SAXSdb — 2pk0

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

Serine/threonine protein phosphatase Stp1

Streptococcus agalactiae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	MAGNESIUM ION × 2 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	MAGNESIUM ION × 2 GLYCEROL × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	MAGNESIUM ION × 3 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	MAGNESIUM ION × 3 CHLORIDE ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q3K363_STRA1
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 6–250； UniProt 1–245 Author chain B； PDBConstruct 6–250； UniProt 1–245 Author chain C； PDBConstruct 6–250； UniProt 1–245 Author chain D； PDBConstruct 6–250； UniProt 1–245

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	2pk0
Deposition date deposition_date	2007-04-17
Structure title title	Structure of the S. agalactiae serine/threonine phosphatase at 2.65 resolution
Keywords keywords	Streptococcus agalactiae, serine, threonine, phosphatase, signaling motif, SIGNALING PROTEIN; SIGNALING PROTEIN
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.

2pk0__assembly_1__model_1

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

Download this curve (.dat)

2pk0__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2pk0__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	18.97 Å
Rg (electron density)	17.73 Å
Total Rg	18.67 Å
Atom count	1888
Residues	247
Excluded volume	33183 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2pk0__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2pk0__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2pk0__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`2pk0__assembly_4__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 (5)

Entity 1 Entity 1 polymer

Description description	Serine/threonine protein phosphatase Stp1
Molecular weight formula_weight	27404.4 kDa
EC 编号 ec_number	3.1.3.16
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	7780

ARKKYMEISLLTDIGQRRSNNQDFINQFENKAGVPLIILADGMGGHRAGNIASEMTVTDLGSDWAETDFSELSEIRDWMLVSIETENRKIYELGQSDDYKGMGTTIEAVAIVGDNIIFAHVGDSRIGIVRQGEYHLLTSDHSLVNELVKAGQLTEEEAASHPQKNIITQSIGQANPVEPDLGVHLLEEGDYLVVNSDGLTNMLSNADIATVLTQEKTLDDKNQDLITLANHRGGLDNITVALVYVESEAV

Source Source

Source organism organism	Streptococcus agalactiae
NCBI taxonomy ID ncbi_taxonomy_id	205921
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	10

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	295

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d2pk0a1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.219 — PP2C-like
Superfamily Superfamily superfamily	d.219.1 — PP2C-like
Family Family family	d.219.1.0 — automated matches

Domain ID domain_id	d2pk0a2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2pk0b1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.219 — PP2C-like
Superfamily Superfamily superfamily	d.219.1 — PP2C-like
Family Family family	d.219.1.0 — automated matches

Domain ID domain_id	d2pk0b2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2pk0c1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.219 — PP2C-like
Superfamily Superfamily superfamily	d.219.1 — PP2C-like
Family Family family	d.219.1.0 — automated matches

Domain ID domain_id	d2pk0c2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2pk0d1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.219 — PP2C-like
Superfamily Superfamily superfamily	d.219.1 — PP2C-like
Family Family family	d.219.1.0 — automated matches

Domain ID domain_id	d2pk0d2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (4 domains)

Domain ID domain_id	2pk0A00
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	40 — Phosphatase 2c; domain 1
Homologous superfamily homologous superfamily	10 — PPM-type phosphatase domain

Domain ID domain_id	2pk0B00
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	40 — Phosphatase 2c; domain 1
Homologous superfamily homologous superfamily	10 — PPM-type phosphatase domain

Domain ID domain_id	2pk0C00
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	40 — Phosphatase 2c; domain 1
Homologous superfamily homologous superfamily	10 — PPM-type phosphatase domain

Domain ID domain_id	2pk0D00
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	40 — Phosphatase 2c; domain 1
Homologous superfamily homologous superfamily	10 — PPM-type phosphatase domain

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Unit-cell length a length_a	139.400 Å
Unit-cell length b length_b	92.100 Å
Unit-cell length c length_c	86.900 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	16

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.650 Å
Low-resolution limit resolution_low	19.650 Å
R factor r_factor	0.2000
R_work r_work	0.1967
R_free r_free	0.2712

Structure of the S. agalactiae serine/threonine phosphatase at 2.65 resolution

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

Serine/threonine protein phosphatase Stp1

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

2pk0__assembly_1__model_1

2pk0__assembly_1__model_1 | I(q)

2pk0__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (8 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Structure of the S. agalactiae serine/threonine phosphatase at 2.65 resolution

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

Serine/threonine protein phosphatase Stp1

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

2pk0__assembly_1__model_1

2pk0__assembly_1__model_1 | I(q)

2pk0__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (8 domains)

CATH v4.4 (4 domains)

7. Citations (1)