SAXSdb — 7p99

▼

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

SUMO-specific isopeptidase USPL1

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 213–516	Not recorded	Small ubiquitin-related modifier × 1 （A0A6J0CIQ7） ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；311 K；0.2M Potassium thiocyanate, 0.1M Sodium Acetate pH 5.0, 8% PEG20000, 8% PEG500MME	Resolution 1.80 Å R-free 0.197

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 7P99	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7ZJU Structure of human USPL1 in covalent complex with SUMO3-2Br probe Deposited 2022-04-12	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 218–502（285 aa）	Not recorded	ZN ZINC ION × 1 GOL GLYCEROL × 1 OXU 2-bromanylethanamine × 1 CL CHLORIDE ION × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.8；293 K；100 mM Tris pH 8.8, 19% PEG6000, 200 mM CaCl2	Resolution 2.17 Å R-free 0.238
7ZJU Structure of human USPL1 in covalent complex with SUMO3-2Br probe Deposited 2022-04-12	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 218–502（285 aa）	Not recorded	ZN ZINC ION × 1 GOL GLYCEROL × 2 OXU 2-bromanylethanamine × 1 CL CHLORIDE ION × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.8；293 K；100 mM Tris pH 8.8, 19% PEG6000, 200 mM CaCl2	Resolution 2.17 Å R-free 0.238
7ZJV Structure of human USPL1 in covalent complex with DeltaN-SUMO2/3-PA probe Deposited 2022-04-12	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 218–502（285 aa）	Not recorded	ZN ZINC ION × 1 AYE prop-2-en-1-amine × 1 CL CHLORIDE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.9；293 K；100 mM CHES pH 8.9, 34% PEG600	Resolution 2.40 Å R-free 0.258

2 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	USPL1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 35–338； UniProt 213–516

Small ubiquitin-related modifier

Peromyscus maniculatus bairdii

UniProt A0A6J0CIQ7

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 19–99	Not recorded	SUMO-specific isopeptidase USPL1 × 1 （Q5W0Q7） ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；311 K；0.2M Potassium thiocyanate, 0.1M Sodium Acetate pH 5.0, 8% PEG20000, 8% PEG500MME	Resolution 1.80 Å R-free 0.197

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	A0A6J0CIQ7_PERMB
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 21–101； UniProt 19–99

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	7p99
Deposition date deposition_date	2021-07-26
Structure title title	Structure of human USPL1 in complex with SUMO2
Keywords keywords	USPL1, SUMO2, HYDROLASE; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	22.20 Å
Radius of gyration Rg (electron density) rg_electron	20.95 Å
Forward intensity I(0) i0	27141400.00
Molecular weight molecular_weight	40179.0 kDa
Excluded volume excluded_volume	50328 Å³
Envelope volume envelope_volume	58605 Å³
Hydration-shell volume shell_volume	23371 Å³
Envelope diameter envelope_diameter	77.7 Å
Shell Rg shell_rg	27.79 Å
Envelope Rg envelope_rg	21.18 Å
Shape Rg shape_rg	20.89 Å
Total Rg total_rg	22.01 Å
Total atoms total_atoms	2824
Residues n_residues	345
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

▼

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

Maximum dimension Dmax dmax	75.7 Å
Rg (real space) rg_real	22.12 Å
Rg uncertainty (real space) rg_real_error	0.50 Å
I(0) (real space) i0_real	2.7140e+07
I(0) uncertainty (real space) i0_real_error	3.7560e+05
Rg (reciprocal space) rg_reciprocal	22.13 Å
I(0) (reciprocal space) i0_reciprocal	27140000.0000
Solution quality estimate total_estimate	0.8715
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	28.3 Å
Skewness Skewness skewness	0.283
Kurtosis Kurtosis kurtosis	-0.230
Angular range angular_range	— – 0.3600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5115000.0000
Real-space data points n_real_points	68
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.780; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.997

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	SUMO-specific isopeptidase USPL1
Molecular weight formula_weight	38686.3 kDa
EC 编号 ec_number	3.4.22.-
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	3000

MGSSHHHHHHSSGLVPRGSHMASMTGGQQMGRGSPLESKCTSFPQALCVQWKNAYALCWLDCILSALVHSEELKNTVTGLCSKEESIFWRLLTKYNQANTLLYTSQLSGVKDGDCKKLTSEIFAEIETCLNEVRDEIFISLQPQLRCTLGDMESPVFAFPLLLKLETHIEKLFLYSFSWDFECSQCGHQYQNRHMKSLVTFTNVIPEWHPLNAAHFGPCNNCNSKSQIRKMVLEKVSPIFMLHFVEGLPQNDLQHYAFHFEGCLYQITSVIQYRANNHFITWILDADGSWLECDDLKGPCSERHKKFEVPASEIHIVIWERKISQVTDKEAACLPLKK

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

Entity 2 Entity 2 polymer

Description description	Small ubiquitin-related modifier
Molecular weight formula_weight	11494.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MGSSHHHHHHSSGLVPRGSHNDHINLKVAGQDGSVVQFKIKRHTPLSKLMKAYSERQGLSMRQIRFRFDGQPINETDTPAQLEMEDEDTIDVFQQQTGAVY

来源 Source

来源生物 organism	Peromyscus maniculatus bairdii
通用名 common_name	Prairie deer mouse
NCBI Class编号 ncbi_taxonomy_id	230844
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	176

▶

8. Citations (1)

▶

Unit-cell length a length_a	50.709 Å
Unit-cell length b length_b	69.884 Å
Unit-cell length c length_c	53.643 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.66 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	41.040 Å
R factor r_factor	0.1756
R_work r_work	0.1745
R_free r_free	0.1974

fit	/app/data/saxs_computation/p9/7p99/7p99.fit
pddf	/app/data/pr_computation/p9/7p99/7p99.pr.out
profile	/app/data/saxs_computation/p9/7p99/7p99.dat

Structure of human USPL1 in complex with SUMO2

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

SUMO-specific isopeptidase USPL1

State in the Current Structure

Other States of the Same Protein in the Database

Small ubiquitin-related modifier

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

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)