SAXSdb — 3r9v

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

Invasin ipaD

Shigella flexneri

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	GLYCEROL × 3 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	(3ALPHA,5BETA,12ALPHA)-3,12-DIHYDROXYCHOLAN-24-OIC ACID × 2 water × 1	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	GLYCEROL × 3 (3ALPHA,5BETA,12ALPHA)-3,12-DIHYDROXYCHOLAN-24-OIC ACID × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	IPAD_SHIFL
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–286； UniProt 39–322 Author chain B； PDBConstruct 3–286； UniProt 39–322

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	3r9v
Deposition date deposition_date	2011-03-26
Structure title title	Cocrystal Structure of Proteolytically Truncated Form of IpaD from Shigella flexneri Bound to Deoxycholate
Keywords keywords	type III secretion system, tip protein, deoxycholate, CELL INVASION; CELL INVASION
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.

3r9v__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3r9v__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3r9v__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	28.66 Å
Rg (electron density)	27.64 Å
Total Rg	28.33 Å
Atom count	2897
Residues	361
Excluded volume	51648 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3r9v__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3r9v__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3r9v__assembly_3__model_1`	dimeric （2）	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 (4)

Entity 1 Entity 1 polymer

Description description	Invasin ipaD
Molecular weight formula_weight	31659.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3123

GSHPVSSLTMLNDTLHNIRTTNQALKKELSQKTLTKTSLEEIALHSSQISMDVNKSAQLLDILSRNEYPINKDARELLHSAPKEAELDGDQMISHRELWAKIANSINDINEQYLKVYEHAVSSYTQMYQDFSAVLSSLAGWISPGGNDGNSVKLQVNSLKKALEELKEKYKDKPLYPANNTVSQEQANKWLTELGGTIGKVSQKNGGYVVSINMTPIDNMLKSLDNLGGNGEVVLDNAKYQAWNAGFSAEDETMKNNLQTLVQKYSNANSIFDNLVKVLSSTISSS

Source Source

Source organism organism	Shigella flexneri
NCBI taxonomy ID ncbi_taxonomy_id	623
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

Description description	(3ALPHA,5BETA,12ALPHA)-3,12-DIHYDROXYCHOLAN-24-OIC ACID
Molecular weight formula_weight	392.6 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	226

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3r9va_
Class class	a — All alpha proteins
Fold Fold fold	a.250 — IpaD-like
Superfamily Superfamily superfamily	a.250.1 — IpaD-like
Family Family family	a.250.1.1 — IpaD-like

Domain ID domain_id	d3r9vb_
Class class	a — All alpha proteins
Fold Fold fold	a.250 — IpaD-like
Superfamily Superfamily superfamily	a.250.1 — IpaD-like
Family Family family	a.250.1.1 — IpaD-like

CATH v4.4 (2 domains)

Domain ID domain_id	3r9vA00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1710 — IpaD-like
Homologous superfamily homologous superfamily	10 — IpaD-like

Domain ID domain_id	3r9vB00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1710 — IpaD-like
Homologous superfamily homologous superfamily	10 — IpaD-like

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Unit-cell length a length_a	62.974 Å
Unit-cell length b length_b	43.719 Å
Unit-cell length c length_c	93.757 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	97.42 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	25.283 Å
R factor r_factor	0.2287
R_work r_work	0.2276
R_free r_free	0.2482

Cocrystal Structure of Proteolytically Truncated Form of IpaD from Shigella flexneri Bound to Deoxycholate

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

Invasin ipaD

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

3r9v__assembly_3__model_1

3r9v__assembly_3__model_1 | I(q)

3r9v__assembly_3__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Cocrystal Structure of Proteolytically Truncated Form of IpaD from Shigella flexneri Bound to Deoxycholate

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

Invasin ipaD

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

3r9v__assembly_3__model_1

3r9v__assembly_3__model_1 | I(q)

3r9v__assembly_3__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)