SAXSdb — 2dvz

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

Putative exported protein

Bordetella pertussis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	CADMIUM ION × 5 GLUTAMIC ACID × 1 water × 1	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	CADMIUM ION × 10 GLUTAMIC ACID × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q7W0A0_BORPE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 13–314； UniProt 26–327

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	2dvz
Deposition date deposition_date	2006-08-01
Structure title title	Structure of a periplasmic transporter
Keywords keywords	periplamsic binding proteins, carboxylate binding, glutamate, Bordetella, TRANSPORT PROTEIN; TRANSPORT 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.

2dvz__assembly_2__model_1

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

Download this curve (.dat)

2dvz__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2dvz__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	29.76 Å
Rg (electron density)	29.41 Å
Total Rg	29.77 Å
Atom count	4526
Residues	584
Excluded volume	81562 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2dvz__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2dvz__assembly_2__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	Putative exported protein
Molecular weight formula_weight	33942.4 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	2465

MRGSHHHHHHGSADAYPSKAIRVIVPFAPGGSTDIIARLVTQRMSQELGQPMVVENKGGAGGAIGASEAARAEPDGYTLSIATVSTMAVNPACRPKDLPYDPIKDFQPVTNFANTANVVAVNPKFPAKDFKGFLEELKKNPGKYSYGSSGTCGVLHLMGESFKMATGTDIVHVPYKGSGPAVADAVGGQIELIFDNLPSSMPQIQAGKLRAMAIAWPTRIDAIKDVPTFADAGFPVLNQPVWYGLLAPKGTPMDVVNKLRDAAVVALKDPKVIKALDDQGSAPSGNTPEEFAKEIKEQYDWAQDVVKKQNIKLD

Source Source

Source organism organism	Bordetella pertussis
NCBI taxonomy ID ncbi_taxonomy_id	520
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	CADMIUM ION
Molecular weight formula_weight	112.4 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 3 Entity 3 non-polymer

Description description	GLUTAMIC ACID
Molecular weight formula_weight	147.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	202

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	2dvzA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily	150 — Bordetella uptake gene, domain 1

Domain ID domain_id	2dvzA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily	10 — Periplasmic binding protein-like II

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Unit-cell length a length_a	53.829 Å
Unit-cell length b length_b	53.829 Å
Unit-cell length c length_c	422.660 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 65 2 2
Space-group number int_tables_number	179
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	15.000 Å
R factor r_factor	0.1801
R_work r_work	0.1763
R_free r_free	0.2492

Structure of a periplasmic transporter

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

Putative exported protein

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

2dvz__assembly_2__model_1

2dvz__assembly_2__model_1 | I(q)

2dvz__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 (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) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Structure of a periplasmic transporter

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

Putative exported protein

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

2dvz__assembly_2__model_1

2dvz__assembly_2__model_1 | I(q)

2dvz__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 (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) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)