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9yc2

Crystal structure of USP49 ZnF-UBP domain

Method: X-RAY DIFFRACTION D_max: 45.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9yc2
deposition_date	2025-09-18
last_revision	2025-10-29
title	Crystal structure of USP49 ZnF-UBP domain
keywords	USP49, deubiquitinase, DUB, protease, ubiquitin, histone, nucleosome, ubiquitin binding domain, PROTEIN BINDING; PROTEIN BINDING
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	14.47 Å
rg_electron	13.13 Å
i0	3660050.00
molecular_weight	12470.0 kDa
excluded_volume	15178 Å³
envelope_volume	17377 Å³
shell_volume	11288 Å³
envelope_diameter	44.0 Å
shell_rg	18.87 Å
envelope_rg	13.42 Å
shape_rg	13.10 Å
total_rg	14.42 Å
total_atoms	1677
n_residues	105
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	45.2 Å
rg_real	14.38 Å
rg_real_error	0.22 Å
i0_real	3.6600e+06
i0_real_error	3.7570e+04
rg_reciprocal	14.39 Å
i0_reciprocal	3660000.0000
total_estimate	0.8994
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	17.7 Å
skewness	0.117
kurtosis	-0.415
angular_range	— – 0.5000 Å⁻¹
current_alpha	0.0000
highest_alpha	501400.0000
n_real_points	80
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.901; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.991

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Ubiquitin carboxyl-terminal hydrolase 49
formula_weight	12068.0 kDa
ec_number	3.4.19.12
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	1949

GPMDRCKHVGRLRLAQDHSILNPQKWCCLECATTESVWACLKCSHVACGRYIEDHALKHFEETGHPLAMEVRDLYVFCYLCKDYVLNDNPEGDLKLLRSSLLAVR

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli BL21

Entity 2 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	3

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	153

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6. Citations (1)

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length_a	35.739 Å
length_b	47.220 Å
length_c	55.247 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	1.400 Å
resolution_low	35.900 Å
r_factor	0.1551
r_work	0.1532
r_free	0.1917

fit	/app/data/saxs_computation/yc/9yc2/9yc2.fit
pddf	/app/data/pr_computation/yc/9yc2/9yc2.pr.out
profile	/app/data/saxs_computation/yc/9yc2/9yc2.dat