6lje

Crystal structure of gelsolin G3 domain (calcium and magnesium condition)

Method: X-RAY DIFFRACTION Dmax: 62.0 Å Quality: REASONABLE

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

Gelsolin

Homo sapiens

UniProt P06396

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 297–397 Fragment:UNP residues 297-397 GOL GLYCEROL × 1 CA CALCIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;PEG3350, ammonium sulphate, calcium chloride, magnesium chloride Resolution 1.40 Å R-free 0.189
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 297–397 Fragment:UNP residues 297-397 GOL GLYCEROL × 1 CA CALCIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;PEG3350, ammonium sulphate, calcium chloride, magnesium chloride Resolution 1.40 Å R-free 0.189

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.

60 other PDB entries and 93 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GELS_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–101; UniProt 297–397 Author chain B; PDBConstruct 1–101; UniProt 297–397

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 6lje

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6lje
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6lje
Deposition date deposition_date2019-12-14
Structure title titleCrystal structure of gelsolin G3 domain (calcium and magnesium condition)
Keywords keywordsfragmin, gelsolin family protein, calcium regulation, actin filament severing, CYTOSOLIC PROTEIN; CYTOSOLIC PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier19.09
Radius of gyration Rg (electron density) rg_electron17.91
Forward intensity I(0) i09117160.00
Molecular weight molecular_weight22758.0 kDa
Excluded volume excluded_volume28753 ų
Envelope volume envelope_volume33969 ų
Hydration-shell volume shell_volume16170 ų
Envelope diameter envelope_diameter62.2
Shell Rg shell_rg23.52
Envelope Rg envelope_rg18.16
Shape Rg shape_rg17.86
Total Rg total_rg19.00
Total atoms total_atoms1600
Residues n_residues202
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 dmax62.0
Rg (real space) rg_real19.03
Rg uncertainty (real space) rg_real_error0.39
I(0) (real space) i0_real9.1170e+06
I(0) uncertainty (real space) i0_real_error1.2260e+05
Rg (reciprocal space) rg_reciprocal19.04
I(0) (reciprocal space) i0_reciprocal9117000.0000
Solution quality estimate total_estimate0.7323
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary24.1
Skewness Skewness skewness0.232
Kurtosis Kurtosis kurtosis-0.404
Angular range angular_range— – 0.4150 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1470000.0000
Real-space data points n_real_points73
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.884; Stabil: 0.999; Sysdev: 0.295; Positv: 1.000; Valcen: 0.997; Smooth: 0.982

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id6ljeA00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology20 — Severin
Homologous superfamily homologous superfamily10 — Severin
Domain ID domain_id6ljeB00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology20 — Severin
Homologous superfamily homologous superfamily10 — Severin

8. Citations (1)

9. Files and Curves (10)