SAXSdb — 9shd

▼

1. Structure Basics

entry_id	9shd
deposition_date	2025-08-26
last_revision	2025-11-19
title	Structure of vaccinia virus A26 (residues 1-397) in complex with Fab 10M2146
keywords	complex antigen-antibody, vaccinia virus, A26, VIRAL PROTEIN; VIRAL PROTEIN
method	X-RAY DIFFRACTION

▼

Download Data

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

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	36.70 Å
rg_electron	36.43 Å
i0	157369000.00
molecular_weight	101370.0 kDa
excluded_volume	126750 Å³
envelope_volume	163100 Å³
shell_volume	39162 Å³
envelope_diameter	128.7 Å
shell_rg	40.69 Å
envelope_rg	36.09 Å
shape_rg	36.39 Å
total_rg	36.82 Å
total_atoms	7148
n_residues	907
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

▼

3. P(r) Analysis (GNOM)

dmax	124.7 Å
rg_real	36.94 Å
rg_real_error	1.13 Å
i0_real	1.5740e+08
i0_real_error	3.0380e+06
rg_reciprocal	36.79 Å
i0_reciprocal	157300000.0000
total_estimate	0.8526
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	34.8 Å
skewness	0.444
kurtosis	-0.490
angular_range	— – 0.2150 Å⁻¹
current_alpha	0.0000
highest_alpha	19280000.0000
n_real_points	44
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.827; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.772; Smooth: 0.826

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (5)

Entity 1 polymer

description	Heavy chain of Fab 10M2146
formula_weight	24551.5 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	H
atom_count	8303

EVQLVQSGAEVKKPGESLKISCKGSGYSFTTHWIGWVRQMPGEGLEWLGIIYPGDSETKYSPSFQGQVTISVDKSINTAYLHWSSLKASDTAMYFCARRPKNYYDASGYYNWLDPWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKS

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 2 polymer

description	Light chain of Fab 10M2146
formula_weight	23410.1 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	L

EIQMTQSPSTLSASVGDRVTITCRASQSLSTWLAWYQQKPGKAPKLLIYKASILESGVPSRFSASGSGTEFTLTISGLQPDDFATYYCQQYNSYLGAFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 3 polymer

description	Anti-Fab VHH
formula_weight	13390.6 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	K

GSQVQLQESGGGLVQPGGSLRLSCAASGRTISRYAMSWFRQAPGKEREFVAVARRSGDGAFYADSVQGRFTVSRDDAKNTVYLQMNSLKPEDTAVYYCAIDSDTFYSGSYDYWGQGTQVTVSS

Source

organism	Lama glama
ncbi_taxonomy_id	9844
host_organism	Escherichia coli

Entity 4 polymer

description	Envelop protein OPG153
formula_weight	52359.9 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	H0Z0

MANIINLWNGIVPTVQDVNVASITAFKSMIDETWDKKIEANTCISRKHRNIIHEVIRDFMKAYPKMDENKKSPLGAPMQWLTQYYILKNEYHKTMLAYDNGSLNTKFKTLNIYMITNVGQYILYIVFCIISGKNHDGTPYIYDSEITSNDKNFINERIKYACKQILHGQLTIALRIRNKFMFIGSPMYLWFNVNGSQVYHDIYDRNAGFHNKEIGRLLYAFMYYLSISGRFLNDFALLKFTYLGESWTFSLSVPEYILYGLGYSVFDTIEKFSNDAILVYIRTNNRNGYDYVEFNKKGIAKVTEDKPDNDKRIHAIRLINDSTDVQHIHFGFRNMVIIDNECANIQSSAENATDTGHHQDSKINIEVEDDVIDDDDYNPKPTPIPEPHPRPPFPRHEGSGLVPRIGSGSAGWSHPQFEKGGGSGGGSGGGSWSHPQFEKGTGGLNDIFEAQKIEWHE

Source

organism	Orthopoxvirus vaccinia
ncbi_taxonomy_id	10245
host_organism	Escherichia coli

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	1067

▶

6. Citations (1)

▶

length_a	122.459 Å
length_b	157.821 Å
length_c	141.434 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	orthorhombic

resolution	1.900 Å
resolution_low	39.930 Å
r_factor	0.1593
r_work	0.1577
r_free	0.1903

fit	/app/data/saxs_computation/sh/9shd/9shd.fit
pddf	/app/data/pr_computation/sh/9shd/9shd.pr.out
profile	/app/data/saxs_computation/sh/9shd/9shd.dat

Structure of vaccinia virus A26 (residues 1-397) in complex with Fab 10M2146

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 (5)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

Entity 5 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)