SAXSdb — 9wuf

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1. Structure Basics

entry_id	9wuf
deposition_date	2025-09-18
title	Cryo-EM structure of Upx
keywords	protein structure, ANTIVIRAL PROTEIN; ANTIVIRAL PROTEIN
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	36.90 Å
rg_electron	36.46 Å
i0	278845000.00
molecular_weight	136130.0 kDa
excluded_volume	170850 Å³
envelope_volume	217730 Å³
shell_volume	49899 Å³
envelope_diameter	125.4 Å
shell_rg	42.65 Å
envelope_rg	36.05 Å
shape_rg	36.46 Å
total_rg	36.86 Å
total_atoms	9585
n_residues	1212
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	119.0 Å
rg_real	36.90 Å
rg_real_error	1.03 Å
i0_real	2.7880e+08
i0_real_error	4.7870e+06
rg_reciprocal	36.90 Å
i0_reciprocal	278800000.0000
total_estimate	0.8833
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	47.1 Å
skewness	0.334
kurtosis	-0.309
angular_range	— – 0.2150 Å⁻¹
current_alpha	0.0000
highest_alpha	79940000.0000
n_real_points	44
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.914; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.745

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4. Crystallography & Experiment

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5. Entities & Polymer Info (1)

Entity 1 polymer

description	Restriction endonuclease
formula_weight	143024.5 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	9585

MNEHLSHMDVHTLFEEMDEQADGITFKYSFDDIAKSNALVVTEFVNFERDSTVALLASLLTLPAHQSQCLRFELLTSLALIHCKGQQIANIDDVKRWYVTIGESSSIVGEDPAEDVFVALVDNKKGDYRVLEGVWEAAGFYTQLMVEIVSDMPDTHRYRSLKLAIQAILRLSDVICARSGLYRFQEGADEFPDSLDTAGLDEKTLCSRVTLSERSLRAEGIKLADLAPFILEPSHISMLGNQVPGEGMLEQRPLLRTRDGIVVVLPTAMTIALRQAVITFAKRTEELSELDKALANVYSLTFSEMPVFGNGGRLRRLTWEKYKMSRTTMVTSIVDAGHLMVLQFVLPSIQQYADTGFNNLLQLDEETTQFLDNSVEQITVDLAKQPGFQRGIVVRIACGWGAGFMGVPPQLPDGWGFEWMSGADFVRFGALPDMSPIAFWRVQDAVETIRQAGVRLINMSGTLNLLGWIRANDGHMVPHDQLPDDRITPEHPLMLMIPTNLLRGIRIAADTGYDRHRISDNNGKWHRVMRPSAEDFFPTERQSKCYASIDDLEAQRLTCVYEGQGNLWVTLEAPEMEDWMLLVELAKMVRTWIGRIGEALEVLSEQPIKKSLKVYLHFDGNDNIGRFDGENFSDDMNTFWRLERIHEHGAIRVVLQDGYLAGFRLPDNRAERALVRALGTAFATLLRMKEPVDKGVTVEQIAVPNDRARSFHIMQAYDFNQYLGRSLTKRLLAIEDIDSAAARIELAWRAVSTDAPSRYQGKKEVGKLLNDVVDVLIQDLLSELSRFDRKQTVMRLLENVVKARCEEAHWRSTAAAVLGLHAGEEGVEETIAQEMSRYAGAALTSRLIIELAICVCPTSGGIEPSDMALSKLLARASLLFRIGGMSDAVRFGALPADIRISPLGDLLFRDELGKMVLEPMLSKVTNERFEEQAAQFEQHYVKTAGGDDENSKQDSVAAETTEDQTDIFLAFWKAEMGFTLEDGMRFIQFLESIGIEQESAIFEMRRSQLADAAKSAGLADETIDAFLNQFILSARPKWDVVPDGFDLSDIYPWRFGRRLSVAVRPLLQIEESHDPLIVIAPGLLNLSLKYVFDGAYTGQFKRDFFRTEGMRDTWLGGAREGHTFEKTLERELREIGWTVRRGIGFPEILRRNLPGDPGDIDLLAWRSDRNQVLVIECKDLSLARNYSEVASQLSEYQGDDIKGKPDKLKKHLKRVLLAKENIDNFAKFTSIANPEIVSWLVFSGASPIAYAQSKIEALAGTNVGRPSDLLNF

Source

organism	Salmonella enterica subsp. enterica serovar Bredeney
ncbi_taxonomy_id	134047
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	3.01 Å
resolution_method	—
num_particles	204860

fit	/app/data/saxs_computation/wu/9wuf/9wuf.fit
pddf	/app/data/pr_computation/wu/9wuf/9wuf.pr.out
profile	/app/data/saxs_computation/wu/9wuf/9wuf.dat

Cryo-EM structure of Upx

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 (1)

Entity 1 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)