SAXSdb — 9ycw

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Ubiquitin carboxyl-terminal hydrolase 16

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 22–144	Not recorded	ZN ZINC ION × 3 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；30% (w/v) Glycerol	Resolution 1.80 Å R-free 0.172
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 22–144	Not recorded	ZN ZINC ION × 3 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；30% (w/v) Glycerol	Resolution 1.80 Å R-free 0.172
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 22–144	Not recorded	ZN ZINC ION × 3 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；30% (w/v) Glycerol	Resolution 1.80 Å R-free 0.172

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 9YCW	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2I50 Solution Structure of Ubp-M Znf-UBP domain Deposited 2006-08-23	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 22–143（122 aa） Fragment：Znf-UBP domain, residues 22-143	Not recorded	ZN ZINC ION × 3	SOLUTION NMR NMR measurement conditions pH 7；300 K；Ionic strength (raw mmCIF value) 100 mM KCl；Pressure 1 NMR sample composition 1mM U-15N,13C, 25 mM Sodium Phosphate, 100 mM KCl, 95% H2O, 5% D2O \| 95% H2O/5% D2O NMR sample composition 1mM U-15N, 25 mM Sodium Phosphate, 100 mM KCl, 95% H2O, 5% D2O \| 95% H2O/5% D2O NMR sample composition 1mM U-15N, 13C, 25 mM Sodium Phosphate, 100 mM KCl, 100% D2O \| 100% D2O NMR sample composition Unlabeled, 25 mM Sodium Phosphate, 100 mM KCl, 100% D2O \| 100% D2O	Resolution not provided
8WG5 Cryo-EM structure of USP16 bound to H2AK119Ub nucleosome Deposited 2023-09-20	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric	Chain M 1–823（823 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.05 Å

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	UBP16_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–125； UniProt 22–144 Author chain B； PDBConstruct 3–125； UniProt 22–144 Author chain C； PDBConstruct 3–125； UniProt 22–144

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9ycw
Deposition date deposition_date	2025-09-19
最后修订 last_revision	2026-05-20
Structure title title	Crystal structure of USP16 ZnF-UBP domain
Keywords keywords	USP16, deubiquitinase, DUB, protease, ubiquitin, histone, nucleosome, ubiquitin binding domain, PROTEIN BINDING; PROTEIN BINDING
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	24.40 Å
Radius of gyration Rg (electron density) rg_electron	23.81 Å
Forward intensity I(0) i0	28001700.00
Molecular weight molecular_weight	37676.0 kDa
Excluded volume excluded_volume	45858 Å³
Envelope volume envelope_volume	59719 Å³
Hydration-shell volume shell_volume	21728 Å³
Envelope diameter envelope_diameter	81.1 Å
Shell Rg shell_rg	29.78 Å
Envelope Rg envelope_rg	23.43 Å
Shape Rg shape_rg	23.83 Å
Total Rg total_rg	24.46 Å
Total atoms total_atoms	5041
Residues n_residues	329
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	76.8 Å
Rg (real space) rg_real	24.35 Å
Rg uncertainty (real space) rg_real_error	0.52 Å
I(0) (real space) i0_real	2.8000e+07
I(0) uncertainty (real space) i0_real_error	3.7500e+05
Rg (reciprocal space) rg_reciprocal	24.36 Å
I(0) (reciprocal space) i0_reciprocal	28000000.0000
Solution quality estimate total_estimate	0.9038
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	23.2 Å
Skewness Skewness skewness	0.180
Kurtosis Kurtosis kurtosis	-0.659
Angular range angular_range	— – 0.3250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5630000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria 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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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Ubiquitin carboxyl-terminal hydrolase 16
Molecular weight formula_weight	14335.3 kDa
EC 编号 ec_number	3.4.19.12
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	5344

GPPVCRHIRKGLEQGNLKKALVNVEWNICQDCKTDNKVKDKAEEETEEKPSVWLCLKCGHQGCGRNSQEQHALKHYLTPRSEPHCLVLSLDNWSVWCYVCDNEVQYCSSNQLGQVVDYVRKQASI

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	9

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	252

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8. Citations (1)

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Unit-cell length a length_a	84.390 Å
Unit-cell length b length_b	84.390 Å
Unit-cell length c length_c	50.432 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	9

Space group space_group	P 31
Space-group number int_tables_number	144
Crystal system crystal_system	trigonal

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	41.510 Å
R factor r_factor	0.1377
R_work r_work	0.1346
R_free 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

1. Protein Identity and Related Structures Protein Identity & Related Structures

Ubiquitin carboxyl-terminal hydrolase 16

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction