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9z7a

;Cryo-EM structure of Secreted extracellular protein A (SepA) from Shigella flexneri complexed with the fragment antigen binding domain of monoclonal antibody 40 ;

Method: ELECTRON MICROSCOPY D_max: 134.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9z7a
deposition_date	2025-11-16
title	;Cryo-EM structure of Secreted extracellular protein A (SepA) from Shigella flexneri complexed with the fragment antigen binding domain of monoclonal antibody 40 ;
keywords	PROTEASE, BETA-HELIX, SECRETED, MONOCLONAL ANTIBODY, HYDROLASE, HYDROLASE-IMMUNE SYSTEM complex; HYDROLASE/IMMUNE SYSTEM
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	40.28 Å
rg_electron	40.40 Å
i0	260912000.00
molecular_weight	127980.0 kDa
excluded_volume	158640 Å³
envelope_volume	205860 Å³
shell_volume	45142 Å³
envelope_diameter	139.5 Å
shell_rg	42.42 Å
envelope_rg	40.88 Å
shape_rg	40.38 Å
total_rg	40.59 Å
total_atoms	9014
n_residues	1204
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	134.8 Å
rg_real	40.38 Å
rg_real_error	1.21 Å
i0_real	2.6090e+08
i0_real_error	4.4420e+06
rg_reciprocal	40.28 Å
i0_reciprocal	260900000.0000
total_estimate	0.8112
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	41.5 Å
skewness	0.330
kurtosis	-0.599
angular_range	— – 0.1950 Å⁻¹
current_alpha	0.0000
highest_alpha	22070000.0000
n_real_points	40
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.896; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.854; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Serine protease SepA autotransporter
formula_weight	109400.4 kDa
ec_number	3.4.21.-
mutation	F684S natural variant compared to Q8VSL2 UniProt entry (F740 in UniProt)
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	9014

ATVSAEIPYQIFRDFAENKGQFTPGTTNISIYDKQGNLVGKLDKAPMADFSSATITTGSLPPGDHTLYSPQYVVTAKHVSGSDTMSFGYAKNTYTAVGTNNNSGLDIKTRRLSKLVTEVAPAEVSDIGAVSGAYQAGGRFTEFYRLGGGMQYVKDKNGNRTQVYTNGGFLVGGTVSALNSYNNGQMITAQTGDIFNPANGPLANYLNMGDSGSPLFAYDSLQKKWVLIGVLSSGTNYGNNWVVTTQDFLGQQPQNDFDKTIAYTSGEGVLQWKYDAANGTGTLTQGNTTWDMHGKKGNDLNAGKNLLFTGNNGEVVLQNSVNQGAGYLQFAGDYRVSALNGQTWMGGGIITDKGTHVLWQVNGVAGDNLHKTGEGTLTVNGTGVNAGGLKVGDGTVILNQQADADGKVQAFSSVGIASGRPTVVLSDSQQVNPDNISWGYRGGRLELNGNNLTFTRLQAADYGAIITNNSEKKSTVTLDLQTLKASDINVPVNTVSIFGGRGAPGDLYYDSSTKQYFILKASSYSPFFSDLNNSSVWQNVGKDRNKAIDTVKQQKIEASSQPYMYHGQLNGNMDVNIPQLSGKDVLALDGSVNLPEGSITKKSGTLIFQGHPVIHAGTTTSSSQSDWETRQFTLEKLKLDAATFHLSRNGKMQGDINATNGSTVILGSSRVFTDRSDGTGNAVSSVEGSATATTVGDQSDYSGNVTLENKSSLQIMERFTGGIEAYDSTVSVTSQNAVFDRVGSFVNSSLTLGKGAKLTAQSGIFSTGAVDVKENASLTLTGMPSAQKQGYYSPVISTTEGINLEDNASFSVKNMGYLSSDIHAGTTAATINLGDSDADAGKTDSPLFSSLMKGYNAVLRGSITGAQSTVNMINALWYSDGKSEAGALKAKGSRIELGDGKHFATLQVKELSADNTTFLMHTNNSRADQLNVTDKLSGSNNSVLVDFLNKPASEMSVTLITAPKGSDEKTFTAGTQQIGFSNVTPVISTEKTDDATKWVLTGYQTTADAGASKAAKDFMASGYKSFLTEVNNL

Source

organism	Shigella flexneri 2a str. 2457T
ncbi_taxonomy_id	198215
host_organism	Escherichia coli DH5[alpha]

Entity 2 polymer

description	Heavy chain of the fragment antigen binding domain of monoclonal antibody 40
formula_weight	23757.5 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

QVQLQESGPGLVKPSETLSLTCTVSGASISSSSYYCIWVRQSPGKGLEWIGTTYYSGTTYHEPSLRSRVSISLDTSKNQFSLMLTSVTAADTARYYCAISYGWGSYVNHWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCD

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 3 polymer

description	Light chain of the fragment antigen binding domain of monoclonal antibody 40
formula_weight	23534.1 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

EIVLTQSPATLSLSPGERATLSCRASQIFGSDLAWYQHKPGQAPRLLIFNTSNRVTGTPARFSGSGSGTDFTLTINSLEPDDVAVYYCHQRSSWPSITFGQGTRLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

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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	triclinic

resolution	1.99 Å
resolution_method	—
num_particles	663017

fit	/app/data/saxs_computation/z7/9z7a/9z7a.fit
pddf	/app/data/pr_computation/z7/9z7a/9z7a.pr.out
profile	/app/data/saxs_computation/z7/9z7a/9z7a.dat

;Cryo-EM structure of Secreted extracellular protein A (SepA) from Shigella flexneri complexed with the fragment antigen binding domain of monoclonal antibody 40 ;

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

EM 3D

5. Entities & Polymer Info (3)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)