SAXSdb — 9qbj

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1. Structure Basics

entry_id	9qbj
deposition_date	2025-03-03
title	Legobody dimer
keywords	legobody, dimer, anti-alfa, BIOSYNTHETIC PROTEIN; BIOSYNTHETIC PROTEIN
method	ELECTRON MICROSCOPY

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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	44.83 Å
rg_electron	44.64 Å
i0	716859000.00
molecular_weight	220780.0 kDa
excluded_volume	276150 Å³
envelope_volume	394690 Å³
shell_volume	73564 Å³
envelope_diameter	145.6 Å
shell_rg	49.46 Å
envelope_rg	43.76 Å
shape_rg	44.62 Å
total_rg	44.96 Å
total_atoms	15562
n_residues	1997
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	141.2 Å
rg_real	45.33 Å
rg_real_error	0.46 Å
i0_real	7.0410e+08
i0_real_error	1.1120e+07
rg_reciprocal	44.83 Å
i0_reciprocal	717100000.0000
total_estimate	0.7165
solution_quality	REASONABLE a REASONABLE solution
n_peaks	1
r_peak_primary	60.5 Å
skewness	0.181
kurtosis	-0.304
angular_range	— – 0.1750 Å⁻¹
current_alpha	1.9050
highest_alpha	64300000.0000
n_real_points	36
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.907; Stabil: 0.924; Sysdev: 0.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.844

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Nanobody ALFA-H6
formula_weight	14813.5 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	C,D
atom_count	15600

EVQLQESGGGLVQPGGSLRLSCTASGVTISALNAMAMGWYRQAPGERRVMVAAVSERGNAMYRESVQGRFTVTRDFTNKMVSLQMDNLKPEDTAVYYCHVLEDRVDSFHDYWGQGTQVTVSSLEGTKHHHHHH

Source

organism	Vicugna pacos
ncbi_taxonomy_id	30538
host_organism	Homo sapiens

Entity 2 polymer

description	Fab antibody 8D3_2_H-H6
formula_weight	25539.6 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	E,G

DVQLVESGGGLVQPGKSLRLSCAASGFTFSNFGMHWVRQAPEMGLEWVAYISSGSTTKYYGDTVKGRFTISRDNPKNTLYLQMNSLRSEDTAMYYCARRPLYDGDYGYPMDYWGQGTSVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCGSGTKHHHHHH

Source

organism	Mus musculus
ncbi_taxonomy_id	10090
host_organism	Homo sapiens

Entity 3 polymer

description	Fa antibody 8D3_2_L
formula_weight	24095.9 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	F,H

NIMLTQSPSSLAVSAGERVTMSCKSTQSILYNSNQKTYLAWYQQKPGQSPKLLIYWASTRASGVPDRFTGSGSGTDFTLTINSVQPEDLAVYYCHQYLSAWTFGGGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Source

organism	Mus musculus
ncbi_taxonomy_id	10090
host_organism	Homo sapiens

Entity 4 polymer

description	Maltose/maltodextrin-binding periplasmic protein,Immunoglobulin G-binding protein A,Immunoglobulin G-binding protein G
formula_weight	59047.1 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	I

MHHHHHHGSKIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSKVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPLGAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDQALAFAQILIMPNLTEEQRNGFIQSLKDDPSVSKEILAEAKKLNEHQAPKGGSGGAGSGDQQSAFYEILNMPNLNEAQRNGFIQSLKDDPSQSTNVLGEAKKLNESQAGGGSGGGSGGSAVTTYKLVINGKTLKGETTTKAVDAETAEKAFKQYANDNGVDGVWTYDDATKTFTVT

Source

organism	;Streptococcus sp. 'group G' ;
ncbi_taxonomy_id	1320
host_organism	Escherichia coli

Entity 5 polymer

description	Maltose/maltodextrin-binding periplasmic protein,Immunoglobulin G-binding protein A,Immunoglobulin G-binding protein G
formula_weight	59176.2 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	J

MHHHHHHGSKIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSKVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPLGAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDQALAFAQILIMPNLTEEQRNGFIQSLKDDPSVSKEILAEAKKLNEHQAPKGGSGGAGSGDQQSAFYEILNMPNLNEAQRNGFIQSLKDDPSQSTNVLGEAKKLNESQAGGGSGGGSGGSAVTTYKLVINGKTLKGETTTKAVDAETAEKAFKQYANDNGVDGVWTYDDATKTFTVTE

Source

organism	;Streptococcus sp. 'group G' ;
ncbi_taxonomy_id	1320
host_organism	Escherichia coli

Entity 6 branched

description	alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose
formula_weight	342.3 kDa
src_method	syn
entity_count	2

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6. Citations (1)

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length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	—

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	3.200 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.20 Å
resolution_method	—
num_particles	114803

fit	/app/data/saxs_computation/qb/9qbj/9qbj.fit
pddf	/app/data/pr_computation/qb/9qbj/9qbj.pr.out
profile	/app/data/saxs_computation/qb/9qbj/9qbj.dat

Legobody dimer

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

EM 3D

5. Entities & Polymer Info (6)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

Entity 5 polymer

Polymer

Source

Entity 6 branched

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)