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9uw1

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

Method: X-RAY DIFFRACTION D_max: 106.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9uw1
deposition_date	2025-05-11
title	Crystal structure of CDC48A-N domain in complex with PUX5 SHP box motif
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	29.92 Å
rg_electron	29.66 Å
i0	62776000.00
molecular_weight	62189.0 kDa
excluded_volume	77976 Å³
envelope_volume	99982 Å³
shell_volume	29856 Å³
envelope_diameter	109.4 Å
shell_rg	34.47 Å
envelope_rg	29.81 Å
shape_rg	29.66 Å
total_rg	30.14 Å
total_atoms	4368
n_residues	548
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	106.3 Å
rg_real	30.11 Å
rg_real_error	1.13 Å
i0_real	6.2780e+07
i0_real_error	1.0540e+06
rg_reciprocal	30.03 Å
i0_reciprocal	62770000.0000
total_estimate	0.8422
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	30.1 Å
skewness	0.513
kurtosis	-0.125
angular_range	— – 0.2650 Å⁻¹
current_alpha	0.0000
highest_alpha	18710000.0000
n_real_points	54
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.749; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.803; Smooth: 0.898

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Cell division control protein 48 homolog A,Plant UBX domain-containing protein 5
formula_weight	21379.5 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	A,B,C
atom_count	4557

GPLGSNRLVVDEAINDDNSVVSLHPATMEKLQLFRGDTILIKGKKRKDTVCIALADETCEEPKIRMNKVVRSNLRVRLGDVISVHQCPDVKYGKRVHILPVDDTVEGVTGNLFDAYLKPYFLEAYRPVRKGDLFLVRGGMRSVEFKVIETDPAEYCVVAPDTEIFCEGEPVKREGGSGGSGGSKNPFQGVGRTL

Source

organism	Arabidopsis thaliana
common_name	thale cress
ncbi_taxonomy_id	3702
host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 2 non-polymer

description	MALONIC ACID
formula_weight	104.1 kDa
src_method	syn
entity_count	7

Entity 3 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	2

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	189

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6. Citations (1)

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length_a	60.070 Å
length_b	101.420 Å
length_c	110.610 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	12

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	1.880 Å
resolution_low	74.750 Å
r_factor	0.1970
r_work	0.1955
r_free	0.2249

fit	/app/data/saxs_computation/uw/9uw1/9uw1.fit
pddf	/app/data/pr_computation/uw/9uw1/9uw1.pr.out
profile	/app/data/saxs_computation/uw/9uw1/9uw1.dat

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

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