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9ycw

Crystal structure of USP16 ZnF-UBP domain

Method: X-RAY DIFFRACTION D_max: 76.8 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9ycw
deposition_date	2025-09-19
last_revision	2026-05-20
title	Crystal structure of USP16 ZnF-UBP domain
keywords	USP16, 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	24.40 Å
rg_electron	23.81 Å
i0	28001700.00
molecular_weight	37676.0 kDa
excluded_volume	45858 Å³
envelope_volume	59719 Å³
shell_volume	21728 Å³
envelope_diameter	81.1 Å
shell_rg	29.78 Å
envelope_rg	23.43 Å
shape_rg	23.83 Å
total_rg	24.46 Å
total_atoms	5041
n_residues	329
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	76.8 Å
rg_real	24.35 Å
rg_real_error	0.52 Å
i0_real	2.8000e+07
i0_real_error	3.7500e+05
rg_reciprocal	24.36 Å
i0_reciprocal	28000000.0000
total_estimate	0.9038
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	3
r_peak_primary	23.2 Å
skewness	0.180
kurtosis	-0.659
angular_range	— – 0.3250 Å⁻¹
current_alpha	0.0000
highest_alpha	5630000.0000
n_real_points	64
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.933; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.973; Smooth: 0.974

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Ubiquitin carboxyl-terminal hydrolase 16
formula_weight	14335.3 kDa
ec_number	3.4.19.12
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	A,B,C
atom_count	5344

GPPVCRHIRKGLEQGNLKKALVNVEWNICQDCKTDNKVKDKAEEETEEKPSVWLCLKCGHQGCGRNSQEQHALKHYLTPRSEPHCLVLSLDNWSVWCYVCDNEVQYCSSNQLGQVVDYVRKQASI

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 2 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	9

Entity 3 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	3

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	252

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6. Citations (1)

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length_a	84.390 Å
length_b	84.390 Å
length_c	50.432 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	9

space_group	P 31
int_tables_number	144
crystal_system	trigonal

resolution	1.800 Å
resolution_low	41.510 Å
r_factor	0.1377
r_work	0.1346
r_free	0.1720

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

Crystal structure of USP16 ZnF-UBP 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