SAXSdb — 3ve2

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

Transferrin-binding protein 2

Neisseria meningitidis serogroup B

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	GLYCEROL × 22 SULFATE ION × 14 ACETATE ION × 2 SODIUM ION × 2 water × 4	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 4	GLYCEROL × 22 SULFATE ION × 14 ACETATE ION × 2 SODIUM ION × 2 water × 4	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	GLYCEROL × 11 SULFATE ION × 7 ACETATE ION × 1 SODIUM ION × 1 water × 2	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	GLYCEROL × 6 SULFATE ION × 1 ACETATE ION × 1 water × 1	Consistent with protein count
5	Protein monomer	Monomer	Protein 1	GLYCEROL × 5 SULFATE ION × 6 SODIUM ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TBB1_NEIMB
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–658； UniProt 56–711 Author chain B； PDBConstruct 3–658； UniProt 56–711

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	3ve2
Deposition date deposition_date	2012-01-06
Structure title title	The 2.1 angstrom crystal structure of Transferrin binding protein B (TbpB) from serogroup B M982 Neisseria meningitidis
Keywords keywords	;Lipoprotein, transferrin receptor, iron acquisition, vaccine candidate, host pathogen interaction, Beta barrel, Receptor, Transferrin, Outermembrane, Transferrin-binding protein ;; Transferrin-binding 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.

3ve2__assembly_1__model_1

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

Download this curve (.dat)

3ve2__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3ve2__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	52.58 Å
Rg (electron density)	52.98 Å
Total Rg	52.97 Å
Atom count	16456
Residues	2066
Excluded volume	289250 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3ve2__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3ve2__assembly_2__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3ve2__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3ve2__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`3ve2__assembly_5__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	Transferrin-binding protein 2
Molecular weight formula_weight	71406.7 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	8868

GSKDQGGYGFAMRLKRRNWYPGAEESEVKLNESDWEATGLPTKPKELPKRQKSVIEKVETDGDSDIYSSPYLTPSNHQNGSAGNGVNQPKNQATGHENFQYVYSGWFYKHAASEKDFSNKKIKSGDDGYIFYHGEKPSRQLPASGKVIYKGVWHFVTDTKKGQDFREIIQPSKKQGDRYSGFSGDGSEEYSNKNESTLKDDHEGYGFTSNLEVDFGNKKLTGKLIRNNASLNNNTNNDKHTTQYYSLDAQITGNRFNGTATATDKKENETKLHPFVSDSSSLSGGFFGPQGEELGFRFLSDDQKVAVVGSAKTKDKLENGAAASGSTGAAASGGAAGTSSENSKLTTVLDAVELTLNDKKIKNLDNFSNAAQLVVDGIMIPLLPKDSESGNTQADKGKNGGTEFTRKFEHTPESDKKDAQAGTQTNGAQTASNTAGDTNGKTKTYEVEVCCSNLNYLKYGMLTRKNSKSAMQAGGNSSQADAKTEQVEQSMFLQGERTDEKEIPTDQNVVYRGSWYGHIANGTSWSGNASDKEGGNRAEFTVNFADKKITGKLTAENRQAQTFTIEGMIQGNGFEGTAKTAESGFDLDQKNTTRTPKAYITDAKVKGGFYGPKAEELGGWFAYPGDKQTEKATATSSDGNSASSATVVFGAKRQQPVQ

Source Source

Source organism organism	Neisseria meningitidis serogroup B
NCBI taxonomy ID ncbi_taxonomy_id	491
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	11

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	7

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	1

Entity 5 Entity 5 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	618

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6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id	3ve2A01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	128 — Lipocalin
Homologous superfamily homologous superfamily	250 —

Domain ID domain_id	3ve2A02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	160 — Porin
Homologous superfamily homologous superfamily	90 —

Domain ID domain_id	3ve2A03
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	128 — Lipocalin
Homologous superfamily homologous superfamily	240 —

Domain ID domain_id	3ve2A04
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	160 — Porin
Homologous superfamily homologous superfamily	90 —

Domain ID domain_id	3ve2B01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	128 — Lipocalin
Homologous superfamily homologous superfamily	250 —

Domain ID domain_id	3ve2B02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	160 — Porin
Homologous superfamily homologous superfamily	90 —

Domain ID domain_id	3ve2B03
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	128 — Lipocalin
Homologous superfamily homologous superfamily	240 —

Domain ID domain_id	3ve2B04
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	160 — Porin
Homologous superfamily homologous superfamily	90 —

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Unit-cell length a length_a	46.604 Å
Unit-cell length b length_b	149.336 Å
Unit-cell length c length_c	199.600 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 2 2 21
Space-group number int_tables_number	17
Crystal system crystal_system	—

Resolution resolution	2.140 Å
Low-resolution limit resolution_low	45.383 Å
R factor r_factor	0.1723
R_work r_work	0.1713
R_free r_free	0.2091

The 2.1 angstrom crystal structure of Transferrin binding protein B (TbpB) from serogroup B M982 Neisseria meningitidis

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

Transferrin-binding protein 2

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

3ve2__assembly_1__model_1

3ve2__assembly_1__model_1 | I(q)

3ve2__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 non-polymer

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) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)

The 2.1 angstrom crystal structure of Transferrin binding protein B (TbpB) from serogroup B M982 Neisseria meningitidis

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

Transferrin-binding protein 2

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

3ve2__assembly_1__model_1

3ve2__assembly_1__model_1 | I(q)

3ve2__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 non-polymer

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) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)