1jyo

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

Method: X-RAY DIFFRACTION

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

SicP

Salmonella typhimurium

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	protein tyrosine phosphatase SptP × 2 （P74873） water × 6	Consistent with protein count

Other States of the Same Protein in the Database

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	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	SicP × 4 （O85300） water × 6	Consistent with protein count

Other States of the Same Protein in the Database

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. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

1jyo__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1jyo__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1jyo__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	37.05 Å
Rg (electron density)	37.56 Å
Total Rg	37.58 Å
Atom count	5706
Residues	726
Excluded volume	102670 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1jyo__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. 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

Source Source

Source organism organism	Salmonella typhimurium
NCBI taxonomy ID ncbi_taxonomy_id	602
Host organism 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

Source Source

Source organism organism	Salmonella typhimurium
NCBI taxonomy ID ncbi_taxonomy_id	602
Host organism 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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6. 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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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

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1jyo__assembly_1__model_1

1jyo__assembly_1__model_1 | I(q)

1jyo__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)

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

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

protein tyrosine phosphatase SptP

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1jyo__assembly_1__model_1

1jyo__assembly_1__model_1 | I(q)

1jyo__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)