SAXSdb — 9qii

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1. Structure Basics

entry_id	9qii
deposition_date	2025-03-17
title	Structure of UBA6 (cluster 3)
keywords	E1, Ligase, SIGNALING PROTEIN; LIGASE
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	34.49 Å
rg_electron	33.82 Å
i0	200993000.00
molecular_weight	114880.0 kDa
excluded_volume	144260 Å³
envelope_volume	189310 Å³
shell_volume	46561 Å³
envelope_diameter	113.6 Å
shell_rg	40.78 Å
envelope_rg	33.31 Å
shape_rg	33.83 Å
total_rg	34.33 Å
total_atoms	8077
n_residues	1011
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	109.6 Å
rg_real	34.37 Å
rg_real_error	0.69 Å
i0_real	2.0100e+08
i0_real_error	3.1060e+06
rg_reciprocal	34.45 Å
i0_reciprocal	201000000.0000
total_estimate	0.9039
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	1
r_peak_primary	42.9 Å
skewness	0.163
kurtosis	-0.570
angular_range	— – 0.2300 Å⁻¹
current_alpha	0.0000
highest_alpha	31070000.0000
n_real_points	47
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.942; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.922

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Ubiquitin-like modifier-activating enzyme 6
formula_weight	118250.8 kDa
ec_number	6.2.1.45
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B
atom_count	8077

GPMEGSEPVAAHQGEEASCSSWGTGSTNKNLPIMSTASVEIDDALYSRQRYVLGDTAMQKMAKSHVFLSGMGGLGLEIAKNLVLAGIKAVTIHDTEKCQAWDLGTNFFLSEDDVVNKRNRAEAVLKHIAELNPYVHVTSSSVPFNETTDLSFLDKYQCVVLTEMKLPLQKKINDFCRSQCPPIKFISADVHGIWSRLFCDFGDEFEVLDTTGEEPKEIFISNITQANPGIVTCLENHPHKLETGQFLTFREINGMTGLNGSIQQITVISPFSFSIGDTTELEPYLHGGIAVQVKTPKTVFFESLERQLKHPKCLIVDFSNPEAPLEIHTAMLALDQFQEKYSRKPNVGCQQDSEELLKLATSISETLEEKPDVNADIVHWLSWTAQGFLSPLAAAVGGVASQEVLKAVTGKFSPLCQWLYLEAADIVESLGKPECEEFLPRGDRYDALRACIGDTLCQKLQNLNIFLVGCGAIGCEMLKNFALLGVGTSKEKGMITVTDPDLIEKSNLNRQFLFRPHHIQKPKSYTAADATLKINSQIKIDAHLNKVCPTTETIYNDEFYTKQDVIITALDNVEARRYVDSRCLANLRPLLDSGTMGTKGHTEVIVPHLTESYNSHRDPPEEEIPFSTLKSFPAAIEHTIQWARDKFESSFSHKPSLFNKFWQTYSSAEEVLQKIQSGHSLEGCFQVIKLLSRRPRNWSQCVELARLKFEKYFNHKALQLLHCFPLDIRLKDGSLFWQSPKRPPSPIKFDLNEPLHLSFLQNAAKLYATVYCIPFAEEDLSADALLNILSEVKIQEFKPSNKVVQTDETARKPDHVPISSEDERNAIFQLEKAILSNEATKSDLQMAVLSFEKDDDHNGHIDFITAASNLRAKMYSIEPADRFKTKRIAGKIIPAIATTTATVSGLVALEMIKVTGGYPFEAYKNCFLNLAIPIVVFTETTEVRKTKIRNGISFTIWDRWTVHGKEDFTLLDFINAVKEKYGIEPTMVVQGVKMLYVPVMPGHAKRLKLTMHKLVKPTTEKKYVDLTVSFAPDIDGDEDLPGPPVRYYFSHDTD

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 2 non-polymer

description	INOSITOL HEXAKISPHOSPHATE
formula_weight	660.0 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	ADENOSINE-5'-TRIPHOSPHATE
formula_weight	507.2 kDa
src_method	syn
entity_count	1

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6. Citations (1)

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resolution	3.99 Å
resolution_method	—
num_particles	17392

fit	/app/data/saxs_computation/qi/9qii/9qii.fit
pddf	/app/data/pr_computation/qi/9qii/9qii.pr.out
profile	/app/data/saxs_computation/qi/9qii/9qii.dat

Structure of UBA6 (cluster 3)

SAXS Profile

P(r) Distribution