SAXSdb — 5feg

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

Profilin-2

Hevea brasiliensis

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 1–131 Chain B； UniProt 1–131	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；0.1M TRIS-HCl, pH 9.0; 2.0 M Ammonium Sulfate	Resolution 2.80 Å R-free 0.250

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.

Other PDB	Difference from Current Entry 5FEG	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5FDS Crystal structure of the monomeric allergen profilin (Hev b 8) Deposited 2015-12-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–131（131 aa）	Not recorded	GOL GLYCEROL × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；291 K；0.1M TRIS-HCL, pH 9.0, 1.6 M Ammonium Sulfate	Resolution 1.90 Å R-free 0.197
7SBD Murine Fab/IgE in complex with profilin from Hevea brasieliensis (Hev b 8) Deposited 2021-09-24	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–131（131 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；2% Tacsimate, pH 6.0, 0.1 M Bis-Tris, pH 6.5, 20% w/v PEG3350	Resolution 3.04 Å R-free 0.254
7SBG Murine Fab/IgE in complex with profilin from Hevea brasieliensis (Hev b 8) Deposited 2021-09-24	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–131（131 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.4；291 K；0.2 M lithium acetate, 20% PEG3350	Resolution 3.34 Å R-free 0.298

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PROF2_HEVBR
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–131； UniProt 1–131 Author chain B； PDBConstruct 1–131； UniProt 1–131

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	5feg
Deposition date deposition_date	2015-12-17
Structure title title	Crystal structure of the dimeric allergen profilin (Hev b 8)
Keywords keywords	Actin Binding Protein, Allergen, Allergy, Cross-reactivity, Hev b 8; ALLERGEN
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	19.92 Å
Radius of gyration Rg (electron density) rg_electron	19.14 Å
Forward intensity I(0) i0	13587900.00
Molecular weight molecular_weight	27248.0 kDa
Excluded volume excluded_volume	33857 Å³
Envelope volume envelope_volume	39066 Å³
Hydration-shell volume shell_volume	17541 Å³
Envelope diameter envelope_diameter	68.2 Å
Shell Rg shell_rg	24.83 Å
Envelope Rg envelope_rg	19.34 Å
Shape Rg shape_rg	19.17 Å
Total Rg total_rg	19.87 Å
Total atoms total_atoms	1914
Residues n_residues	260
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	66.7 Å
Rg (real space) rg_real	19.94 Å
Rg uncertainty (real space) rg_real_error	0.52 Å
I(0) (real space) i0_real	1.3590e+07
I(0) uncertainty (real space) i0_real_error	1.7180e+05
Rg (reciprocal space) rg_reciprocal	19.93 Å
I(0) (reciprocal space) i0_reciprocal	13590000.0000
Solution quality estimate total_estimate	0.6098
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.6 Å
Skewness Skewness skewness	0.403
Kurtosis Kurtosis kurtosis	-0.284
Angular range angular_range	— – 0.4000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5142000.0000
Real-space data points n_real_points	72
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.777; Stabil: 0.999; Sysdev: 0.210; Positv: 1.000; Valcen: 0.968; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d5fega_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.110 — Profilin-like
Superfamily Superfamily superfamily	d.110.1 — Profilin (actin-binding protein)
Family Family family	d.110.1.0 — automated matches

Domain ID domain_id	d5fegb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.110 — Profilin-like
Superfamily Superfamily superfamily	d.110.1 — Profilin (actin-binding protein)
Family Family family	d.110.1.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id	5fegA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	450 — Beta-Lactamase
Homologous superfamily homologous superfamily	30 — Dynein light chain 2a, cytoplasmic

Domain ID domain_id	5fegB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	450 — Beta-Lactamase
Homologous superfamily homologous superfamily	30 — Dynein light chain 2a, cytoplasmic

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8. Citations (1)

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Unit-cell length a length_a	58.558 Å
Unit-cell length b length_b	58.558 Å
Unit-cell length c length_c	87.340 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 32
Space-group number int_tables_number	145
Crystal system crystal_system	—

Resolution resolution	2.802 Å
Low-resolution limit resolution_low	33.092 Å
R factor r_factor	0.2097
R_work r_work	0.2067
R_free r_free	0.2497

Description description	Profilin-2
Molecular weight formula_weight	14162.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	1914

Crystal structure of the dimeric allergen profilin (Hev b 8)

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

Profilin-2

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Hevea brasiliensis
通用名 common_name	Para rubber tree
NCBI Class编号 ncbi_taxonomy_id	3981
宿主生物 host_organism	Escherichia coli

fit	/app/data/saxs_computation/fe/5feg/5feg.fit
pddf	/app/data/pr_computation/fe/5feg/5feg.pr.out
profile	/app/data/saxs_computation/fe/5feg/5feg.dat