SAXSdb — 4mel

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

Ubiquitin carboxyl-terminal hydrolase 11

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 67–288	Fragment：DUSP-UBL domains, UNP residues 67-288	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.5；292 K；0.1 M MES/imidazole, 30 mM Na Nitrate, 30 mM Na phosphate and 30 mM Na sulphate, 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD., pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K	Resolution 2.90 Å R-free 0.297
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 67–288	Fragment：DUSP-UBL domains, UNP residues 67-288	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.5；292 K；0.1 M MES/imidazole, 30 mM Na Nitrate, 30 mM Na phosphate and 30 mM Na sulphate, 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD., pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K	Resolution 2.90 Å R-free 0.297
3	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 67–288 Chain B； UniProt 67–288	Fragment：DUSP-UBL domains, UNP residues 67-288	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.5；292 K；0.1 M MES/imidazole, 30 mM Na Nitrate, 30 mM Na phosphate and 30 mM Na sulphate, 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD., pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K	Resolution 2.90 Å R-free 0.297

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 4MEL	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8OYP Crystal structure of Ubiquitin specific protease 11 (USP11) in complex with a substrate mimetic Deposited 2023-05-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 295–489（195 aa） Chain A 778–937（160 aa）	Mutation：C318S Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：C318S Non-standard monomer：Yes (specific site not provided by mmCIF)	CD CADMIUM ION × 1 CL CHLORIDE ION × 1 NO3 NITRATE ION × 2 PO4 PHOSPHATE ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293.15 K；100 mM Tris/Bicine pH 8.5, 30 mM sodium nitrate, 30 mM sodium phosphate dibasic, 30 mM ammonium sulphate, 11.25% v/v MPD; 11.25% PEG 1000; 11.25% w/v PEG 3350 with 5 mM CdCl2	Resolution 2.44 Å R-free 0.235
8OYP Crystal structure of Ubiquitin specific protease 11 (USP11) in complex with a substrate mimetic Deposited 2023-05-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 295–489（195 aa） Chain B 778–937（160 aa）	Mutation：C318S Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：C318S Non-standard monomer：Yes (specific site not provided by mmCIF)	CD CADMIUM ION × 1 CL CHLORIDE ION × 1 NO3 NITRATE ION × 2 PO4 PHOSPHATE ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293.15 K；100 mM Tris/Bicine pH 8.5, 30 mM sodium nitrate, 30 mM sodium phosphate dibasic, 30 mM ammonium sulphate, 11.25% v/v MPD; 11.25% PEG 1000; 11.25% w/v PEG 3350 with 5 mM CdCl2	Resolution 2.44 Å R-free 0.235

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

View Construct and Data Evidence

UniProt name	UBP11_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–223； UniProt 67–288 Author chain B； PDBConstruct 2–223； UniProt 67–288

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	4mel
Deposition date deposition_date	2013-08-27
Structure title title	Crystal Structure of the human USP11 DUSP-UBL domains
Keywords keywords	;DOMAIN PRESENT IN UBIQUITIN SPECIFIC PROTEASES (DUSP), UBIQUITIN-LIKE DOMAIN (UBL), DEUBIQUITINATING ENZYME, DUB, DU FINGER, UBIQUITIN THIOLESTERASE, HYDROLASE ;; HYDROLASE
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	31.21 Å
Radius of gyration Rg (electron density) rg_electron	30.06 Å
Forward intensity I(0) i0	38720900.00
Molecular weight molecular_weight	48489.0 kDa
Excluded volume excluded_volume	60573 Å³
Envelope volume envelope_volume	82514 Å³
Hydration-shell volume shell_volume	23777 Å³
Envelope diameter envelope_diameter	98.9 Å
Shell Rg shell_rg	35.82 Å
Envelope Rg envelope_rg	29.37 Å
Shape Rg shape_rg	30.08 Å
Total Rg total_rg	30.58 Å
Total atoms total_atoms	3438
Residues n_residues	426
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	94.4 Å
Rg (real space) rg_real	31.11 Å
Rg uncertainty (real space) rg_real_error	0.77 Å
I(0) (real space) i0_real	3.8720e+07
I(0) uncertainty (real space) i0_real_error	6.1970e+05
Rg (reciprocal space) rg_reciprocal	31.16 Å
I(0) (reciprocal space) i0_reciprocal	38720000.0000
Solution quality estimate total_estimate	0.6943
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	46.3 Å
Skewness Skewness skewness	0.028
Kurtosis Kurtosis kurtosis	-0.790
Angular range angular_range	— – 0.2550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4386000.0000
Real-space data points n_real_points	52
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.942; Stabil: 1.000; Sysdev: 0.115; Positv: 1.000; Valcen: 0.964; Smooth: 0.888

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	4melA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2230 — DUSP-like
Homologous superfamily homologous superfamily	10 — DUSP-like

Domain ID domain_id	4melA02
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

Domain ID domain_id	4melB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2230 — DUSP-like
Homologous superfamily homologous superfamily	10 — DUSP-like

Domain ID domain_id	4melB02
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

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8. Citations (1)

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Unit-cell length a length_a	27.725 Å
Unit-cell length b length_b	131.982 Å
Unit-cell length c length_c	72.029 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	96.71 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	2.899 Å
Low-resolution limit resolution_low	37.474 Å
R factor r_factor	0.2341
R_work r_work	0.2311
R_free r_free	0.2967

Description description	Ubiquitin carboxyl-terminal hydrolase 11
Molecular weight formula_weight	26804.9 kDa
EC 编号 ec_number	3.4.19.12
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3449

Crystal Structure of the human USP11 DUSP-UBL domains

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

Ubiquitin carboxyl-terminal hydrolase 11

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

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

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	4

fit	/app/data/saxs_computation/me/4mel/4mel.fit
pddf	/app/data/pr_computation/me/4mel/4mel.pr.out
profile	/app/data/saxs_computation/me/4mel/4mel.dat