SAXSdb — 4wfu

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

Allergen Bos d 2

Bos taurus

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 17–172	Fragment：UNP Residues 17-172	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；4.0 M sodium formate	Resolution 1.75 Å R-free 0.232

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 4WFU	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BJ7 BOVINE LIPOCALIN ALLERGEN BOS D 2 Deposited 1998-07-02	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 17–172（156 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 4；pH 4	Resolution 1.80 Å R-free 0.232
4WFV Bovine allergen Bos d 2 in the monoclinic space group C2. Deposited 2014-09-17	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: Monomeric	Chain A 17–172（156 aa） Fragment：UNP Residues 17-172	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；293 K；2.5 M 1,6-hexanediol, 0.1 M sodium citrate	Resolution 1.40 Å R-free 0.213

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

View Construct and Data Evidence

UniProt name	ALL2_BOVIN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–156； UniProt 17–172

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	4wfu
Deposition date deposition_date	2014-09-17
Structure title title	Bovine allergen Bos d 2 in the trigonal space group P3221.
Keywords keywords	Allergen, Lipocalin; 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	15.93 Å
Radius of gyration Rg (electron density) rg_electron	14.41 Å
Forward intensity I(0) i0	5901950.00
Molecular weight molecular_weight	17314.0 kDa
Excluded volume excluded_volume	21591 Å³
Envelope volume envelope_volume	24205 Å³
Hydration-shell volume shell_volume	13949 Å³
Envelope diameter envelope_diameter	47.8 Å
Shell Rg shell_rg	20.64 Å
Envelope Rg envelope_rg	14.73 Å
Shape Rg shape_rg	14.39 Å
Total Rg total_rg	15.66 Å
Total atoms total_atoms	1217
Residues n_residues	151
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	48.6 Å
Rg (real space) rg_real	15.79 Å
Rg uncertainty (real space) rg_real_error	0.24 Å
I(0) (real space) i0_real	5.9020e+06
I(0) uncertainty (real space) i0_real_error	5.9070e+04
Rg (reciprocal space) rg_reciprocal	15.81 Å
I(0) (reciprocal space) i0_reciprocal	5902000.0000
Solution quality estimate total_estimate	0.8955
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	22.2 Å
Skewness Skewness skewness	0.017
Kurtosis Kurtosis kurtosis	-0.459
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1555000.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.889; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.982; Smooth: 0.991

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d4wfua_
Class class	b — All beta proteins
Fold Fold fold	b.60 — Lipocalins
Superfamily Superfamily superfamily	b.60.1 — Lipocalins
Family Family family	b.60.1.1 — Retinol binding protein-like

CATH v4.4 (1 domains)

Domain ID domain_id	4wfuA00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	128 — Lipocalin
Homologous superfamily homologous superfamily	20 — Calycin beta-barrel core domain

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8. Citations (1)

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Unit-cell length a length_a	75.500 Å
Unit-cell length b length_b	75.500 Å
Unit-cell length c length_c	95.190 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 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	1.750 Å
Low-resolution limit resolution_low	38.480 Å
R factor r_factor	0.2119
R_work r_work	0.2109
R_free r_free	0.2315

Description description	Allergen Bos d 2
Molecular weight formula_weight	17868.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1338

Bovine allergen Bos d 2 in the trigonal space group P3221.

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

Allergen Bos d 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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Bos taurus
通用名 common_name	Bovine
NCBI Class编号 ncbi_taxonomy_id	9913
宿主生物 host_organism	Komagataella pastoris

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	90

fit	/app/data/saxs_computation/wf/4wfu/4wfu.fit
pddf	/app/data/pr_computation/wf/4wfu/4wfu.pr.out
profile	/app/data/saxs_computation/wf/4wfu/4wfu.dat