SAXSdb — 3f5e

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

Micronemal protein 1

Toxoplasma gondii

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Monomer	Protein 1 其他Polymer 1	N-acetyl-alpha-neuraminic acid-(2-3)-2-deoxy-2-fluoro-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CHLORIDE ION × 1 ACETATE ION × 8 GLYCEROL × 5 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MIC1_TOXGO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–246； UniProt 17–262

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	3f5e
Deposition date deposition_date	2008-11-03
Structure title title	Crystal structure of Toxoplasma gondii micronemal protein 1 bound to 2'F-3'SiaLacNAc1-3
Keywords keywords	;cellular adhesion, micronemal protein 1, toxoplasma gondii, carbohydrate, fluorine, Cell adhesion, Cytoplasmic vesicle, Lectin, Virulence ;; CELL ADHESION
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.

3f5e__assembly_1__model_1

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

Download this curve (.dat)

3f5e__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3f5e__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	20.21 Å
Rg (electron density)	19.47 Å
Total Rg	20.27 Å
Atom count	1849
Residues	226
Excluded volume	32265 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3f5e__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 (6)

Entity 1 Entity 1 polymer

Description description	Micronemal protein 1
Molecular weight formula_weight	27266.0 kDa
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	2054

VGPEAYGEASHSHSPASGRYIQQMLDQRCQEIAAELCQSGLRKMCVPSSRIVARNAVGITHQNTLQWRCFDTASLLESNQENNGVNCVDDCGHTIPCPGGVHRQNSNHATRHEILSKLVEEGVQRFCSPYQASANKYCNDKFPGTIARRSKGFGNNVEVAWRCYEKASLLYSVYAECASNCGTTWYCPGGRRGTSTELDKRHYTEEEGIRQAIGSVDSPCSEVEVCLPKDENPPLCLDESGQISRT

Source Source

Source organism organism	Toxoplasma gondii
NCBI taxonomy ID ncbi_taxonomy_id	383379
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 branched

Description description	N-acetyl-alpha-neuraminic acid-(2-3)-2-deoxy-2-fluoro-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	676.6 kDa
Source method src_method	man
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

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

Entity 4 Entity 4 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 5 Entity 5 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	191

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	3f5eA01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	640 — Actin; Chain A, domain 4
Homologous superfamily homologous superfamily	70 —

Domain ID domain_id	3f5eA02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	640 — Actin; Chain A, domain 4
Homologous superfamily homologous superfamily	70 —

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Unit-cell length a length_a	66.325 Å
Unit-cell length b length_b	66.325 Å
Unit-cell length c length_c	172.091 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	8

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	29.660 Å
R factor r_factor	0.1687
R_work r_work	0.1650
R_free r_free	0.2035

Crystal structure of Toxoplasma gondii micronemal protein 1 bound to 2'F-3'SiaLacNAc1-3

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

Micronemal protein 1

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

3f5e__assembly_1__model_1

3f5e__assembly_1__model_1 | I(q)

3f5e__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (2)

Crystal structure of Toxoplasma gondii micronemal protein 1 bound to 2'F-3'SiaLacNAc1-3

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

Micronemal protein 1

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

3f5e__assembly_1__model_1

3f5e__assembly_1__model_1 | I(q)

3f5e__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (2)