SAXSdb — 4yx1

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

Surface presentation of antigens protein SpaO

Salmonella 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 232–297 Chain B； UniProt 232–297	Fragment：UNP Residues 232-297 Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；SpaO(232-297) was concentrated to 8mg/mL and crystallized with 35% PEG400, 200mM calcium acetate, 100mM sodium acetate pH=5.0. Crystals were cryoprotected in the mother liquor. Microseeding was employed to enhance crystal uniformity and diffraction. Briefly, crystals to be seeded were harvested in precipitant solution and vortexed in a microfuge tube with a small stir bar for ~60 seconds. The slurry of microseeds was serially dilluted (5-10-fold steps) in precipitant solution and 5 selected microseed-precipitant mixtures were mixed with fresh protein as in a normal hanging drop experiment.	Resolution 1.35 Å R-free 0.205

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 4YX1	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4YX5 SpaO(SPOA1,2) Deposited 2015-03-22	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 145–213（69 aa） Fragment：UNP Residues 145-213 Chain B 232–297（66 aa） Fragment：UNP Residues 232-297	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；SpaO(145-213) + SpaO (232-297) was concentrated to 12mg/mL and crystallized with 25% PEG400, 10% isopropanol, 100mM sodium citrate pH=5.6 at 277K. Microseeding was employed to enhance crystal uniformity and diffraction. Briefly, crystals to be seeded were harvested in precipitant solution and vortexed in a microfuge tube with a small stir bar for ~60 seconds. The slurry of microseeds was serially dilluted (5-10-fold steps) in precipitant solution and 5 selected microseed-precipitant mixtures were mixed with fresh protein as in a normal hanging drop experiment. Crystals were cryoprotected in mother liquor with the PEG400 concentration raised to 37.5%.	Resolution 2.90 Å R-free 0.279
4YX7 Complex of SpaO(SPOA1,2) and OrgB(APAR)::T4lysozyme fusion protein Deposited 2015-03-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 145–213（69 aa） Fragment：UNP Residues 145-213 Chain B 232–297（66 aa） Fragment：UNP Residues 232-297	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；SpaO(145-213) + SpaO (232-297) + OrgB(1-30)::T4 lysozyme was concentrated to 18.5mg/mL and crystallized with 25% PEG3350, 200mM ammonium formate, 100mM sodium acetate pH=5.0. Microseeding was employed to enhance crystal uniformity and diffraction. Briefly, crystals to be seeded were harvested in precipitant solution and vortexed in a microfuge tube with a small stir bar for ~60 seconds. The slurry of microseeds was serially dilluted (5-10-fold steps) in precipitant solution and 5 selected microseed-precipitant mixtures were mixed with fresh protein as in a normal hanging drop experiment. Crystals were cryoprotected in 30% PEG3350, 10% glycerol, 200mM ammonium acetate, 100mM sodium acetate pH=5.0.	Resolution 2.00 Å R-free 0.210
4YX7 Complex of SpaO(SPOA1,2) and OrgB(APAR)::T4lysozyme fusion protein Deposited 2015-03-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 145–213（69 aa） Fragment：UNP Residues 145-213 Chain E 232–297（66 aa） Fragment：UNP Residues 232-297	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；SpaO(145-213) + SpaO (232-297) + OrgB(1-30)::T4 lysozyme was concentrated to 18.5mg/mL and crystallized with 25% PEG3350, 200mM ammonium formate, 100mM sodium acetate pH=5.0. Microseeding was employed to enhance crystal uniformity and diffraction. Briefly, crystals to be seeded were harvested in precipitant solution and vortexed in a microfuge tube with a small stir bar for ~60 seconds. The slurry of microseeds was serially dilluted (5-10-fold steps) in precipitant solution and 5 selected microseed-precipitant mixtures were mixed with fresh protein as in a normal hanging drop experiment. Crystals were cryoprotected in 30% PEG3350, 10% glycerol, 200mM ammonium acetate, 100mM sodium acetate pH=5.0.	Resolution 2.00 Å R-free 0.210
4YXA Complex of SpaO(SPOA1,2 SeMet) and OrgB(APAR)::T4lysozyme fusion protein Deposited 2015-03-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 145–213（69 aa） Fragment：UNP Residues 145-213 Chain B 232–297（66 aa） Fragment：UNP Residues 232-297	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；SpaO(145-213, SeMet) + SpaO (232-297, SeMet) + OrgB(1-30)::T4 lysozyme (native) was concentrated to 18mg/mL, supplemented with 50mM maltose, and crystallized with 25% PEG3350, 200mM ammonium formate, 100mM sodium acetate pH=5.0. Microseeding was employed to enhance crystal uniformity and diffraction. Briefly, crystals to be seeded were harvested in precipitant solution and vortexed in a microfuge tube with a small stir bar for ~60 seconds. The slurry of microseeds was serially dilluted (5-10-fold steps) in precipitant solution and 5 selected microseed-precipitant mixtures were mixed with fresh protein as in a normal hanging drop experiment. Crystals were cryoprotected in 25% PEG3350, 10% ethylene glycol, 200mM ammonium formate, 100mM sodium acetate pH=5.0, 50mM maltose.	Resolution 2.35 Å R-free 0.262
4YXA Complex of SpaO(SPOA1,2 SeMet) and OrgB(APAR)::T4lysozyme fusion protein Deposited 2015-03-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 145–213（69 aa） Fragment：UNP Residues 145-213 Chain E 232–297（66 aa） Fragment：UNP Residues 232-297	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；SpaO(145-213, SeMet) + SpaO (232-297, SeMet) + OrgB(1-30)::T4 lysozyme (native) was concentrated to 18mg/mL, supplemented with 50mM maltose, and crystallized with 25% PEG3350, 200mM ammonium formate, 100mM sodium acetate pH=5.0. Microseeding was employed to enhance crystal uniformity and diffraction. Briefly, crystals to be seeded were harvested in precipitant solution and vortexed in a microfuge tube with a small stir bar for ~60 seconds. The slurry of microseeds was serially dilluted (5-10-fold steps) in precipitant solution and 5 selected microseed-precipitant mixtures were mixed with fresh protein as in a normal hanging drop experiment. Crystals were cryoprotected in 25% PEG3350, 10% ethylene glycol, 200mM ammonium formate, 100mM sodium acetate pH=5.0, 50mM maltose.	Resolution 2.35 Å R-free 0.262

3 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SPAO_SALTY
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–70； UniProt 232–297 Author chain B； PDBConstruct 5–70； UniProt 232–297

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	4yx1
Deposition date deposition_date	2015-03-21
Structure title title	SpaO(SPOA2)
Keywords keywords	Type III Secretion System, PROTEIN TRANSPORT; PROTEIN TRANSPORT
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	16.17 Å
Radius of gyration Rg (electron density) rg_electron	14.98 Å
Forward intensity I(0) i0	4741750.00
Molecular weight molecular_weight	15502.0 kDa
Excluded volume excluded_volume	19321 Å³
Envelope volume envelope_volume	22411 Å³
Hydration-shell volume shell_volume	12885 Å³
Envelope diameter envelope_diameter	51.0 Å
Shell Rg shell_rg	20.43 Å
Envelope Rg envelope_rg	15.31 Å
Shape Rg shape_rg	15.00 Å
Total Rg total_rg	16.01 Å
Total atoms total_atoms	1064
Residues n_residues	131
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	52.2 Å
Rg (real space) rg_real	16.08 Å
Rg uncertainty (real space) rg_real_error	0.29 Å
I(0) (real space) i0_real	4.7420e+06
I(0) uncertainty (real space) i0_real_error	6.2030e+04
Rg (reciprocal space) rg_reciprocal	16.09 Å
I(0) (reciprocal space) i0_reciprocal	4742000.0000
Solution quality estimate total_estimate	0.6592
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	20.7 Å
Skewness Skewness skewness	0.186
Kurtosis Kurtosis kurtosis	-0.299
Angular range angular_range	— – 0.4900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	634200.0000
Real-space data points n_real_points	79
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.838; Stabil: 1.000; Sysdev: 0.353; Positv: 1.000; Valcen: 0.993; 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	Surface presentation of antigens protein SpaO
Molecular weight formula_weight	7851.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	1286

GPVDVKLEFVLYRKNVTLAELEAMGQQQLLSLPTNAELNVEIMANGVLLGNGELVQMNDTLGVEIHEWLS

来源 Source

来源生物 organism	Salmonella typhimurium
NCBI Class编号 ncbi_taxonomy_id	99287
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	222

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	4yx1A00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	330 — Surface presentation of antigens (SPOA)
Homologous superfamily homologous superfamily	10 — SpoA-like

Domain ID domain_id	4yx1B00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	330 — Surface presentation of antigens (SPOA)
Homologous superfamily homologous superfamily	10 — SpoA-like

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8. Citations (1)

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Unit-cell length a length_a	35.000 Å
Unit-cell length b length_b	41.270 Å
Unit-cell length c length_c	48.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	103.92 °
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	1.350 Å
Low-resolution limit resolution_low	31.262 Å
R factor r_factor	0.1747
R_work r_work	0.1724
R_free r_free	0.2053

fit	/app/data/saxs_computation/yx/4yx1/4yx1.fit
pddf	/app/data/pr_computation/yx/4yx1/4yx1.pr.out
profile	/app/data/saxs_computation/yx/4yx1/4yx1.dat

SpaO(SPOA2)

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

Surface presentation of antigens protein SpaO

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