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9v9o

Crystal structure of CDC48A-N domain in complex with PUX5 SHP box motif and UBX domain

Method: X-RAY DIFFRACTION D_max: 153.4 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9v9o
deposition_date	2025-06-01
title	Crystal structure of CDC48A-N domain in complex with PUX5 SHP box motif and UBX domain
keywords	ATPase, Ubiquitination, cofactor, PLANT PROTEIN; PLANT PROTEIN
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	42.66 Å
rg_electron	42.69 Å
i0	207818000.00
molecular_weight	117780.0 kDa
excluded_volume	147870 Å³
envelope_volume	204270 Å³
shell_volume	42955 Å³
envelope_diameter	155.7 Å
shell_rg	43.52 Å
envelope_rg	42.02 Å
shape_rg	42.69 Å
total_rg	42.76 Å
total_atoms	8279
n_residues	1056
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	153.4 Å
rg_real	42.98 Å
rg_real_error	2.13 Å
i0_real	2.0780e+08
i0_real_error	4.6050e+06
rg_reciprocal	42.66 Å
i0_reciprocal	207700000.0000
total_estimate	0.8390
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	45.6 Å
skewness	0.475
kurtosis	-0.349
angular_range	— – 0.1850 Å⁻¹
current_alpha	0.0000
highest_alpha	16330000.0000
n_real_points	38
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.754; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.766; Smooth: 0.874

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Cell division control protein 48 homolog A,Plant UBX domain-containing protein 5
formula_weight	32592.1 kDa
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	8378

GSNRLVVDEAINDDNSVVSLHPATMEKLQLFRGDTILIKGKKRKDTVCIALADETCEEPKIRMNKVVRSNLRVRLGDVISVHQCPDVKYGKRVHILPVDDTVEGVTGNLFDAYLKPYFLEAYRPVRKGDLFLVRGGMRSVEFKVIETDPAEYCVVAPDTEIFCEGEPVKREGGSGGSGGSKNPFQGVGRTLGASGSGSSSAPQASSAPMNVAPAPSRGLVVDPAAPTTSIQLRLADGTRLVSRFNNHHTVRDVRGFIDASRPGGSKEYQLLTMGFPPKQLTELDQTIEQAGIANAVVIQKF

Source

organism	Arabidopsis thaliana
common_name	thale cress
ncbi_taxonomy_id	3702
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	syn
entity_count	7

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	99

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6. Citations (1)

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length_a	34.880 Å
length_b	87.110 Å
length_c	95.970 Å
angle_alpha	88.59 °
angle_beta	86.67 °
angle_gamma	89.89 °
z_pdb	4

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	2.200 Å
resolution_low	95.780 Å
r_factor	0.2260
r_work	0.2237
r_free	0.2681

fit	/app/data/saxs_computation/v9/9v9o/9v9o.fit
pddf	/app/data/pr_computation/v9/9v9o/9v9o.pr.out
profile	/app/data/saxs_computation/v9/9v9o/9v9o.dat

Crystal structure of CDC48A-N domain in complex with PUX5 SHP box motif and UBX domain

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