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9qtf

Simkania negevensis CE-clan virulence factor SnCE1 C256A catalytically inactive mutant

Method: X-RAY DIFFRACTION D_max: 173.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qtf
deposition_date	2025-04-08
title	Simkania negevensis CE-clan virulence factor SnCE1 C256A catalytically inactive mutant
keywords	cysteine protease, CE-clan, Ubl protease, deSUMOylase, SUMO pathway, virulence factor, bacterial virulence, pathogenesis, HYDROLASE; HYDROLASE
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	49.41 Å
rg_electron	49.83 Å
i0	473472000.00
molecular_weight	191000.0 kDa
excluded_volume	242770 Å³
envelope_volume	325290 Å³
shell_volume	56502 Å³
envelope_diameter	169.4 Å
shell_rg	49.92 Å
envelope_rg	49.34 Å
shape_rg	49.80 Å
total_rg	49.95 Å
total_atoms	26850
n_residues	1593
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	173.6 Å
rg_real	50.00 Å
rg_real_error	2.46 Å
i0_real	4.7350e+08
i0_real_error	9.8460e+06
rg_reciprocal	49.41 Å
i0_reciprocal	473100000.0000
total_estimate	0.8086
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	48.8 Å
skewness	0.489
kurtosis	-0.488
angular_range	— – 0.1600 Å⁻¹
current_alpha	0.0000
highest_alpha	21680000.0000
n_real_points	33
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.707; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.768; Smooth: 0.620

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Deubiquitinase and deneddylase ChlaDub2
formula_weight	28360.2 kDa
mutation	C256A
src_method	man
entity_count	8

Polymer

type	polypeptide(L)
strand_id	A,B,C,D,E,F,G,H
atom_count	27774

GPLGSSLTSKAICRYSLSSVESIQPKTQVKAIEPKGEKDRFLIDERNWLNNQHLGLYSLFLQEKYGPEVFFPFGGWTYVFPGLTDRFFKEDSYHILDVRAKRIKSFLDYKSITYPLFIGGNHWGLLFIDREKRTVEYYDSKINYGNYEEGLQGIKDVAAKFTKYDPGEKPYTYLEKIKKKLQPDGYQAGPWALYFLEHRLENPEVDFNQLDLNEAQNMIAKYRFAVRDKLLELQKNGNTLYC

Source

organism	Simkania negevensis Z
ncbi_taxonomy_id	331113
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
formula_weight	122.1 kDa
src_method	syn
entity_count	8

Entity 3 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	syn
entity_count	3

Entity 4 non-polymer

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

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	881

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6. Citations (1)

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length_a	78.626 Å
length_b	151.173 Å
length_c	80.777 Å
angle_alpha	90.00 °
angle_beta	105.07 °
angle_gamma	90.00 °
z_pdb	16

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	2.205 Å
resolution_low	48.550 Å
r_factor	—
r_work	0.1550
r_free	0.1906

fit	/app/data/saxs_computation/qt/9qtf/9qtf.fit
pddf	/app/data/pr_computation/qt/9qtf/9qtf.pr.out
profile	/app/data/saxs_computation/qt/9qtf/9qtf.dat