SAXSdb — 9yc2

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

Ubiquitin carboxyl-terminal hydrolase 49

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 1–103	Not recorded	SO4 SULFATE ION × 2 GOL GLYCEROL × 1 ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.5；281 K；0.2 M sodium chloride; 2 M ammonium sulphate; 0.1 M sodium cacodylate	Resolution 1.40 Å R-free 0.192

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	UBP49_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–105； UniProt 1–103

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	9yc2
Deposition date deposition_date	2025-09-18
最后修订 last_revision	2025-10-29
Structure title title	Crystal structure of USP49 ZnF-UBP domain
Keywords keywords	USP49, 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	14.47 Å
Radius of gyration Rg (electron density) rg_electron	13.13 Å
Forward intensity I(0) i0	3660050.00
Molecular weight molecular_weight	12470.0 kDa
Excluded volume excluded_volume	15178 Å³
Envelope volume envelope_volume	17377 Å³
Hydration-shell volume shell_volume	11288 Å³
Envelope diameter envelope_diameter	44.0 Å
Shell Rg shell_rg	18.87 Å
Envelope Rg envelope_rg	13.42 Å
Shape Rg shape_rg	13.10 Å
Total Rg total_rg	14.42 Å
Total atoms total_atoms	1677
Residues n_residues	105
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	45.2 Å
Rg (real space) rg_real	14.38 Å
Rg uncertainty (real space) rg_real_error	0.22 Å
I(0) (real space) i0_real	3.6600e+06
I(0) uncertainty (real space) i0_real_error	3.7570e+04
Rg (reciprocal space) rg_reciprocal	14.39 Å
I(0) (reciprocal space) i0_reciprocal	3660000.0000
Solution quality estimate total_estimate	0.8994
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	17.7 Å
Skewness Skewness skewness	0.117
Kurtosis Kurtosis kurtosis	-0.415
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	501400.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria 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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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Ubiquitin carboxyl-terminal hydrolase 49
Molecular weight formula_weight	12068.0 kDa
EC 编号 ec_number	3.4.19.12
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1949

GPMDRCKHVGRLRLAQDHSILNPQKWCCLECATTESVWACLKCSHVACGRYIEDHALKHFEETGHPLAMEVRDLYVFCYLCKDYVLNDNPEGDLKLLRSSLLAVR

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

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	2

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	1

Entity 4 Entity 4 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	153

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8. Citations (1)

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Unit-cell length a length_a	35.739 Å
Unit-cell length b length_b	47.220 Å
Unit-cell length c length_c	55.247 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	orthorhombic

Resolution resolution	1.400 Å
Low-resolution limit resolution_low	35.900 Å
R factor r_factor	0.1551
R_work r_work	0.1532
R_free 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

Crystal structure of USP49 ZnF-UBP domain

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

Ubiquitin carboxyl-terminal hydrolase 49

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