34
Rg uncertainty (real space) rg_real_error0.41
I(0) (real space) i0_real3.0350e+07
I(0) uncertainty (real space) i0_real_error4.0880e+05
Rg (reciprocal space) rg_reciprocal21.37
I(0) (reciprocal space) i0_reciprocal30350000.0000
Solution quality estimate total_estimate0.8876
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary27.5
Skewness Skewness skewness0.098
Kurtosis Kurtosis kurtosis-0.459
Angular range angular_range— – 0.3700 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha5579000.0000
Real-space data points n_real_points69
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.850; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.991

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 1 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd7b7xa_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.69 — alpha/beta-Hydrolases
Superfamily Superfamily superfamilyc.69.1 — alpha/beta-Hydrolases
Family Family familyc.69.1.42 — Pectinacetylesterase-like

8. Citations (1)

9. Files and Curves (10)