SAXSdb — 1ypt

▼

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

PROTEIN-TYROSINE PHOSPHATASE YERSINIA (CATALYTIC DOMAIN)

Yersinia enterocolitica

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	YOPH_YEREN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–305； UniProt 164–468 Author chain B； PDBConstruct 1–305； UniProt 164–468

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	1ypt
Deposition date deposition_date	1994-09-16
Structure title title	CRYSTAL STRUCTURE OF YERSINIA PROTEIN TYROSINE PHOSPHATASE AT 2.5 ANGSTROMS AND THE COMPLEX WITH TUNGSTATE
Keywords keywords	HYDROLASE, PROTEIN TYROSINE PHOSPHATASE; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

▼

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.

1ypt__assembly_1__model_1

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

Download this curve (.dat)

1ypt__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1ypt__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	28.56 Å
Rg (electron density)	27.67 Å
Total Rg	28.27 Å
Atom count	4290
Residues	558
Excluded volume	75568 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1ypt__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (2)

▼

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1ypta_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.45 — (Phosphotyrosine protein) phosphatases II
Superfamily Superfamily superfamily	c.45.1 — (Phosphotyrosine protein) phosphatases II
Family Family family	c.45.1.2 — Higher-molecular-weight phosphotyrosine protein phosphatases

Domain ID domain_id	d1yptb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.45 — (Phosphotyrosine protein) phosphatases II
Superfamily Superfamily superfamily	c.45.1 — (Phosphotyrosine protein) phosphatases II
Family Family family	c.45.1.2 — Higher-molecular-weight phosphotyrosine protein phosphatases

CATH v4.4 (2 domains)

Domain ID domain_id	1yptA00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	190 — Protein-Tyrosine Phosphatase; Chain A
Homologous superfamily homologous superfamily	10 — Protein tyrosine phosphatase superfamily

Domain ID domain_id	1yptB00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	190 — Protein-Tyrosine Phosphatase; Chain A
Homologous superfamily homologous superfamily	10 — Protein tyrosine phosphatase superfamily

▶

Unit-cell length a length_a	71.530 Å
Unit-cell length b length_b	71.530 Å
Unit-cell length c length_c	107.480 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 32
Space-group number int_tables_number	145
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	7.000 Å
R factor r_factor	0.1680
R_work r_work	0.1680
R_free r_free	0.2220

Description description	PROTEIN-TYROSINE PHOSPHATASE YERSINIA (CATALYTIC DOMAIN)
Molecular weight formula_weight	33422.7 kDa
EC 编号 ec_number	3.1.3.48
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	4355

CRYSTAL STRUCTURE OF YERSINIA PROTEIN TYROSINE PHOSPHATASE AT 2.5 ANGSTROMS AND THE COMPLEX WITH TUNGSTATE

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

PROTEIN-TYROSINE PHOSPHATASE YERSINIA (CATALYTIC DOMAIN)

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

1ypt__assembly_1__model_1

1ypt__assembly_1__model_1 | I(q)

1ypt__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (2)

Source organism organism	Yersinia enterocolitica
NCBI taxonomy ID ncbi_taxonomy_id	630

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	65

CRYSTAL STRUCTURE OF YERSINIA PROTEIN TYROSINE PHOSPHATASE AT 2.5 ANGSTROMS AND THE COMPLEX WITH TUNGSTATE

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

PROTEIN-TYROSINE PHOSPHATASE YERSINIA (CATALYTIC DOMAIN)

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

1ypt__assembly_1__model_1

1ypt__assembly_1__model_1 | I(q)

1ypt__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (2)