3dtd

Crystal structure of invasion associated protein b from bartonella henselae

Method: X-RAY DIFFRACTION

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

Invasion-associated protein B

Bartonella henselae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 12	GLYCEROL × 18 water × 12	Consistent with protein count
10	Protein monomer	Monomer	Protein 1	GLYCEROL × 4 water × 1	Consistent with protein count
11	Protein monomer	Monomer	Protein 1	GLYCEROL × 1 water × 1	Consistent with protein count
12	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
13	Protein monomer	Monomer	Protein 1	GLYCEROL × 1 water × 1	Consistent with protein count
14	Protein monomer	Monomer	Protein 1	GLYCEROL × 1 water × 1	Consistent with protein count
15	Protein monomer	Monomer	Protein 1	GLYCEROL × 2 water × 1	Consistent with protein count
16	Protein monomer	Monomer	Protein 1	GLYCEROL × 3 water × 1	Consistent with protein count
17	Protein monomer	Monomer	Protein 1	GLYCEROL × 1 water × 1	Consistent with protein count
18	Protein monomer	Monomer	Protein 1	GLYCEROL × 1 water × 1	Consistent with protein count
19	Protein monomer	Monomer	Protein 1	GLYCEROL × 2 water × 1	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	GLYCEROL × 2 water × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	GLYCEROL × 3 water × 2	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 2	GLYCEROL × 5 water × 2	Consistent with protein count
5	Protein homooligomer	Homooligomer	Protein 2	GLYCEROL × 1 water × 2	Consistent with protein count
6	Protein homooligomer	Homooligomer	Protein 2	GLYCEROL × 4 water × 2	Consistent with protein count
7	Protein homooligomer	Homooligomer	Protein 2	GLYCEROL × 3 water × 2	Consistent with protein count
8	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
9	Protein monomer	Monomer	Protein 1	GLYCEROL × 2 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q6G4Y3_BARHE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–167； UniProt 23–186 Author chain B； PDBConstruct 4–167； UniProt 23–186 Author chain C； PDBConstruct 4–167； UniProt 23–186 Author chain D； PDBConstruct 4–167； UniProt 23–186 Author chain E； PDBConstruct 4–167； UniProt 23–186 Author chain F； PDBConstruct 4–167； UniProt 23–186 Author chain G； PDBConstruct 4–167； UniProt 23–186 Author chain H； PDBConstruct 4–167； UniProt 23–186 Author chain I； PDBConstruct 4–167； UniProt 23–186 Author chain J； PDBConstruct 4–167； UniProt 23–186 Author chain K； PDBConstruct 4–167； UniProt 23–186 Author chain L； PDBConstruct 4–167； UniProt 23–186

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	3dtd
Deposition date deposition_date	2008-07-14
Structure title title	Crystal structure of invasion associated protein b from bartonella henselae
Keywords keywords	;STRUCTURAL GENOMICS, INVASION ASSOCIATED PROTEIN, PSI-2, PROTEIN STRUCTURE INITIATIVE, NEW YORK STRUCTURAL GENOMIX RESEARCH CONSORTIUM, NYSGXRC, UNKNOWN FUNCTION, New York SGX Research Center for Structural Genomics ;; STRUCTURAL GENOMICS, UNKNOWN FUNCTION
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.

3dtd__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3dtd__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3dtd__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	24.21 Å
Rg (electron density)	23.37 Å
Total Rg	24.13 Å
Atom count	2169
Residues	285
Excluded volume	39237 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3dtd__assembly_1__model_1`	dodecameric （12）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3dtd__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3dtd__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3dtd__assembly_4__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`3dtd__assembly_5__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`3dtd__assembly_6__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
7	1	`3dtd__assembly_7__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
8	1	`3dtd__assembly_8__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
9	1	`3dtd__assembly_9__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
10	1	`3dtd__assembly_10__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
11	1	`3dtd__assembly_11__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
12	1	`3dtd__assembly_12__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
13	1	`3dtd__assembly_13__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
14	1	`3dtd__assembly_14__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
15	1	`3dtd__assembly_15__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
16	1	`3dtd__assembly_16__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
17	1	`3dtd__assembly_17__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
18	1	`3dtd__assembly_18__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
19	1	`3dtd__assembly_19__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	Invasion-associated protein B
Molecular weight formula_weight	18841.7 kDa
Source method src_method	man
Copy count entity_count	12

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L
Atom count atom_count	13760

MSLSNSKSTTTKDTVATLPNGASSLTETYGLWSINCGIQEGKKVCFMHRQEVNDQNRVVVAMSVVLNADGVVSGNLTVPFGILVSKPVRLQVDEGKAVIETGIRTCVPAGCIVPIVFDKNYVAALRAGKHLKLAMTIAAPGEPPLNDLFVQLNGFSNALNRLIALQKEGHHHHHH

Source Source

Source organism organism	Bartonella henselae
NCBI taxonomy ID ncbi_taxonomy_id	38323
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	18

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	416

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6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

Domain ID domain_id	3dtdA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1880 — Invasion associated locus B (IalB) protein

Domain ID domain_id	3dtdB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1880 — Invasion associated locus B (IalB) protein

Domain ID domain_id	3dtdC00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1880 — Invasion associated locus B (IalB) protein

Domain ID domain_id	3dtdD00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1880 — Invasion associated locus B (IalB) protein

Domain ID domain_id	3dtdE00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1880 — Invasion associated locus B (IalB) protein

Domain ID domain_id	3dtdF00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1880 — Invasion associated locus B (IalB) protein

Domain ID domain_id	3dtdG00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1880 — Invasion associated locus B (IalB) protein

Domain ID domain_id	3dtdH00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1880 — Invasion associated locus B (IalB) protein

Domain ID domain_id	3dtdI00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1880 — Invasion associated locus B (IalB) protein

Domain ID domain_id	3dtdJ00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1880 — Invasion associated locus B (IalB) protein

Domain ID domain_id	3dtdK00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1880 — Invasion associated locus B (IalB) protein

Domain ID domain_id	3dtdL00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1880 — Invasion associated locus B (IalB) protein

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Unit-cell length a length_a	95.707 Å
Unit-cell length b length_b	139.951 Å
Unit-cell length c length_c	179.075 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	48

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

Resolution resolution	2.350 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2359
R_work r_work	0.2350
R_free r_free	0.2652

Crystal structure of invasion associated protein b from bartonella henselae

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

Invasion-associated protein B

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

3dtd__assembly_2__model_1

3dtd__assembly_2__model_1 | I(q)

3dtd__assembly_2__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) 12 domains

CATH v4.4 (12 domains)

7. Citations (1)

Crystal structure of invasion associated protein b from bartonella henselae

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

Invasion-associated protein B

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

3dtd__assembly_2__model_1

3dtd__assembly_2__model_1 | I(q)

3dtd__assembly_2__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) 12 domains

CATH v4.4 (12 domains)

7. Citations (1)