SAXSdb — 5my5

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

ABC transporter periplasmic substrate-binding protein

Desulfovibrio alaskensis (strain G20)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	SODIUM ION × 1 CHLORIDE ION × 2 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q316W1_DESAG
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 24–274； UniProt 21–271

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	5my5
Deposition date deposition_date	2017-01-25
Structure title title	Tungstate binding protein - TupA - from Desulfovibrio alaskensis G20
Keywords keywords	;susbtrate binding protein, TupA, tungstate, Desulfovibrio alaskensis G20, ABC transporter, tungsten detection, sulphate reducing bacteria, 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.

5my5__assembly_1__model_1

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

Download this curve (.dat)

5my5__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5my5__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	20.15 Å
Rg (electron density)	19.36 Å
Total Rg	20.19 Å
Atom count	1883
Residues	250
Excluded volume	33761 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5my5__assembly_1__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	ABC transporter periplasmic substrate-binding protein
Molecular weight formula_weight	29697.9 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	2226

MAHHHHHHVDDDDKMLEVLFQGPEAPVLMMATTTSTDNTGLLDDLAPQFTKDTGIELRWTAVGTGKALKMGENCDVDILLVHAPAAEKAFVDAGFGTARTQLMYNDFVIIGPAADPAGVKGMTVAAALGKIAADNAVFVSRGDNSGTHKMEKSLWKQIEGPSPEKEAWYVQTGQGMLRTINVAAEKGGYTMTDRGTYIKYEASMDGNPPLKILVEGDKILFNQYSAIPVNPAHCPKVKKDLADKFVNWMASPATQKTIGDFKLMGKALFTPNAE

Source Source

Source organism organism	Desulfovibrio alaskensis (strain G20)
NCBI taxonomy ID ncbi_taxonomy_id	207559
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

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

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 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	332

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	5my5A01
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

Domain ID domain_id	5my5A02
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	52.323 Å
Unit-cell length b length_b	42.530 Å
Unit-cell length c length_c	54.753 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	95.45 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

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

Resolution resolution	1.400 Å
Low-resolution limit resolution_low	42.530 Å
R factor r_factor	0.1781
R_work r_work	0.1761
R_free r_free	0.2175

Tungstate binding protein - TupA - from Desulfovibrio alaskensis G20

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

ABC transporter 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

5my5__assembly_1__model_1

5my5__assembly_1__model_1 | I(q)

5my5__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) 2 domains

CATH v4.4 (2 domains)

7. Citations (2)

Tungstate binding protein - TupA - from Desulfovibrio alaskensis G20

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

ABC transporter 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

5my5__assembly_1__model_1

5my5__assembly_1__model_1 | I(q)

5my5__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) 2 domains

CATH v4.4 (2 domains)

7. Citations (2)