SAXSdb — 2vpo

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

PERIPLASMIC SUBSTRATE BINDING PROTEIN

HALOMONAS ELONGATA

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	(4S,5S)-5-HYDROXY-2-METHYL-1,4,5,6-TETRAHYDROPYRIMIDINE-4-CARBOXYLIC ACID × 1 MAGNESIUM ION × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	(4S,5S)-5-HYDROXY-2-METHYL-1,4,5,6-TETRAHYDROPYRIMIDINE-4-CARBOXYLIC ACID × 1 MAGNESIUM ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8VPB3_HALEL
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–316； UniProt 26–341 Author chain B； PDBConstruct 1–316； UniProt 26–341

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	2vpo
Deposition date deposition_date	2008-03-03
Structure title title	High resolution structure of the periplasmic binding protein TeaA from TeaABC TRAP transporter of Halomonas elongata in complex with hydroxyectoine
Keywords keywords	SBP, ECTOINE, HYDROXYECTOINE, TRAP TRANSPORTER, PERIPLASMIC BINDING PROTEIN, TRANSPORT; TRANSPORT
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.

2vpo__assembly_1__model_1

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

Download this curve (.dat)

2vpo__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2vpo__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	20.46 Å
Rg (electron density)	19.05 Å
Total Rg	19.94 Å
Atom count	2466
Residues	307
Excluded volume	43488 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2vpo__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2vpo__assembly_2__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 (4)

Entity 1 Entity 1 polymer

Description description	PERIPLASMIC SUBSTRATE BINDING PROTEIN
Molecular weight formula_weight	35713.2 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	5292

DNWRYAHEEYEGDVQDVFAQAFKGYVEDNSDHTVQVYRFGELGESDDIMEQTQNGILQFVNQSPGFTGSLIPSAQIFFIPYLMPTDMDTVLEFFDESKAINEMFPKLYAEHGLELLKMYPEGEMVVTADEPITSPEDFDNKKIRTMTNPLLAETYKAFGATPTPLPWGEVYGGLQTGIIDGQENPIFWIESGGLYEVSPNLTFTSHGWFTTAMMANQDFYEGLSEEDQQLVQDAADAAYDHTIEHIKGLSEESLEKIKAASDEVTVTRLNDEQIQAFKERAPQVEEKFIEMTGEQGQELLDQFKADLKAVQSESEG

Source Source

Source organism organism	HALOMONAS ELONGATA
NCBI taxonomy ID ncbi_taxonomy_id	2746
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	(4S,5S)-5-HYDROXY-2-METHYL-1,4,5,6-TETRAHYDROPYRIMIDINE-4-CARBOXYLIC ACID
Molecular weight formula_weight	158.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 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	303

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2vpoa_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.94 — Periplasmic binding protein-like II
Superfamily Superfamily superfamily	c.94.1 — Periplasmic binding protein-like II
Family Family family	c.94.1.0 — automated matches

Domain ID domain_id	d2vpob_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.94 — Periplasmic binding protein-like II
Superfamily Superfamily superfamily	c.94.1 — Periplasmic binding protein-like II
Family Family family	c.94.1.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id	2vpoA00
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	170 — Bacterial extracellular solute-binding protein, family 7

Domain ID domain_id	2vpoB00
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	170 — Bacterial extracellular solute-binding protein, family 7

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Unit-cell length a length_a	48.600 Å
Unit-cell length b length_b	52.100 Å
Unit-cell length c length_c	63.700 Å
Unit-cell angle α angle_alpha	80.80 °
Unit-cell angle β angle_beta	85.70 °
Unit-cell angle γ angle_gamma	78.00 °
Molecules per unit cell Z z_pdb	2

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

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	19.820 Å
R factor r_factor	0.1820
R_work r_work	0.1790
R_free r_free	0.2250

High resolution structure of the periplasmic binding protein TeaA from TeaABC TRAP transporter of Halomonas elongata in complex with hydroxyectoine

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

PERIPLASMIC SUBSTRATE BINDING 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

2vpo__assembly_1__model_1

2vpo__assembly_1__model_1 | I(q)

2vpo__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 (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)

High resolution structure of the periplasmic binding protein TeaA from TeaABC TRAP transporter of Halomonas elongata in complex with hydroxyectoine

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

PERIPLASMIC SUBSTRATE BINDING 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

2vpo__assembly_1__model_1

2vpo__assembly_1__model_1 | I(q)

2vpo__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 (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)