SAXSdb — 1jyo

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

SicP

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 heterocomplex Heteromer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain A； UniProt 2–116 Chain B； UniProt 2–116 Chain C； UniProt 2–116 Chain D； UniProt 2–116	Not recorded	protein tyrosine phosphatase SptP × 2 （P74873）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；2M sodium chloride, 5-10% polyethylene glycol molecular weight 6000 (PEG6000), supplemented with 2mM DTT and 15% glycerol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 1.90 Å R-free 0.258

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	SICP_SALTY
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 16–130； UniProt 2–116 Author chain B； PDBConstruct 16–130； UniProt 2–116 Author chain C； PDBConstruct 16–130； UniProt 2–116 Author chain D； PDBConstruct 16–130； UniProt 2–116

protein tyrosine phosphatase SptP

Salmonella typhimurium

UniProt P74873

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 heterocomplex Heteromer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain E； UniProt 35–139 Chain F； UniProt 35–139	Not recorded	SicP × 4 （O85300）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；2M sodium chloride, 5-10% polyethylene glycol molecular weight 6000 (PEG6000), supplemented with 2mM DTT and 15% glycerol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 1.90 Å R-free 0.258

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 1JYO	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1G4U CRYSTAL STRUCTURE OF THE SALMONELLA TYROSINE PHOSPHATASE AND GTPASE ACTIVATING PROTEIN SPTP BOUND TO RAC1 Deposited 2000-10-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain S 161–543（383 aa） Fragment：SPTP RESIDUES 161-543	Not recorded	MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 AF3 ALUMINUM FLUORIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.7；18 %PEG 400, 0.1M MES, 15mM sodium flouride, 0.1mM aluminum chloride, 2mM DTT, 2mM magnesium chloride, pH 5.7, VAPOR DIFFUSION, HANGING DROP	Resolution 2.30 Å R-free 0.258
1G4W CRYSTAL STRUCTURE OF THE SALMONELLA TYROSINE PHOSPHATASE AND GTPASE ACTIVATING PROTEIN SPTP Deposited 2000-10-28	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain R 161–543（383 aa） Fragment：SPTP RESIDUES 161-543	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；295 K；3.5M sodium formate, 2mM DTT, 0.1M Tris pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.20 Å R-free 0.314

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

View Construct and Data Evidence

UniProt name	SPTP_SALTY
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain E； PDBConstruct 1–105； UniProt 35–139 Author chain F； PDBConstruct 1–105； UniProt 35–139

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	1jyo
Deposition date deposition_date	2001-09-12
Structure title title	Structure of the Salmonella Virulence Effector SptP in Complex with its Secretion Chaperone SicP
Keywords keywords	;Salmonella, bacterial pathogenesis, infectious disease, virulence factor, type III secretion, chaperone, unfolded, protein folding, SptP, SicP ;; CHAPERONE
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	37.05 Å
Radius of gyration Rg (electron density) rg_electron	37.56 Å
Forward intensity I(0) i0	95273900.00
Molecular weight molecular_weight	81119.0 kDa
Excluded volume excluded_volume	102670 Å³
Envelope volume envelope_volume	132400 Å³
Hydration-shell volume shell_volume	32160 Å³
Envelope diameter envelope_diameter	134.7 Å
Shell Rg shell_rg	39.06 Å
Envelope Rg envelope_rg	37.65 Å
Shape Rg shape_rg	37.58 Å
Total Rg total_rg	37.58 Å
Total atoms total_atoms	5706
Residues n_residues	726
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	131.7 Å
Rg (real space) rg_real	37.65 Å
Rg uncertainty (real space) rg_real_error	1.94 Å
I(0) (real space) i0_real	9.5270e+07
I(0) uncertainty (real space) i0_real_error	2.0380e+06
Rg (reciprocal space) rg_reciprocal	37.29 Å
I(0) (reciprocal space) i0_reciprocal	95240000.0000
Solution quality estimate total_estimate	0.7061
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	27.6 Å
Skewness Skewness skewness	0.588
Kurtosis Kurtosis kurtosis	-0.469
Angular range angular_range	— – 0.2150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	31730000.0000
Real-space data points n_real_points	44
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.407; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.236; Smooth: 0.723

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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	SicP
Molecular weight formula_weight	14457.4 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	6335

LQAHQDIIANIGEKLGLPLTFDDNNQCLLLLDSDIFTSIEAKDDIWLLNGMIIPLSPVCGDSIWRQIMVINGELAANNEGTLAYIDAAETLLLIHAITDLTNTYHIISQLESFVNQQEALKNILQEYAKV

来源 Source

来源生物 organism	Salmonella typhimurium
NCBI Class编号 ncbi_taxonomy_id	602
宿主生物 host_organism	Escherichia coli BL21

Entity 2 Entity 2 polymer

Description description	protein tyrosine phosphatase SptP
Molecular weight formula_weight	11966.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,F

TDKAYVAPEKFSSKVLTWLGKMPLFKNTEVVQKHTENIRVQDQKILQTFLHALTEKYGETAVNDALLMSRINMNKPLTQRLAVQITECVKAADEGFINLIKSKDN

来源 Source

来源生物 organism	Salmonella typhimurium
NCBI Class编号 ncbi_taxonomy_id	602
宿主生物 host_organism	Escherichia coli BL21

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	629

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7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1jyoa_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.198 — Secretion chaperone-like
Superfamily Superfamily superfamily	d.198.1 — Type III secretory system chaperone-like
Family Family family	d.198.1.1 — Type III secretory system chaperone

Domain ID domain_id	d1jyob_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.198 — Secretion chaperone-like
Superfamily Superfamily superfamily	d.198.1 — Type III secretory system chaperone-like
Family Family family	d.198.1.1 — Type III secretory system chaperone

Domain ID domain_id	d1jyoc_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.198 — Secretion chaperone-like
Superfamily Superfamily superfamily	d.198.1 — Type III secretory system chaperone-like
Family Family family	d.198.1.1 — Type III secretory system chaperone

Domain ID domain_id	d1jyod_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.198 — Secretion chaperone-like
Superfamily Superfamily superfamily	d.198.1 — Type III secretory system chaperone-like
Family Family family	d.198.1.1 — Type III secretory system chaperone

Domain ID domain_id	d1jyoe_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.184 — Non-globular alpha+beta subunits of globular proteins
Superfamily Superfamily superfamily	d.184.1 — Non-globular alpha+beta subunits of globular proteins
Family Family family	d.184.1.2 — Type III secretory system effector

Domain ID domain_id	d1jyof_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.184 — Non-globular alpha+beta subunits of globular proteins
Superfamily Superfamily superfamily	d.184.1 — Non-globular alpha+beta subunits of globular proteins
Family Family family	d.184.1.2 — Type III secretory system effector

CATH v4.4 (6 domains)

Domain ID domain_id	1jyoA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1460 — Yope Regulator; Chain: A,
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1jyoB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1460 — Yope Regulator; Chain: A,
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1jyoC00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1460 — Yope Regulator; Chain: A,
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1jyoD00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1460 — Yope Regulator; Chain: A,
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1jyoE00
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	1330 — non globular Virulence effector SptP fold
Homologous superfamily homologous superfamily	10 — non globular Virulence effector SptP domain

Domain ID domain_id	1jyoF00
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	1330 — non globular Virulence effector SptP fold
Homologous superfamily homologous superfamily	10 — non globular Virulence effector SptP domain

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8. Citations (1)

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Unit-cell length a length_a	167.489 Å
Unit-cell length b length_b	49.582 Å
Unit-cell length c length_c	138.142 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	121.95 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2260
R_work r_work	0.2240
R_free r_free	0.2580

fit	/app/data/saxs_computation/jy/1jyo/1jyo.fit
pddf	/app/data/pr_computation/jy/1jyo/1jyo.pr.out
profile	/app/data/saxs_computation/jy/1jyo/1jyo.dat

Structure of the Salmonella Virulence Effector SptP in Complex with its Secretion Chaperone SicP

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

SicP

State in the Current Structure

Other States of the Same Protein in the Database

protein tyrosine phosphatase SptP

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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)