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9ux0

Crystal structure of the virulence effector VepA in complex with its secretion chaperone VecA

Method: X-RAY DIFFRACTION D_max: 98.3 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9ux0
deposition_date	2025-05-13
title	Crystal structure of the virulence effector VepA in complex with its secretion chaperone VecA
keywords	Vibrio parahaemolyticus, Type 3 secretion system, effector, TOXIN; TOXIN
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	30.60 Å
rg_electron	29.92 Å
i0	89351100.00
molecular_weight	74222.0 kDa
excluded_volume	92917 Å³
envelope_volume	120240 Å³
shell_volume	34062 Å³
envelope_diameter	106.3 Å
shell_rg	36.32 Å
envelope_rg	30.11 Å
shape_rg	29.91 Å
total_rg	30.55 Å
total_atoms	5218
n_residues	668
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	98.3 Å
rg_real	30.61 Å
rg_real_error	0.62 Å
i0_real	8.9350e+07
i0_real_error	1.1980e+06
rg_reciprocal	30.61 Å
i0_reciprocal	89350000.0000
total_estimate	0.9039
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	34.0 Å
skewness	0.299
kurtosis	-0.536
angular_range	— – 0.2600 Å⁻¹
current_alpha	0.0000
highest_alpha	27650000.0000
n_real_points	53
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.933; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.973; Smooth: 0.975

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4. Crystallography & Experiment

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5. Entities & Polymer Info (2)

Entity 1 polymer

description	Cation transporter
formula_weight	53156.4 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	5218

GMVNTTQKISQSPVPDLEQFRAIAAQKDDRVISKRGEVKEPSTFHKGHKFASVSEGVLRKKYTKFFQENIKTHLDLKQALLKEEKPETALLAYSLVSPSGYRGEPLTERKILEVVSLLDEVKVEGDTYQQLKNTFDSISKDPRMQVSLENQYPGKMDGFGAQLLEMGKEKLKGSGVNAAINLALPGVGLLVATGRELHKASVNGDAEAYHHQLEQISQLPGRDQRLSMPMQQTLAIGHAMLSAEGAVGATLGMATGGLGTFGVSSVATAGVTPIAKEAIGTALATGIISGGGFVAGQAGAYGLNNEVQDQLKQGPMSGVLPRLEISNVKGDFTFSMQEPAAVRALMAYLGPKEDTSMSSPQAPKEAQEMEAARLTLKQMLGSSPNEHLVPDVDSLLKLSDEDMPSQTESTANGAFKKLLSEDWDWLMPAVRAMDKGEANKINEKLTYKLPLDAANGRVYLDKSPNLSGAQLDALDKLGSPSQLRLMYLAEGWI

Source

organism	Vibrio parahaemolyticus
ncbi_taxonomy_id	670
host_organism	Escherichia coli

Entity 2 polymer

description	CesT family type III secretion system chaperone
formula_weight	17553.8 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,C

GPLGSMNTIQPLLDEFCRLNELPPLILEDGNRCQLLVDDRFVLYFTATEDDALMLSVAFGGLEKSGELRVRGLELLARANYQRVGSGNLALSLAPNGRQLVLAGRQPTEHLNSANLTVWFHEIIEQTELWQARFAMLDQDLSATSNHEQSHVQPLRV

Source

organism	Vibrio parahaemolyticus
ncbi_taxonomy_id	670
host_organism	Escherichia coli

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6. Citations (1)

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length_a	109.848 Å
length_b	152.934 Å
length_c	101.120 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	16

space_group	C 2 2 21
int_tables_number	20
crystal_system	orthorhombic

resolution	2.490 Å
resolution_low	48.260 Å
r_factor	0.2441
r_work	0.2406
r_free	0.2764

fit	/app/data/saxs_computation/ux/9ux0/9ux0.fit
pddf	/app/data/pr_computation/ux/9ux0/9ux0.pr.out
profile	/app/data/saxs_computation/ux/9ux0/9ux0.dat

Crystal structure of the virulence effector VepA in complex with its secretion chaperone VecA

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 (2)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)