SAXSdb — 9h6w

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

E3 ubiquitin-protein ligase SspH1

Salmonella enterica subsp. enterica serovar Typhimurium

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 161–700	Not recorded	TLA L(+)-TARTARIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；293.15 K；0.225 M sodium tartrate, 22% PEG 3350, 11 mM sarcosine	Resolution 2.90 Å R-free 0.316
2	Protein homooligomer Homooligomer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain A； UniProt 161–700	Not recorded	TLA L(+)-TARTARIC ACID × 6	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；293.15 K；0.225 M sodium tartrate, 22% PEG 3350, 11 mM sarcosine	Resolution 2.90 Å R-free 0.316

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 9H6W	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4NKG Crystal structure of SspH1 LRR domain in complex PKN1 HR1b domain Deposited 2013-11-12	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 161–405（245 aa） Fragment：LRR domains, UNP residues 161-405	Not recorded	HEZ HEXANE-1,6-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；293 K；26% PEG3350, 0.18M tri-Ammonium citrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.90 Å R-free 0.242
4NKG Crystal structure of SspH1 LRR domain in complex PKN1 HR1b domain Deposited 2013-11-12	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 161–405（245 aa） Fragment：LRR domains, UNP residues 161-405	Not recorded	HEZ HEXANE-1,6-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；293 K；26% PEG3350, 0.18M tri-Ammonium citrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.90 Å R-free 0.242
4NKH Crystal structure of SspH1 LRR domain Deposited 2013-11-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 161–398（238 aa） Fragment：LRR domains, UNP residues 161-398 Chain F 161–398（238 aa） Fragment：LRR domains, UNP residues 161-398	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；293 K；0.95M Ammonium sulphate, 0.5% PEG 8000, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.75 Å R-free 0.280
4NKH Crystal structure of SspH1 LRR domain Deposited 2013-11-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 161–398（238 aa） Fragment：LRR domains, UNP residues 161-398 Chain E 161–398（238 aa） Fragment：LRR domains, UNP residues 161-398	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；293 K；0.95M Ammonium sulphate, 0.5% PEG 8000, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.75 Å R-free 0.280
4NKH Crystal structure of SspH1 LRR domain Deposited 2013-11-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 161–398（238 aa） Fragment：LRR domains, UNP residues 161-398 Chain D 161–398（238 aa） Fragment：LRR domains, UNP residues 161-398	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；293 K；0.95M Ammonium sulphate, 0.5% PEG 8000, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.75 Å R-free 0.280
4NKH Crystal structure of SspH1 LRR domain Deposited 2013-11-12	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 161–398（238 aa） Fragment：LRR domains, UNP residues 161-398	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；293 K；0.95M Ammonium sulphate, 0.5% PEG 8000, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.75 Å R-free 0.280
4NKH Crystal structure of SspH1 LRR domain Deposited 2013-11-12	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 161–398（238 aa） Fragment：LRR domains, UNP residues 161-398	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；293 K；0.95M Ammonium sulphate, 0.5% PEG 8000, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.75 Å R-free 0.280
4NKH Crystal structure of SspH1 LRR domain Deposited 2013-11-12	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 161–398（238 aa） Fragment：LRR domains, UNP residues 161-398	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；293 K；0.95M Ammonium sulphate, 0.5% PEG 8000, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.75 Å R-free 0.280
4NKH Crystal structure of SspH1 LRR domain Deposited 2013-11-12	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 7 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 161–398（238 aa） Fragment：LRR domains, UNP residues 161-398	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；293 K；0.95M Ammonium sulphate, 0.5% PEG 8000, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.75 Å R-free 0.280
4NKH Crystal structure of SspH1 LRR domain Deposited 2013-11-12	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 8 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain E 161–398（238 aa） Fragment：LRR domains, UNP residues 161-398	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；293 K；0.95M Ammonium sulphate, 0.5% PEG 8000, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.75 Å R-free 0.280
4NKH Crystal structure of SspH1 LRR domain Deposited 2013-11-12	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 9 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain F 161–398（238 aa） Fragment：LRR domains, UNP residues 161-398	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；293 K；0.95M Ammonium sulphate, 0.5% PEG 8000, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.75 Å R-free 0.280

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

View Construct and Data Evidence

UniProt name	SSPH1_SALT1
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–540； UniProt 161–700

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	9h6w
Deposition date deposition_date	2024-10-25
Structure title title	Crystal structure of the Salmonella effector SspH1
Keywords keywords	E3 ubiquitin ligase, Salmonella effector protein, NEL proteins, LIGASE; LIGASE
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	32.10 Å
Radius of gyration Rg (electron density) rg_electron	32.17 Å
Forward intensity I(0) i0	59185800.00
Molecular weight molecular_weight	59657.0 kDa
Excluded volume excluded_volume	74342 Å³
Envelope volume envelope_volume	97357 Å³
Hydration-shell volume shell_volume	28572 Å³
Envelope diameter envelope_diameter	127.1 Å
Shell Rg shell_rg	34.28 Å
Envelope Rg envelope_rg	32.68 Å
Shape Rg shape_rg	32.18 Å
Total Rg total_rg	32.34 Å
Total atoms total_atoms	4207
Residues n_residues	540
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	120.8 Å
Rg (real space) rg_real	32.66 Å
Rg uncertainty (real space) rg_real_error	1.36 Å
I(0) (real space) i0_real	5.9190e+07
I(0) uncertainty (real space) i0_real_error	1.1010e+06
Rg (reciprocal space) rg_reciprocal	32.42 Å
I(0) (reciprocal space) i0_reciprocal	59170000.0000
Solution quality estimate total_estimate	0.5704
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	29.6 Å
Skewness Skewness skewness	0.729
Kurtosis Kurtosis kurtosis	0.290
Angular range angular_range	— – 0.2450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	7842000.0000
Real-space data points n_real_points	50
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.585; Stabil: 1.000; Sysdev: 0.096; Positv: 1.000; Valcen: 0.519; Smooth: 0.848

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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	E3 ubiquitin-protein ligase SspH1
Molecular weight formula_weight	59603.9 kDa
EC 编号 ec_number	2.3.2.27
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	4251

AEYDAVWSKWERDAPAGESPGRAAVVQEMRDCLNNGNPVLNVGASGLTTLPDRLPPHITTLVIPDNNLTSLPELPEGLRELEVSGNLQLTSLPSLPQGLQKLWAYNNWLASLPTLPPGLGDLAVSNNQLTSLPEMPPALRELRVSGNNLTSLPALPSGLQKLWAYNNRLTSLPEMSPGLQELDVSHNQLTRLPQSLTGLSSAARVYLDGNPLSVRTLQALRDIIGHSGIRIHFDMAGPSVPREARALHLAVADWLTSAREGEAAQADRWQAFGLEDNAAAFSLVLDRLRETENFKKDAGFKAQISSWLTQLAEDAALRAKTFAMATEATSTCEDRVTHALHQMNNVQLVHNAEKGEYDNNLQGLVSTGREMFRLATLEQIAREKAGTLALVDDVEVYLAFQNKLKESLELTSVTSEMRFFDVSGVTVSDLQAAELQVKTAENSGFSKWILQWGPLHSVLERKVPERFNALREKQISDYEDTYRKLYDEVLKSSGLVDDTDAERTIGVSAMDSAKKEFLDGLRALVDEVLGSYLTARWRLN

来源 Source

来源生物 organism	Salmonella enterica subsp. enterica serovar Typhimurium
NCBI Class编号 ncbi_taxonomy_id	90371
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	L(+)-TARTARIC ACID
Molecular weight formula_weight	150.1 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	44

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8. Citations (1)

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Unit-cell length a length_a	170.772 Å
Unit-cell length b length_b	170.772 Å
Unit-cell length c length_c	94.800 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 6 2 2
Space-group number int_tables_number	177
Crystal system crystal_system	—

Resolution resolution	2.900 Å
Low-resolution limit resolution_low	58.310 Å
R factor r_factor	0.2620
R_work r_work	0.2595
R_free r_free	0.3158

fit	/app/data/saxs_computation/h6/9h6w/9h6w.fit
pddf	/app/data/pr_computation/h6/9h6w/9h6w.pr.out
profile	/app/data/saxs_computation/h6/9h6w/9h6w.dat

Crystal structure of the Salmonella effector SspH1

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

E3 ubiquitin-protein ligase SspH1

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