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9z7o

Structure of Escherichia VapS-VapC complex

Method: X-RAY DIFFRACTION D_max: 125.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9z7o
deposition_date	2025-11-17
title	Structure of Escherichia VapS-VapC complex
keywords	toxin-antitoxin, PIN domain, STAS domain, 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	36.96 Å
rg_electron	36.71 Å
i0	325165000.00
molecular_weight	147920.0 kDa
excluded_volume	185870 Å³
envelope_volume	234170 Å³
shell_volume	53075 Å³
envelope_diameter	131.8 Å
shell_rg	42.81 Å
envelope_rg	36.46 Å
shape_rg	36.71 Å
total_rg	37.10 Å
total_atoms	10400
n_residues	1288
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	125.6 Å
rg_real	36.96 Å
rg_real_error	1.10 Å
i0_real	3.2520e+08
i0_real_error	6.3040e+06
rg_reciprocal	36.96 Å
i0_reciprocal	325200000.0000
total_estimate	0.8790
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	43.8 Å
skewness	0.354
kurtosis	-0.238
angular_range	— – 0.2150 Å⁻¹
current_alpha	0.0000
highest_alpha	81700000.0000
n_real_points	44
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.846; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.973; Smooth: 0.912

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Escherichia VapS
formula_weight	15829.8 kDa
mutation	N-terminal His6-TEV tag
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,E,F
atom_count	10400

MKSSHHHHHHENLYFQSNAKILIKDFIGTRCILKEDGQKLFEEISRHLESKDEVILDFSNVKMFASPFFNYSIGQLFNKFSENEIRNNLHLDNLEVVGHSIIERVVENASRFKSDLDYKKIVDEILEQQARESD

Source

organism	Escherichia
ncbi_taxonomy_id	561
host_organism	Escherichia coli

Entity 2 polymer

description	Escherichia VapC
formula_weight	23135.5 kDa
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	C,D,G,H

MAFSGVILANVFNIGNYTPTKDDKFLVDTNVWYWMTYTKGIPSNRQYLNTYIKFISDCISKESQLFHSGLSLAELAHIIESTEREIHEATIKSRIMTKEFRYKYAKERQLAMKEVEVSWAQVKQIAPQVDLTICQDLTDSCASKMTSNTLDGYDLMIHETMLKHGITNIITDDGDYTSVPGINVFTINKNVIVSAATQKKLMN

Source

organism	Escherichia
ncbi_taxonomy_id	561
host_organism	Escherichia coli

Entity 3 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	4

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6. Citations (1)

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length_a	159.082 Å
length_b	159.082 Å
length_c	176.198 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	36

space_group	H 3
int_tables_number	146
crystal_system	trigonal

resolution	3.400 Å
resolution_low	74.220 Å
r_factor	0.2409
r_work	0.2397
r_free	0.2641

fit	/app/data/saxs_computation/z7/9z7o/9z7o.fit
pddf	/app/data/pr_computation/z7/9z7o/9z7o.pr.out
profile	/app/data/saxs_computation/z7/9z7o/9z7o.dat

Structure of Escherichia VapS-VapC complex

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 (3)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)