← Back to search

9uwz

Crystal structure of the type III secretion chaperone VecA from Vibrio parahaemolyticus

Method: X-RAY DIFFRACTION D_max: 69.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9uwz
deposition_date	2025-05-13
title	Crystal structure of the type III secretion chaperone VecA from Vibrio parahaemolyticus
keywords	Vibrio parahaemolyticus, Type 3 secretion system, chaperone; CHAPERONE
method	X-RAY DIFFRACTION

▼

Download Data

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

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	20.68 Å
rg_electron	19.74 Å
i0	21787500.00
molecular_weight	31886.0 kDa
excluded_volume	37907 Å³
envelope_volume	46540 Å³
shell_volume	19948 Å³
envelope_diameter	74.3 Å
shell_rg	25.96 Å
envelope_rg	20.07 Å
shape_rg	19.64 Å
total_rg	20.79 Å
total_atoms	2119
n_residues	264
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	69.3 Å
rg_real	20.61 Å
rg_real_error	0.59 Å
i0_real	2.1790e+07
i0_real_error	3.0220e+05
rg_reciprocal	20.62 Å
i0_reciprocal	21790000.0000
total_estimate	0.7786
solution_quality	GOOD a GOOD solution
n_peaks	3
r_peak_primary	27.1 Å
skewness	0.108
kurtosis	-0.455
angular_range	— – 0.3850 Å⁻¹
current_alpha	0.0000
highest_alpha	369500.0000
n_real_points	70
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.708; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.000

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (4)

Entity 1 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	A,B
atom_count	2137

GPLGSMNTIQPLLDEFCRLNELPPLILEDGNRCQLLVDDRFVLYFTATEDDALMLSVAFGGLEKSGELRVRGLELLARANYQRVGSGNLALSLAPNGRQLVLAGRQPTEHLNSANLTVWFHEIIEQTELWQARFAMLDQDLSATSNHEQSHVQPLRV

Source

organism	Vibrio parahaemolyticus
ncbi_taxonomy_id	670
host_organism	Escherichia coli

Entity 2 non-polymer

description	PHOSPHATE ION
formula_weight	95.0 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	HEXATANTALUM DODECABROMIDE
formula_weight	2044.5 kDa
src_method	nat
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	18

▶

6. Citations (1)

▶

length_a	73.754 Å
length_b	73.754 Å
length_c	109.906 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	16

space_group	P 41 21 2
int_tables_number	92
crystal_system	tetragonal

resolution	2.200 Å
resolution_low	32.810 Å
r_factor	0.2448
r_work	0.2393
r_free	0.2949

fit	/app/data/saxs_computation/uw/9uwz/9uwz.fit
pddf	/app/data/pr_computation/uw/9uwz/9uwz.pr.out
profile	/app/data/saxs_computation/uw/9uwz/9uwz.dat

Crystal structure of the type III secretion chaperone VecA from Vibrio parahaemolyticus

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