SAXSdb — 9y0a

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1. Structure Basics

entry_id	9y0a
deposition_date	2025-08-28
title	Crystal structure of Bet v 1.0101 in complex with human IgE Fab 2H22
keywords	allergen, human IgE, IgE Fab, allergen-antibody complex, ALLERGEN-IMMUNE SYSTEM complex; ALLERGEN/IMMUNE SYSTEM
method	X-RAY DIFFRACTION

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	30.78 Å
rg_electron	30.71 Å
i0	66034100.00
molecular_weight	64284.0 kDa
excluded_volume	80482 Å³
envelope_volume	102270 Å³
shell_volume	30042 Å³
envelope_diameter	115.0 Å
shell_rg	35.14 Å
envelope_rg	30.84 Å
shape_rg	30.70 Å
total_rg	31.15 Å
total_atoms	4533
n_residues	598
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	108.2 Å
rg_real	31.11 Å
rg_real_error	1.21 Å
i0_real	6.6030e+07
i0_real_error	1.1020e+06
rg_reciprocal	30.97 Å
i0_reciprocal	66030000.0000
total_estimate	0.8140
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	29.7 Å
skewness	0.620
kurtosis	-0.069
angular_range	— – 0.2550 Å⁻¹
current_alpha	0.0000
highest_alpha	13140000.0000
n_real_points	52
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.713; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.675; Smooth: 0.765

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4. Crystallography & Experiment

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5. Entities & Polymer Info (8)

Entity 1 polymer

description	Major pollen allergen Bet v 1-A
formula_weight	17592.8 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C
atom_count	4927

MGVFNYETETTSVIPAARLFKAFILDGDNLFPKVAPQAISSVENIEGNGGPGTIKKISFPEGFPFKYVKDRVDEVDHTNFKYNYSVIEGGPIGDTLEKISNEIKIVATPDGGSILKISNKYHTKGDHEVKAEQVKASKEMGETLLRAVESYLLAHSDAYN

Source

organism	Betula pendula
common_name	European white birch
ncbi_taxonomy_id	3505
host_organism	Escherichia coli

Entity 2 polymer

description	hIgE Fab 2H22 heavy chain
formula_weight	23953.7 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A

EVQLQESGPGLVKPSETLSLTCTVSGGSISTNGYYWGWIRQPPGKGLDWIGSISYSGNTYYNPSLQSRVSISVDTSKKQFSLKLSSVTASDTAVYYCARHGANWEGVVGWFDPWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Cricetulus griseus

Entity 3 polymer

description	hIgE Fab 2H22 light chain
formula_weight	22630.1 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

QSVLPQPPSVSAAPGQNVTISCSGSISNIGNNYVSWYQRLPGTAPKLLIYGNNNRPSGIPDRFSGSKSATSATLGITGLQAGDEAVYYCGTWDSSLRAGVFGGGTQLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Cricetulus griseus

Entity 4 branched

description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	424.4 kDa
src_method	man
entity_count	1

Entity 5 non-polymer

description	DI(HYDROXYETHYL)ETHER
formula_weight	106.1 kDa
src_method	syn
entity_count	3

Entity 6 non-polymer

description	TETRAETHYLENE GLYCOL
formula_weight	194.2 kDa
src_method	syn
entity_count	2

Entity 7 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	1

Entity 8 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	372

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6. Citations (1)

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length_a	81.928 Å
length_b	117.535 Å
length_c	158.622 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	C 2 2 21
int_tables_number	20
crystal_system	—

resolution	2.120 Å
resolution_low	39.694 Å
r_factor	—
r_work	0.1708
r_free	0.2183

fit	/app/data/saxs_computation/y0/9y0a/9y0a.fit
pddf	/app/data/pr_computation/y0/9y0a/9y0a.pr.out
profile	/app/data/saxs_computation/y0/9y0a/9y0a.dat

Crystal structure of Bet v 1.0101 in complex with human IgE Fab 2H22

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

Diffraction

5. Entities & Polymer Info (8)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 branched

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)