SAXSdb — 3d8k

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

Protein phosphatase 2C

Toxoplasma gondii

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	SULFATE ION × 4 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A4GX63_TOXGO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–369； UniProt 79–444 Author chain B； PDBConstruct 4–369； UniProt 79–444 Author chain C； PDBConstruct 4–369； UniProt 79–444 Author chain D； PDBConstruct 4–369； UniProt 79–444

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	3d8k
Deposition date deposition_date	2008-05-23
Structure title title	Crystal structure of a phosphatase from a toxoplasma gondii
Keywords keywords	;9110a1, NYSGRC, PSI-II, Phosphatase, Toxoplasma gondii., Structural Genomics, Protein Structure Initiative, New York Structural GenomiX Research Consortium, NYSGXRC, HYDROLASE, New York SGX Research Center for Structural Genomics ;; 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.

3d8k__assembly_1__model_1

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

Download this curve (.dat)

3d8k__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3d8k__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	37.84 Å
Rg (electron density)	37.49 Å
Total Rg	37.85 Å
Atom count	10711
Residues	1353
Excluded volume	189190 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3d8k__assembly_1__model_1`	tetrameric （4）	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	Protein phosphatase 2C
Molecular weight formula_weight	42012.8 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	10892

MSLRHLYIEEGRTVCASATSRNRRPTSESPHSDDVVVVEGMLRGRPETRVHAMFDGFQGRHSAMWLAQNVMNYLNDLRDVNEEEITRQFERMDGDLRAANLPGGSSALIIFVRYEKKPTEARVVGRQIVPEGAKEFTSVAEALGGPLMPVVAMNFRRDPRAAKGIYTIHVASLGNSRCVLKSGRTAIHLSTPHTASSHKERHRVQAAGGVFTTVNGELLLGGVVPMTRAFGSFDFKKGGQGKLQQDLVSAVPDVTTFFAYPGDDIVAGTAGAFAHFRSHAAIAAAIALYPVSPETVLDAAKAMVVNAKRRKVTKNISTFVRHLPESRTRSQKMLEGTSGENGEEDFSIDRTNELTQALQAGFFSFLLYYEGHHHHHH

Source Source

Source organism organism	Toxoplasma gondii
NCBI taxonomy ID ncbi_taxonomy_id	5811
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	181

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	3d8kA00
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	3d8kB00
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	3d8kC00
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	3d8kD00
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	57.882 Å
Unit-cell length b length_b	169.052 Å
Unit-cell length c length_c	87.012 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	104.47 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.710 Å
Low-resolution limit resolution_low	46.710 Å
R factor r_factor	0.2510
R_work r_work	0.2510
R_free r_free	0.3040

Crystal structure of a phosphatase from a toxoplasma gondii

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

Protein phosphatase 2C

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

3d8k__assembly_1__model_1

3d8k__assembly_1__model_1 | I(q)

3d8k__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) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of a phosphatase from a toxoplasma gondii

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

Protein phosphatase 2C

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

3d8k__assembly_1__model_1

3d8k__assembly_1__model_1 | I(q)

3d8k__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) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)