SAXSdb — 3f9a

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

Tyrosine-protein phosphatase yopH

Yersinia enterocolitica (type O:9)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	TUNGSTATE(VI)ION × 2 water × 1	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 2–306； 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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3f9a
Deposition date deposition_date	2008-11-13
Structure title title	W354F Yersinia enterocolitica PTPase complexed with tungstate
Keywords keywords	Hydrolase, P-loop, WPD-loop, Protein Phosphatase, tungstate, Membrane, Outer membrane, Secreted, Virulence; HYDROLASE
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.

3f9a__assembly_1__model_1

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

Download this curve (.dat)

3f9a__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3f9a__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	19.31 Å
Rg (electron density)	18.11 Å
Total Rg	18.99 Å
Atom count	2173
Residues	282
Excluded volume	38267 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3f9a__assembly_1__model_1`	monomeric （1）	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	Tyrosine-protein phosphatase yopH
Molecular weight formula_weight	33514.8 kDa
EC 编号 ec_number	3.1.3.48
Mutation mutation	C235R, W354F
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2546

MRERPHTSGHHGAGEARATAPSTVSPYGPEARAELSSRLTTLRNTLAPATNDPRYLQACGGEKLNRFRDIQCRRQTAVRADLNANYIQVGNTRTIACQYPLQSQLESHFRMLAENRTPVLAVLASSSEIANQRFGMPDYFRQSGTYGSITVESKMTQQVGLGDGIMADMYTLTIREAGQKTISVPVVHVGNFPDQTAVSSEVTKALASLVDQTAETKRNMYESKGSSAVADDSKLRPVIHCRAGVGRTAQLIGAMCMNDSRNSQLSVEDMVSQMRVQRNGIMVQKDEQLDVLIKLAEGQGRPLLNS

Source Source

Source organism organism	Yersinia enterocolitica (type O:9)
NCBI taxonomy ID ncbi_taxonomy_id	34055
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	TUNGSTATE(VI)ION
Molecular weight formula_weight	247.8 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	373

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d3f9aa_
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 (1 domains)

Domain ID domain_id	3f9aA00
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

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Unit-cell length a length_a	54.431 Å
Unit-cell length b length_b	58.263 Å
Unit-cell length c length_c	90.622 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.690 Å
Low-resolution limit resolution_low	26.410 Å
R factor r_factor	0.1750
R_work r_work	0.1730
R_free r_free	0.2070

W354F Yersinia enterocolitica PTPase complexed with tungstate

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

Tyrosine-protein phosphatase yopH

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

3f9a__assembly_1__model_1

3f9a__assembly_1__model_1 | I(q)

3f9a__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 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)

W354F Yersinia enterocolitica PTPase complexed with tungstate

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

Tyrosine-protein phosphatase yopH

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

3f9a__assembly_1__model_1

3f9a__assembly_1__model_1 | I(q)

3f9a__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 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)