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9r3t

C-terminal domain of SdeA Legionella effector

Method: X-RAY DIFFRACTION D_max: 135.8 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9r3t
deposition_date	2025-05-06
last_revision	2026-05-20
title	C-terminal domain of SdeA Legionella effector
keywords	Legionella, Ubiquitin ligase, membrane binding, secretion signal, 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	35.35 Å
rg_electron	36.11 Å
i0	22577800.00
molecular_weight	36797.0 kDa
excluded_volume	45961 Å³
envelope_volume	66605 Å³
shell_volume	17711 Å³
envelope_diameter	145.2 Å
shell_rg	35.62 Å
envelope_rg	37.65 Å
shape_rg	36.09 Å
total_rg	36.13 Å
total_atoms	5243
n_residues	319
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	135.8 Å
rg_real	36.17 Å
rg_real_error	2.00 Å
i0_real	2.2580e+07
i0_real_error	4.1860e+05
rg_reciprocal	35.66 Å
i0_reciprocal	22570000.0000
total_estimate	0.6525
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	21.1 Å
skewness	0.675
kurtosis	-0.234
angular_range	— – 0.2250 Å⁻¹
current_alpha	0.0000
highest_alpha	1473000.0000
n_real_points	46
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.171; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.040; Smooth: 0.923

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Ubiquitinating/deubiquitinating enzyme SdeA
formula_weight	39717.2 kDa
ec_number	3.4.22.-,2.3.2.-,2.4.2.31
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	5314

GSHMDFSDVEKLEQQIQVIDTKLADAYLLEVTKQISALDNTKPKNQTELKTKIAAFLDRTTDIEMLRNERIKKHGSSKDPLDLSDLDKLSGSLQRINQSLVSDLITTIRVSINQMEAKTFHEQEKEIQQNFELLAKLEKTLDKSKTSEKLREDIPKLNDLLVAKQKAYPQMVQMQLKSEVFVTQLREVCQANHDDLDKTRNARLRELDRLDREAGITRMVGNLIWGLTNKVGLTTDERLDIRTKQQSLARFKNELFNDKIDTDQLISNLARKRPSELQEGLGISTDNAMELHLLLTELAGKTTSPDELEERMKAIDDISTKIGREPEHLKFVMVEEDESNKKTIGF

Source

organism	Legionella pneumophila
ncbi_taxonomy_id	446
host_organism	Escherichia coli

Entity 2 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	4

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	61

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6. Citations (1)

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length_a	110.956 Å
length_b	110.956 Å
length_c	218.708 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	18

space_group	H 3 2
int_tables_number	155
crystal_system	trigonal

resolution	1.980 Å
resolution_low	55.480 Å
r_factor	0.2250
r_work	0.2237
r_free	0.2504

fit	/app/data/saxs_computation/r3/9r3t/9r3t.fit
pddf	/app/data/pr_computation/r3/9r3t/9r3t.pr.out
profile	/app/data/saxs_computation/r3/9r3t/9r3t.dat

C-terminal domain of SdeA Legionella effector

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