SAXSdb — 5lnb

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

Ubiquitin-like-specific protease 2

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

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 B； UniProt 411–710	Not recorded	ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；277 K；0.2 M di-ammonium hydrogen citrate, 20 % PEG 3350, protein concentration 3 mg/ml	Resolution 2.30 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 5LNB	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5V1A Structure of S. cerevisiae Ulp2:Csm1 complex Deposited 2017-03-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 821–845（25 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；100 mM M HEPES pH 7.5 and 20% PEG 3350, 25% Glycerol	Resolution 2.14 Å R-free 0.278

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

View Construct and Data Evidence

UniProt name	ULP2_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain B； PDBConstruct 2–301； UniProt 411–710

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	5lnb
Deposition date deposition_date	2016-08-03
Structure title title	Crystal structure of the de-sumoylating protease
Keywords keywords	Protease, de-sumoylation, 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	20.57 Å
Radius of gyration Rg (electron density) rg_electron	19.48 Å
Forward intensity I(0) i0	15294700.00
Molecular weight molecular_weight	30876.0 kDa
Excluded volume excluded_volume	39327 Å³
Envelope volume envelope_volume	46097 Å³
Hydration-shell volume shell_volume	19946 Å³
Envelope diameter envelope_diameter	69.5 Å
Shell Rg shell_rg	25.77 Å
Envelope Rg envelope_rg	19.98 Å
Shape Rg shape_rg	19.43 Å
Total Rg total_rg	20.60 Å
Total atoms total_atoms	2181
Residues n_residues	259
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	67.3 Å
Rg (real space) rg_real	20.52 Å
Rg uncertainty (real space) rg_real_error	0.49 Å
I(0) (real space) i0_real	1.5290e+07
I(0) uncertainty (real space) i0_real_error	1.9090e+05
Rg (reciprocal space) rg_reciprocal	20.53 Å
I(0) (reciprocal space) i0_reciprocal	15290000.0000
Solution quality estimate total_estimate	0.8080
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	26.4 Å
Skewness Skewness skewness	0.307
Kurtosis Kurtosis kurtosis	-0.224
Angular range angular_range	— – 0.3850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3273000.0000
Real-space data points n_real_points	70
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.834; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Ubiquitin-like-specific protease 2
Molecular weight formula_weight	36613.5 kDa
EC 编号 ec_number	3.4.22.68
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B
Atom count atom_count	2380

SSNSEFDDATTEFETPELFKPSLCYKFNDGSSYTITNQDFKCLFNKDWVNDSILDFFTKFYIESSIEKSIIKREQVHLMSSFFYTKLISNPADYYSNVKKWVNNTDLFSKKYVVIPINISYHWFSCIITNLDAILDFHQNKDKNDAINSDEISINNPLVNILTFDSLRQTHSREIDPIKEFLISYALDKYSIQLDKTQIKMKTCPVPQQPNMSDCGVHVILNIRKFFENPVETIDVWKNSKIKSKHFTAKMINKYFDKNERNSARKNLRHTLKLLQLNYISYLKKENLYEEVMQMEEKKSTGGGHHHHHH

来源 Source

来源生物 organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
通用名 common_name	;Baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	559292
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	199

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8. Citations (1)

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Unit-cell length a length_a	42.540 Å
Unit-cell length b length_b	55.580 Å
Unit-cell length c length_c	172.780 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	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	86.390 Å
R factor r_factor	0.1607
R_work r_work	0.1571
R_free r_free	0.1968

fit	/app/data/saxs_computation/ln/5lnb/5lnb.fit
pddf	/app/data/pr_computation/ln/5lnb/5lnb.pr.out
profile	/app/data/saxs_computation/ln/5lnb/5lnb.dat

Crystal structure of the de-sumoylating protease

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

Ubiquitin-like-specific protease 2

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