SAXSdb — 1pm4

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

YPM

Yersinia pseudotuberculosis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 3	water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q57221_YERPS
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–119； UniProt 33–151 Author chain B； PDBConstruct 1–119； UniProt 33–151 Author chain C； PDBConstruct 1–119； UniProt 33–151

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	1pm4
Deposition date deposition_date	2003-06-09
Structure title title	Crystal structure of Yersinia pseudotuberculosis-derived mitogen (YPM)
Keywords keywords	Jelly roll fold, TOXIN; TOXIN
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.

1pm4__assembly_1__model_1

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

Download this curve (.dat)

1pm4__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1pm4__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.19 Å
Rg (electron density)	20.85 Å
Total Rg	21.80 Å
Atom count	2730
Residues	351
Excluded volume	48240 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1pm4__assembly_1__model_1`	trimeric （3）	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 (2)

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1pm4a_
Class class	b — All beta proteins
Fold Fold fold	b.135 — Superantigen (mitogen) Ypm
Superfamily Superfamily superfamily	b.135.1 — Superantigen (mitogen) Ypm
Family Family family	b.135.1.1 — Superantigen (mitogen) Ypm

Domain ID domain_id	d1pm4b_
Class class	b — All beta proteins
Fold Fold fold	b.135 — Superantigen (mitogen) Ypm
Superfamily Superfamily superfamily	b.135.1 — Superantigen (mitogen) Ypm
Family Family family	b.135.1.1 — Superantigen (mitogen) Ypm

Domain ID domain_id	d1pm4c_
Class class	b — All beta proteins
Fold Fold fold	b.135 — Superantigen (mitogen) Ypm
Superfamily Superfamily superfamily	b.135.1 — Superantigen (mitogen) Ypm
Family Family family	b.135.1.1 — Superantigen (mitogen) Ypm

CATH v4.4 (3 domains)

Domain ID domain_id	1pm4A00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	510 — Mitogen Ypm

Domain ID domain_id	1pm4B00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	510 — Mitogen Ypm

Domain ID domain_id	1pm4C00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	510 — Mitogen Ypm

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Unit-cell length a length_a	138.651 Å
Unit-cell length b length_b	78.652 Å
Unit-cell length c length_c	32.901 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	91.97 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

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

Resolution resolution	1.755 Å
Low-resolution limit resolution_low	34.710 Å
R factor r_factor	0.1844
R_work r_work	0.1820
R_free r_free	0.2293

Description description	YPM
Molecular weight formula_weight	13223.8 kDa
Source method src_method	man
Copy count entity_count	3

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	3087

Crystal structure of Yersinia pseudotuberculosis-derived mitogen (YPM)

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

YPM

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

1pm4__assembly_1__model_1

1pm4__assembly_1__model_1 | I(q)

1pm4__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (1)

Source organism organism	Yersinia pseudotuberculosis
NCBI taxonomy ID ncbi_taxonomy_id	633
Host organism host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	339

Crystal structure of Yersinia pseudotuberculosis-derived mitogen (YPM)

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

YPM

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

1pm4__assembly_1__model_1

1pm4__assembly_1__model_1 | I(q)

1pm4__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (1)