SAXSdb — 9qug

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1. Structure Basics

entry_id	9qug
deposition_date	2025-04-10
last_revision	2026-01-21
title	Structure of a UBC-Ubiquitin conjugate
keywords	E2/E3 enzyme UBC domain conjugated to ubiquitin, LIGASE; LIGASE
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	22.28 Å
rg_electron	21.20 Å
i0	27746000.00
molecular_weight	41922.0 kDa
excluded_volume	53213 Å³
envelope_volume	61817 Å³
shell_volume	24171 Å³
envelope_diameter	87.5 Å
shell_rg	28.15 Å
envelope_rg	21.64 Å
shape_rg	21.18 Å
total_rg	22.18 Å
total_atoms	2954
n_residues	359
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	80.5 Å
rg_real	22.20 Å
rg_real_error	0.69 Å
i0_real	2.7750e+07
i0_real_error	3.7570e+05
rg_reciprocal	22.22 Å
i0_reciprocal	27750000.0000
total_estimate	0.7638
solution_quality	GOOD a GOOD solution
n_peaks	3
r_peak_primary	28.1 Å
skewness	0.286
kurtosis	-0.114
angular_range	— – 0.3550 Å⁻¹
current_alpha	0.0000
highest_alpha	7921000.0000
n_real_points	67
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.646; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Polyubiquitin-B
formula_weight	8576.8 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C
atom_count	3162

MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 polymer

description	(E3-independent) E2 ubiquitin-conjugating enzyme
formula_weight	42364.7 kDa
ec_number	2.3.2.24
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A

MTFTSAKGEVFSVLEFAPSNHSFKKIEFQPPEAKKFFSTVRKEMALLATSLPEGIMVKTFEDRMDLFSALIKGPTRTPYEDGLYLFDIQLPNIYPAVPPHFCYLSQCSGRLNPNLYDNGKVKVSLLGTWIGKGTERWTSKSSLLQVLISIQGLILVNEPYYNEAGFDSDRGLQEGYENSRCYNEMALIRVVQSMTQLVRRPPEVFEQEIRQHFSTGGWRLVNRIESWLETHALLEKAQALPNGVPKASSSPEPPAVAELSDSGQQEPEDGGPAPGEASQGSDSEGGAQGLASASRDHTDQTSETAPDASVPPSVKPKKRRKSYRSFLPEKSGYPDIGFPLFPLSKGFIKSIRGVLTQFRAALLEAGMPECTEDKGSHHHHHH

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 3 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	4

Entity 4 non-polymer

description	polyethylene glycol
formula_weight	662.8 kDa
src_method	syn
entity_count	2

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	192

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6. Citations (1)

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length_a	61.577 Å
length_b	82.845 Å
length_c	98.657 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 21 21 21
int_tables_number	19
crystal_system	orthorhombic

resolution	1.800 Å
resolution_low	49.330 Å
r_factor	0.1682
r_work	0.1670
r_free	0.1916

fit	/app/data/saxs_computation/qu/9qug/9qug.fit
pddf	/app/data/pr_computation/qu/9qug/9qug.pr.out
profile	/app/data/saxs_computation/qu/9qug/9qug.dat

Structure of a UBC-Ubiquitin conjugate

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

5. Entities & Polymer Info (5)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)