SAXSdb — 9z7a

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

Serine protease SepA autotransporter

Shigella flexneri 2a str. 2457T

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 heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 57–1089	Mutation：F684S natural variant compared to Q8VSL2 UniProt entry (F740 in UniProt)	Heavy chain of the fragment antigen binding domain of monoclonal antibody 40 × 1 Light chain of the fragment antigen binding domain of monoclonal antibody 40 × 1	ELECTRON MICROSCOPY mmCIF provides none of the parsed experimental conditions	Resolution 1.99 Å

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	SEPA_SHIFL
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–1033； UniProt 57–1089

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	9z7a
Deposition date deposition_date	2025-11-16
Structure title 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 keywords	PROTEASE, BETA-HELIX, SECRETED, MONOCLONAL ANTIBODY, HYDROLASE, HYDROLASE-IMMUNE SYSTEM complex; HYDROLASE/IMMUNE SYSTEM
Experimental Method method	ELECTRON MICROSCOPY

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	40.28 Å
Radius of gyration Rg (electron density) rg_electron	40.40 Å
Forward intensity I(0) i0	260912000.00
Molecular weight molecular_weight	127980.0 kDa
Excluded volume excluded_volume	158640 Å³
Envelope volume envelope_volume	205860 Å³
Hydration-shell volume shell_volume	45142 Å³
Envelope diameter envelope_diameter	139.5 Å
Shell Rg shell_rg	42.42 Å
Envelope Rg envelope_rg	40.88 Å
Shape Rg shape_rg	40.38 Å
Total Rg total_rg	40.59 Å
Total atoms total_atoms	9014
Residues n_residues	1204
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	134.8 Å
Rg (real space) rg_real	40.38 Å
Rg uncertainty (real space) rg_real_error	1.21 Å
I(0) (real space) i0_real	2.6090e+08
I(0) uncertainty (real space) i0_real_error	4.4420e+06
Rg (reciprocal space) rg_reciprocal	40.28 Å
I(0) (reciprocal space) i0_reciprocal	260900000.0000
Solution quality estimate total_estimate	0.8112
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	41.5 Å
Skewness Skewness skewness	0.330
Kurtosis Kurtosis kurtosis	-0.599
Angular range angular_range	— – 0.1950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	22070000.0000
Real-space data points n_real_points	40
GNOM version gnom_version	4.1.3
Quality Criteria 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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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Serine protease SepA autotransporter
Molecular weight formula_weight	109400.4 kDa
EC 编号 ec_number	3.4.21.-
Mutation mutation	F684S natural variant compared to Q8VSL2 UniProt entry (F740 in UniProt)
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	9014

ATVSAEIPYQIFRDFAENKGQFTPGTTNISIYDKQGNLVGKLDKAPMADFSSATITTGSLPPGDHTLYSPQYVVTAKHVSGSDTMSFGYAKNTYTAVGTNNNSGLDIKTRRLSKLVTEVAPAEVSDIGAVSGAYQAGGRFTEFYRLGGGMQYVKDKNGNRTQVYTNGGFLVGGTVSALNSYNNGQMITAQTGDIFNPANGPLANYLNMGDSGSPLFAYDSLQKKWVLIGVLSSGTNYGNNWVVTTQDFLGQQPQNDFDKTIAYTSGEGVLQWKYDAANGTGTLTQGNTTWDMHGKKGNDLNAGKNLLFTGNNGEVVLQNSVNQGAGYLQFAGDYRVSALNGQTWMGGGIITDKGTHVLWQVNGVAGDNLHKTGEGTLTVNGTGVNAGGLKVGDGTVILNQQADADGKVQAFSSVGIASGRPTVVLSDSQQVNPDNISWGYRGGRLELNGNNLTFTRLQAADYGAIITNNSEKKSTVTLDLQTLKASDINVPVNTVSIFGGRGAPGDLYYDSSTKQYFILKASSYSPFFSDLNNSSVWQNVGKDRNKAIDTVKQQKIEASSQPYMYHGQLNGNMDVNIPQLSGKDVLALDGSVNLPEGSITKKSGTLIFQGHPVIHAGTTTSSSQSDWETRQFTLEKLKLDAATFHLSRNGKMQGDINATNGSTVILGSSRVFTDRSDGTGNAVSSVEGSATATTVGDQSDYSGNVTLENKSSLQIMERFTGGIEAYDSTVSVTSQNAVFDRVGSFVNSSLTLGKGAKLTAQSGIFSTGAVDVKENASLTLTGMPSAQKQGYYSPVISTTEGINLEDNASFSVKNMGYLSSDIHAGTTAATINLGDSDADAGKTDSPLFSSLMKGYNAVLRGSITGAQSTVNMINALWYSDGKSEAGALKAKGSRIELGDGKHFATLQVKELSADNTTFLMHTNNSRADQLNVTDKLSGSNNSVLVDFLNKPASEMSVTLITAPKGSDEKTFTAGTQQIGFSNVTPVISTEKTDDATKWVLTGYQTTADAGASKAAKDFMASGYKSFLTEVNNL

来源 Source

来源生物 organism	Shigella flexneri 2a str. 2457T
NCBI Class编号 ncbi_taxonomy_id	198215
宿主生物 host_organism	Escherichia coli DH5[alpha]

Entity 2 Entity 2 polymer

Description description	Heavy chain of the fragment antigen binding domain of monoclonal antibody 40
Molecular weight formula_weight	23757.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

QVQLQESGPGLVKPSETLSLTCTVSGASISSSSYYCIWVRQSPGKGLEWIGTTYYSGTTYHEPSLRSRVSISLDTSKNQFSLMLTSVTAADTARYYCAISYGWGSYVNHWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCD

来源 Source

来源生物 organism	Homo sapiens
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Homo sapiens

Entity 3 Entity 3 polymer

Description description	Light chain of the fragment antigen binding domain of monoclonal antibody 40
Molecular weight formula_weight	23534.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

EIVLTQSPATLSLSPGERATLSCRASQIFGSDLAWYQHKPGQAPRLLIFNTSNRVTGTPARFSGSGSGTDFTLTINSLEPDDVAVYYCHQRSSWPSITFGQGTRLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

来源 Source

来源生物 organism	Homo sapiens
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Homo sapiens

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	triclinic

Resolution resolution	1.99 Å
Resolution测定方法 resolution_method	—
颗粒数 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

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

Serine protease SepA autotransporter

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

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)