SAXSdb — 9soc

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1. Structure Basics

entry_id	9soc
deposition_date	2025-09-12
last_revision	2026-02-18
title	Murine RanBP10-Twa1 complex
keywords	RanBPM, CTLH complex, Gid complex, E3 ligase, 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	37.64 Å
rg_electron	36.97 Å
i0	358862000.00
molecular_weight	150560.0 kDa
excluded_volume	187460 Å³
envelope_volume	259360 Å³
shell_volume	58416 Å³
envelope_diameter	138.6 Å
shell_rg	42.95 Å
envelope_rg	36.82 Å
shape_rg	36.97 Å
total_rg	37.36 Å
total_atoms	10581
n_residues	1330
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	129.7 Å
rg_real	37.56 Å
rg_real_error	0.93 Å
i0_real	3.5890e+08
i0_real_error	5.1920e+06
rg_reciprocal	37.61 Å
i0_reciprocal	358900000.0000
total_estimate	0.8627
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	46.3 Å
skewness	0.331
kurtosis	-0.034
angular_range	— – 0.2100 Å⁻¹
current_alpha	0.0000
highest_alpha	43830000.0000
n_real_points	43
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.771; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.899

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Ran-binding protein 10
formula_weight	65162.2 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,C
atom_count	10581

GLPSPGEQELSRRLQRLYPAVNQHETPLPRSWSPKDKYNYIGLSQGNLRVHYKGHGKNHKDAASVRATHPIPAACGIYYFEVKIVSKGRDGYMGIGLSAQGVNMNRLPGWDKHSYGYHGDDGHSFCSSGTGQPYGPTFTTGDVIGCCVNLINGTCFYTKNGHSLGIAFTDLPANLYPTVGLQTPGEIVDANFGQQPFLFDIEDYMREWRAKVQGTVHGFPISARLGEWQAVLQNMVSSYLVHHGYCSTATAFARMTETPIQEEQASIKNRQKIQKLVLEGRVGEAIETTQRFYPGLLEHNPNLLFMLKCRQFVEMVNGTDSEVRSLSSRSPKSQDSYPGSPSLSPRHGPSSSHIHNTGADSPSCSNGVASTKNKQNHSKYPAPSSSSSSSSSSSSSSPSSVNYSESNSTDSTKSQPHSSTSNQETSDSEMEMEAEHYPNGVLESVSTRIVNGAYKHDDLQTDESSMDDGHPRRQLCGGNQAATERIILFGRELQALSEQLGREYGKNLAHTEMLQDAFSLLAYSDPWSCPVGHQLDPIQREPVCAALNSAILESQNLPKQPPLMLALGQASECLRLMARAGLGSCSFARVDDYLH

Source

organism	Mus musculus
common_name	house mouse
ncbi_taxonomy_id	10090
host_organism	Escherichia coli

Entity 2 polymer

description	Glucose-induced degradation protein 8 homolog
formula_weight	26812.6 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,D

MSYAEKPDEITKDEWMEKLNNLHVQRADMNRLIMNYLVTEGFKEAAEKFRMESGIEPSVDLETLDERIKIREMILKGQIQEAIALINSLHPELLDTNRYLYFHLQQQHLIELIRQRETEAALEFAQTQLAEQGEESRECLTEMERTLALLAFDSPEESPFGDLLHMMQRQKVWSEVNQAVLDYENRESTPKLAKLLKLLLWAQNELDQKKVKYPKMTDLSKGVIEEPK

Source

organism	Mus musculus
common_name	house mouse
ncbi_taxonomy_id	10090
host_organism	Escherichia coli

Entity 3 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	COBALT (II) ION
formula_weight	58.9 kDa
src_method	syn
entity_count	1

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6. Citations (1)

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length_a	124.920 Å
length_b	124.920 Å
length_c	479.645 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	24

space_group	P 61 2 2
int_tables_number	178
crystal_system	hexagonal

resolution	3.180 Å
resolution_low	20.000 Å
r_factor	0.2998
r_work	0.2993
r_free	0.3120

fit	/app/data/saxs_computation/so/9soc/9soc.fit
pddf	/app/data/pr_computation/so/9soc/9soc.pr.out
profile	/app/data/saxs_computation/so/9soc/9soc.dat

Murine RanBP10-Twa1 complex

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 (4)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 non-polymer

Entity 4 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)