SAXSdb — 5fds

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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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–131	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

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 5FDS	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5FEG Crystal structure of the dimeric allergen profilin (Hev b 8) Deposited 2015-12-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–131（131 aa） Chain B 1–131（131 aa）	Not recorded	No recorded non-water small molecule	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
7SBD Murine Fab/IgE in complex with profilin from Hevea brasieliensis (Hev b 8) Deposited 2021-09-24	Different oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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

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	5fds
Deposition date deposition_date	2015-12-16
Structure title title	Crystal structure of the monomeric 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	15.13 Å
Radius of gyration Rg (electron density) rg_electron	13.57 Å
Forward intensity I(0) i0	4206920.00
Molecular weight molecular_weight	14332.0 kDa
Excluded volume excluded_volume	17813 Å³
Envelope volume envelope_volume	19526 Å³
Hydration-shell volume shell_volume	12163 Å³
Envelope diameter envelope_diameter	44.4 Å
Shell Rg shell_rg	19.43 Å
Envelope Rg envelope_rg	13.83 Å
Shape Rg shape_rg	13.56 Å
Total Rg total_rg	14.79 Å
Total atoms total_atoms	1003
Residues n_residues	131
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	46.5 Å
Rg (real space) rg_real	14.99 Å
Rg uncertainty (real space) rg_real_error	0.23 Å
I(0) (real space) i0_real	4.2070e+06
I(0) uncertainty (real space) i0_real_error	4.7520e+04
Rg (reciprocal space) rg_reciprocal	15.01 Å
I(0) (reciprocal space) i0_reciprocal	4207000.0000
Solution quality estimate total_estimate	0.8956
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	20.0 Å
Skewness Skewness skewness	0.033
Kurtosis Kurtosis kurtosis	-0.432
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	709500.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.893; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.981; Smooth: 0.980

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Profilin-2
Molecular weight formula_weight	14162.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1187

MSWQAYVDDHLMCEIEGNHLSAAAIIGQDGSVWAQSANFPQFKSEEITGIMSDFHEPGTLAPTGLYIGGTKYMVIQGEPGAVIRGKKGPGGVTVKKTNQALIIGIYDEPMTPGQCNMIVERLGDYLIDQGY

来源 Source

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

Entity 2 Entity 2 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	131

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d5fdsa_
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 (1 domains)

Domain ID domain_id	5fdsA00
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	59.037 Å
Unit-cell length b length_b	59.037 Å
Unit-cell length c length_c	132.891 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	33.220 Å
R factor r_factor	0.1742
R_work r_work	0.1730
R_free r_free	0.1968

fit	/app/data/saxs_computation/fd/5fds/5fds.fit
pddf	/app/data/pr_computation/fd/5fds/5fds.pr.out
profile	/app/data/saxs_computation/fd/5fds/5fds.dat

Crystal structure of the monomeric 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