SAXSdb — 5ysk

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

Ubiquitinating/deubiquitinating enzyme SdeA

Legionella pneumophila subsp. pneumophila

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 756–905	Mutation：E860A, E862A Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；PEG400, Tris	Resolution 2.40 Å R-free 0.261
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 756–905	Mutation：E860A, E862A Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；PEG400, Tris	Resolution 2.40 Å R-free 0.261
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 756–905	Mutation：E860A, E862A Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；PEG400, Tris	Resolution 2.40 Å R-free 0.261
4	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 756–905	Mutation：E860A, E862A Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；PEG400, Tris	Resolution 2.40 Å R-free 0.261

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 5YSK	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5YSJ SdeA mART-C domain WT apo Deposited 2017-11-14	Different mutation/modification Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 756–905（150 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG400, Tris	Resolution 2.06 Å R-free 0.269
5YSJ SdeA mART-C domain WT apo Deposited 2017-11-14	Different mutation/modification Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 756–905（150 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG400, Tris	Resolution 2.06 Å R-free 0.269
5YSJ SdeA mART-C domain WT apo Deposited 2017-11-14	Different mutation/modification Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 756–905（150 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG400, Tris	Resolution 2.06 Å R-free 0.269
5YSJ SdeA mART-C domain WT apo Deposited 2017-11-14	Different mutation/modification Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 756–905（150 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG400, Tris	Resolution 2.06 Å R-free 0.269
6G0C Crystal structure of SdeA catalytic core Deposited 2018-03-17	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 213–907（695 aa）	Not recorded	1PS 3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE × 1 EDO 1,2-ETHANEDIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；300 K；100mM Bis Tris Propane pH 7.0-8.0, 0.1-0.2M sodium citrate tribasic dihydrate, 20-30% PEG 3350	Resolution 2.80 Å R-free 0.293
6WTG SdeA DUB Domain in complex with Ubiquitin Deposited 2020-05-02	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–193（193 aa）	Mutation：C118A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；298 K；0.1 M bicine pH 9.0, 65% (v/v) MPD	Resolution 2.63 Å R-free 0.243
7MIR Cryo-EM structure of SidJ-SdeA-CaM reaction intermediate complex Deposited 2021-04-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 231–1190（960 aa）	Not recorded	AMP ADENOSINE MONOPHOSPHATE × 1 MG MAGNESIUM ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 6.5；25 mM Bis-tris pH 6.5, 100 mM NaCl, 1 mM TCEP, 2 mM MgCl2, 1 mM ATP cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.50 Å
7PPO Structure of SidJ/CaM bound to SdeA in pre-glutamylation state Deposited 2021-09-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 231–1190（960 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	MG MAGNESIUM ION × 1 CA CALCIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.91 Å
7PQE Structure of SidJ/CaM bound to SdeA in post-catalysis state Deposited 2021-09-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 231–1190（960 aa）	Not recorded	MG MAGNESIUM ION × 1 CA CALCIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å
9R3T C-terminal domain of SdeA Legionella effector Deposited 2025-05-06	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1158–1499（342 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M sodium chloride, 0.1 M sodium/ potassium phosphate pH-7.5, 50% PEG 200	Resolution 1.98 Å R-free 0.250
9R3T C-terminal domain of SdeA Legionella effector Deposited 2025-05-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1158–1499（342 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 24	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M sodium chloride, 0.1 M sodium/ potassium phosphate pH-7.5, 50% PEG 200	Resolution 1.98 Å R-free 0.250

7 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SDEA_LEGPH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–152； UniProt 756–905 Author chain B； PDBConstruct 3–152； UniProt 756–905 Author chain C； PDBConstruct 3–152； UniProt 756–905 Author chain D； PDBConstruct 3–152； UniProt 756–905

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	5ysk
Deposition date deposition_date	2017-11-14
Structure title title	SdeA mART-C domain EE/AA apo
Keywords keywords	E3 ligase, 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	27.64 Å
Radius of gyration Rg (electron density) rg_electron	26.71 Å
Forward intensity I(0) i0	61967500.00
Molecular weight molecular_weight	61721.0 kDa
Excluded volume excluded_volume	77269 Å³
Envelope volume envelope_volume	95529 Å³
Hydration-shell volume shell_volume	30050 Å³
Envelope diameter envelope_diameter	88.9 Å
Shell Rg shell_rg	34.11 Å
Envelope Rg envelope_rg	26.44 Å
Shape Rg shape_rg	26.72 Å
Total Rg total_rg	27.47 Å
Total atoms total_atoms	8451
Residues n_residues	538
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	84.9 Å
Rg (real space) rg_real	27.63 Å
Rg uncertainty (real space) rg_real_error	0.52 Å
I(0) (real space) i0_real	6.1970e+07
I(0) uncertainty (real space) i0_real_error	9.0580e+05
Rg (reciprocal space) rg_reciprocal	27.64 Å
I(0) (reciprocal space) i0_reciprocal	61970000.0000
Solution quality estimate total_estimate	0.9005
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	31.3 Å
Skewness Skewness skewness	0.313
Kurtosis Kurtosis kurtosis	-0.491
Angular range angular_range	— – 0.2850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6653000.0000
Real-space data points n_real_points	58
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.955; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.840

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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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8. Citations (1)

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Unit-cell length a length_a	43.750 Å
Unit-cell length b length_b	85.360 Å
Unit-cell length c length_c	70.795 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	97.11 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	2.403 Å
Low-resolution limit resolution_low	32.420 Å
R factor r_factor	0.1926
R_work r_work	0.1852
R_free r_free	0.2614

Description description	Ubiquitinating/deubiquitinating enzyme SdeA
Molecular weight formula_weight	16923.6 kDa
EC 编号 ec_number	3.4.22.-
Mutation mutation	E860A, E862A
Source method src_method	man
Copy count entity_count	4

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	8570

SdeA mART-C domain EE/AA apo

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

Ubiquitinating/deubiquitinating enzyme SdeA

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

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Legionella pneumophila subsp. pneumophila
NCBI Class编号 ncbi_taxonomy_id	272624
宿主生物 host_organism	Escherichia coli BL21(DE3)

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	119

fit	/app/data/saxs_computation/ys/5ysk/5ysk.fit
pddf	/app/data/pr_computation/ys/5ysk/5ysk.pr.out
profile	/app/data/saxs_computation/ys/5ysk/5ysk.dat