SAXSdb — 9qpv

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1. Structure Basics

entry_id	9qpv
deposition_date	2025-03-29
title	Pseudomonas aeruginosa Ptx2 toxin
keywords	toxin, soluble protein, pre-pore state; 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	33.62 Å
rg_electron	33.08 Å
i0	188879000.00
molecular_weight	110150.0 kDa
excluded_volume	137970 Å³
envelope_volume	171060 Å³
shell_volume	43340 Å³
envelope_diameter	126.7 Å
shell_rg	39.34 Å
envelope_rg	33.79 Å
shape_rg	33.06 Å
total_rg	33.60 Å
total_atoms	7776
n_residues	1000
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	119.4 Å
rg_real	33.73 Å
rg_real_error	1.12 Å
i0_real	1.8890e+08
i0_real_error	3.2460e+06
rg_reciprocal	33.66 Å
i0_reciprocal	188900000.0000
total_estimate	0.8487
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	35.6 Å
skewness	0.499
kurtosis	-0.092
angular_range	— – 0.2350 Å⁻¹
current_alpha	0.0000
highest_alpha	67760000.0000
n_real_points	48
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.732; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.867; Smooth: 0.966

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4. Crystallography & Experiment

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5. Entities & Polymer Info (1)

Entity 1 polymer

description	Ptx2 toxin
formula_weight	131467.6 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	7776

MGSSHHHHHHSQDPNSSSMTAQATPRRDSANLAANEASSSDSRSPSGTCPLMNAKVQLLPLRYGLTEGVDPSAELAMPFALKSRPLGLRLVRNGYLYVIDGGTGKLHEYRIDKGAIDKLLWQDAEVRADVRSRAVGEPQLVFPRTSVLYVAYSELQWTARKCMQVLASPKDREHFMQAVDLRRADPQQGGPHLLTRRQAETWLAEVVQNKVHRDEQGQQRFPPHQQRPASPPAAHPDERRDYVWEDPPLFRDTQLGELTAQVLPQYEHDALFLALRDDIGVMRDLAAYQDEVVGWLEEWLQGGAQAGANERDYVIACYIESLTQIRAAELPKLADESAQPLFDDLDRLPPPERERSRQALLDYLNGEPLPKPMDPAMPEPLHRPVERHFTKRKMAVADPAFVERNLDALIRLKKSHGEKVDDALHGAKFGQRGIDDLIDRPAMDSFLAANRPNLARWNALLEQISADRTQMLTEQRFHRAAWYYDFQQAEQLGLAFATQYACLKDICRSDEASEAVLAFLEENPQYDRPLFQTLPLNTQAELIAQYAQLGPPGHLWLSKLKEWAQQRDSLELGKLPALDGLPEATRALADSAQATLNPALTLGISRTMEGFFKSVGQQQAPDLDALFRKLPKALPGRLLDAAVREGVTFTIASEAEKAILQADLKEVLEQRAELRRLVRQRKQVKSQAGHKSTDARALLADIQRVRLQLNALEPRLAAALSPIAELPDNSIRLAGATPGRAGITLILPSAQLQEVASGIRNLRNGYSSAAAFNKVGDGIGLAVFVAQFVNMVQVWRGVIATSPDKRELMPLAGSIFTTISAGVAAAQAIADTALQARSVQLAQGLQNHAVEVAHVQMGKLHLRLGFVGYAAGFFAAAVATQTHYGEWLGAIRSGNAQAQQGAALAMVGSSGMLASSAYGVWHTGYALKGVLRAATPAAERTAWALAGTRLSSIFARFNIAGAIFTALELVGTYWYNRSNTTPHDDWLLSTPWSRDIGGRLNQSLEIYQQRLLGIVQTPRGEVKHASHGSWWRDLLSSSATAEISLALPGISLGALQQTLAGRPEVRLSLAAYRIRSVKYERGSPMVRWFPVTEVVGDSLQVASAEPLVLLVPRLAPLEGVTGGSVTEDLLLAVQIERLNPQGQYHADRHMVRLSPHSEGDYPASPQRIQGQEASWMLIDPRLLPDFADAPER

Source

organism	Pseudomonas aeruginosa
ncbi_taxonomy_id	287
host_organism	Escherichia coli

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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	—

resolution	3.300 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.30 Å
resolution_method	—
num_particles	684417

fit	/app/data/saxs_computation/qp/9qpv/9qpv.fit
pddf	/app/data/pr_computation/qp/9qpv/9qpv.pr.out
profile	/app/data/saxs_computation/qp/9qpv/9qpv.dat

Pseudomonas aeruginosa Ptx2 toxin

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

EM 3D

5. Entities & Polymer Info (1)

Entity 1 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)