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9r8g

Pseudomonas putida Pore-Forming Toxin Tke5 in complex with its cognate Type VI adaptor protein Tap3

Method: ELECTRON MICROSCOPY D_max: 138.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9r8g
deposition_date	2025-05-16
title	Pseudomonas putida Pore-Forming Toxin Tke5 in complex with its cognate Type VI adaptor protein Tap3
keywords	Pseudomonas putida T6SS effector, Pore-Forming Toxin, MIX family domain, adaptor protein, TOXIN; TOXIN
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	39.33 Å
rg_electron	39.11 Å
i0	239301000.00
molecular_weight	124490.0 kDa
excluded_volume	155130 Å³
envelope_volume	211750 Å³
shell_volume	47002 Å³
envelope_diameter	140.8 Å
shell_rg	42.67 Å
envelope_rg	39.65 Å
shape_rg	39.15 Å
total_rg	39.16 Å
total_atoms	8811
n_residues	1211
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	138.2 Å
rg_real	39.73 Å
rg_real_error	1.67 Å
i0_real	2.3930e+08
i0_real_error	4.4320e+06
rg_reciprocal	39.49 Å
i0_reciprocal	239200000.0000
total_estimate	0.8343
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	38.0 Å
skewness	0.542
kurtosis	-0.276
angular_range	— – 0.2000 Å⁻¹
current_alpha	0.0000
highest_alpha	39650000.0000
n_real_points	41
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.738; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.812; Smooth: 0.815

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4. Crystallography & Experiment

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5. Entities & Polymer Info (2)

Entity 1 polymer

description	Toxin VasX N-terminal region domain-containing protein
formula_weight	109903.4 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	8811

MTNASVSSATSGPACSARVPILPVRYAIVPRTADAPACRYADAGFNLEQGFPTLQHSAYTLRALRPGYVYVFMKGPRGEKLVIHEYVGAGLYKELRYQGLEDYHRRERYLSGQSTGWVWADTCQDTAEEVWIGYSPHLWTNAITARITGSAALRKRHMRQLDMAELVSGNQAPSTQPHVLPVSALQTWVEDFKPTERRMPLTWSSDPVTETLPIGNLHAIARHYPWTQPKVPVVVALADAEGMALDLSLSVSAYQHQLRDLMPAEQLEHTKPAQPPEQERVPACYRLDAEQLSPQSRDFHHRNLVAMLLNKTLESLYPADAPSPELAAFRLGTSRRGPALSPAESHFQALTHEDYSPNGARLAQRLDVDKYRRFLAERDALERRIAALRNLALQASNDHDAWLATAEPQHIDNPYSLAAALACYDRDERTSARGLEISLALLIHPMGQPTPGTEDHDRRFKRLEQWLDQHDSPLYTALAPFNPFKDKADSIGTLFGASDNVIEGLAGRFPAMADITDLTAQSVNTVVLKRLRGQTRWDASHGLRRQVQLAAREANAEKALGLLAARYRITEQAITENPFSQEVQRYLKSGMAQVEEMKALRISGSRTVSIELTTTARAKPNFLGLLTSGGGGGLNAGMLWFNILSLKTAYNSLQKSDAPEYTLGFASSVFGVIGAAAATLVSVRATQKAMMLKWISTAPGMAFGNGIINFLTSNLFARASGYPAIIMGFSSDIFKAIRQWQNGNLISGLYTAAASATTALGSILVLEGSLAIAGTTVLIPFAGWTAAGIALIGATLIGGGLFLYSKAHSRLHSPLELWASRSIFGTRENDGEIRDNIKLDFDKKLPPFRHIHEEIKSWQIEFFSPKALLAPYSEQLGLGALTTHLDINNKWPTPDWATIIHTQVTKQNATLELTILLPEFVVGQSEWSGSLVSQNLDRQTTPLQINPDCHITQAGLLLHYKTDARQIRSATLTINYYANQGLDDDTPSTTTIHLER

Source

organism	Pseudomonas putida KT2440
ncbi_taxonomy_id	160488
host_organism	Escherichia coli BL21(DE3)

Entity 2 polymer

description	DUF4123 domain-containing protein
formula_weight	35710.5 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

MGSSHHHHHHSMTTLSSPPPRSEDFAHNCRFLLLMTSAIENWAYRPIPQEGELVPAYAPSVLDLINAVSRNTQKAWLWKNSALDDRHEFGPLLVDVADAHELLAHAITTWMPIGGAIALDAEVGLAALADHFTSLVQVVLPDHSVATHHVTPDHLAAWLNALDDDHRKAWLGPVSRLAWRVNWGPAHEWKTHENKPIAARSKSELPLTLQQLELDRLQAGMHEHFVLSLAHEVLAMPPHANHTLADIRLWIETLLPQLTALNFRSEEVAGQFIRLIAGHMWLMSNDKAGKIYTNLEESPQARLRELQALVESKEPAHD

Source

organism	Pseudomonas putida KT2440
ncbi_taxonomy_id	160488
host_organism	Escherichia coli BL21(DE3)

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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	2.77 Å
resolution_method	—
num_particles	381732

fit	/app/data/saxs_computation/r8/9r8g/9r8g.fit
pddf	/app/data/pr_computation/r8/9r8g/9r8g.pr.out
profile	/app/data/saxs_computation/r8/9r8g/9r8g.dat

Pseudomonas putida Pore-Forming Toxin Tke5 in complex with its cognate Type VI adaptor protein Tap3

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 (2)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)