SAXSdb — 4nkh

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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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 161–398 Chain F； UniProt 161–398	Fragment：LRR domains, UNP residues 161-398	No other associated polymer	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	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 161–398 Chain E； UniProt 161–398	Fragment：LRR domains, UNP residues 161-398	No other associated polymer	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
3	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 161–398 Chain D； UniProt 161–398	Fragment：LRR domains, UNP residues 161-398	No other associated polymer	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
4	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 161–398	Fragment：LRR domains, UNP residues 161-398	No other associated polymer	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
5	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 161–398	Fragment：LRR domains, UNP residues 161-398	No other associated polymer	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
6	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 161–398	Fragment：LRR domains, UNP residues 161-398	No other associated polymer	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
7	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 161–398	Fragment：LRR domains, UNP residues 161-398	No other associated polymer	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
8	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain E； UniProt 161–398	Fragment：LRR domains, UNP residues 161-398	No other associated polymer	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
9	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain F； UniProt 161–398	Fragment：LRR domains, UNP residues 161-398	No other associated polymer	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

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 4NKH	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
9H6W Crystal structure of the Salmonella effector SspH1 Deposited 2024-10-25	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 161–700（540 aa）	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
9H6W Crystal structure of the Salmonella effector SspH1 Deposited 2024-10-25	Different construct 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 161–700（540 aa）	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

2 other PDB entries and 4 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 2–239； UniProt 161–398 Author chain B； PDBConstruct 2–239； UniProt 161–398 Author chain C； PDBConstruct 2–239； UniProt 161–398 Author chain D； PDBConstruct 2–239； UniProt 161–398 Author chain E； PDBConstruct 2–239； UniProt 161–398 Author chain F； PDBConstruct 2–239； UniProt 161–398

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	4nkh
Deposition date deposition_date	2013-11-12
Structure title title	Crystal structure of SspH1 LRR domain
Keywords keywords	Leucine-rich repeat, E3 ligase substrate interaction domain, 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	36.17 Å
Radius of gyration Rg (electron density) rg_electron	35.24 Å
Forward intensity I(0) i0	339164000.00
Molecular weight molecular_weight	148320.0 kDa
Excluded volume excluded_volume	185740 Å³
Envelope volume envelope_volume	246380 Å³
Hydration-shell volume shell_volume	57536 Å³
Envelope diameter envelope_diameter	120.6 Å
Shell Rg shell_rg	42.56 Å
Envelope Rg envelope_rg	34.57 Å
Shape Rg shape_rg	35.25 Å
Total Rg total_rg	35.74 Å
Total atoms total_atoms	10455
Residues n_residues	1416
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	112.2 Å
Rg (real space) rg_real	35.93 Å
Rg uncertainty (real space) rg_real_error	0.62 Å
I(0) (real space) i0_real	3.3920e+08
I(0) uncertainty (real space) i0_real_error	5.2060e+06
Rg (reciprocal space) rg_reciprocal	36.08 Å
I(0) (reciprocal space) i0_reciprocal	339200000.0000
Solution quality estimate total_estimate	0.8996
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	48.4 Å
Skewness Skewness skewness	0.087
Kurtosis Kurtosis kurtosis	-0.487
Angular range angular_range	— – 0.2200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	42150000.0000
Real-space data points n_real_points	45
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.916; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.979; Smooth: 0.965

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	4nkhA00
Class class	3 — Alpha Beta
Architecture architecture	80 — Alpha-Beta Horseshoe
Topology topology	10 — Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
Homologous superfamily homologous superfamily	10 — Ribonuclease Inhibitor

Domain ID domain_id	4nkhB00
Class class	3 — Alpha Beta
Architecture architecture	80 — Alpha-Beta Horseshoe
Topology topology	10 — Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
Homologous superfamily homologous superfamily	10 — Ribonuclease Inhibitor

Domain ID domain_id	4nkhC00
Class class	3 — Alpha Beta
Architecture architecture	80 — Alpha-Beta Horseshoe
Topology topology	10 — Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
Homologous superfamily homologous superfamily	10 — Ribonuclease Inhibitor

Domain ID domain_id	4nkhD00
Class class	3 — Alpha Beta
Architecture architecture	80 — Alpha-Beta Horseshoe
Topology topology	10 — Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
Homologous superfamily homologous superfamily	10 — Ribonuclease Inhibitor

Domain ID domain_id	4nkhE00
Class class	3 — Alpha Beta
Architecture architecture	80 — Alpha-Beta Horseshoe
Topology topology	10 — Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
Homologous superfamily homologous superfamily	10 — Ribonuclease Inhibitor

Domain ID domain_id	4nkhF00
Class class	3 — Alpha Beta
Architecture architecture	80 — Alpha-Beta Horseshoe
Topology topology	10 — Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
Homologous superfamily homologous superfamily	10 — Ribonuclease Inhibitor

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8. Citations (1)

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Unit-cell length a length_a	114.930 Å
Unit-cell length b length_b	114.930 Å
Unit-cell length c length_c	252.170 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	48

Space group space_group	P 42 21 2
Space-group number int_tables_number	94
Crystal system crystal_system	—

Resolution resolution	2.750 Å
Low-resolution limit resolution_low	49.860 Å
R factor r_factor	0.2446
R_work r_work	0.2427
R_free r_free	0.2802

Description description	E3 ubiquitin-protein ligase sspH1
Molecular weight formula_weight	25782.2 kDa
EC 编号 ec_number	6.3.2.-
Source method src_method	man
Copy count entity_count	6

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	10455

Crystal structure of SspH1 LRR domain

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

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Salmonella enterica subsp. enterica serovar Typhimurium
NCBI Class编号 ncbi_taxonomy_id	588858
宿主生物 host_organism	Escherichia coli

fit	/app/data/saxs_computation/nk/4nkh/4nkh.fit
pddf	/app/data/pr_computation/nk/4nkh/4nkh.pr.out
profile	/app/data/saxs_computation/nk/4nkh/4nkh.dat