2yvx

Crystal structure of magnesium transporter MgtE

Method: X-RAY DIFFRACTION

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

Mg2+ transporter MgtE

Thermus thermophilus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	MAGNESIUM ION × 9	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	MAGNESIUM ION × 9	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q5SMG8_THET8
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 24–473； UniProt 1–450 Author chain B； PDBConstruct 24–473； UniProt 1–450 Author chain C； PDBConstruct 24–473； UniProt 1–450 Author chain D； PDBConstruct 24–473； UniProt 1–450

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	2yvx
Deposition date deposition_date	2007-04-18
Structure title title	Crystal structure of magnesium transporter MgtE
Keywords keywords	membrane protein, 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.

2yvx__assembly_1__model_1

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

Download this curve (.dat)

2yvx__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2yvx__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	31.63 Å
Rg (electron density)	31.29 Å
Total Rg	31.96 Å
Atom count	6949
Residues	884
Excluded volume	125780 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2yvx__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2yvx__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 (2)

Entity 1 Entity 1 polymer

Description description	Mg2+ transporter MgtE
Molecular weight formula_weight	52491.5 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	13898

MGSSHHHHHHSSGLGVLPGGPLHMEEKLAVSLQEALQEGDTRALREVLEEIHPQDLLALWDELKGEHRYVVLTLLPKAKAAEVLSHLSPEEQAEYLKTLPPWRLREILEELSLDDLADALQAVRKEDPAYFQRLKDLLDPRTRAEVEALARYEEDEAGGLMTPEYVAVREGMTVEEVLRFLRRAAPDAETIYYIYVVDEKGRLKGVLSLRDLIVADPRTRVAEIMNPKVVYVRTDTDQEEVARLMADYDFTVLPVVDEEGRLVGIVTVDDVLDVLEAEATEDIHKLGAVDVPDLVYSEAGPVALWLARVRWLVILILTGMVTSSILQGFESVLEAVTALAFYVPVLLGTGGNTGNQSATLIIRALATRDLDLRDWRRVFLKEMGVGLLLGLTLSFLLVGKVYWDGHPLLLPVVGVSLVLIVFFANLVGAMLPFLLRRLGVDPALVSNPLVATLSDVTGLLIYLSVARLLLEAV

Source Source

Source organism organism	Thermus thermophilus
NCBI taxonomy ID ncbi_taxonomy_id	300852
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	18

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6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d2yvxa1
Class class	a — All alpha proteins
Fold Fold fold	a.118 — alpha-alpha superhelix
Superfamily Superfamily superfamily	a.118.26 — MgtE N-terminal domain-like
Family Family family	a.118.26.1 — MgtE N-terminal domain-like

Domain ID domain_id	d2yvxa2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.37 — CBS-domain pair
Superfamily Superfamily superfamily	d.37.1 — CBS-domain pair
Family Family family	d.37.1.1 — CBS-domain pair

Domain ID domain_id	d2yvxa3
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.57 — MgtE membrane domain-like
Superfamily Superfamily superfamily	f.57.1 — MgtE membrane domain-like
Family Family family	f.57.1.1 — MgtE membrane domain-like

Domain ID domain_id	d2yvxb1
Class class	a — All alpha proteins
Fold Fold fold	a.118 — alpha-alpha superhelix
Superfamily Superfamily superfamily	a.118.26 — MgtE N-terminal domain-like
Family Family family	a.118.26.1 — MgtE N-terminal domain-like

Domain ID domain_id	d2yvxb2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.37 — CBS-domain pair
Superfamily Superfamily superfamily	d.37.1 — CBS-domain pair
Family Family family	d.37.1.1 — CBS-domain pair

Domain ID domain_id	d2yvxb3
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.57 — MgtE membrane domain-like
Superfamily Superfamily superfamily	f.57.1 — MgtE membrane domain-like
Family Family family	f.57.1.1 — MgtE membrane domain-like

Domain ID domain_id	d2yvxc1
Class class	a — All alpha proteins
Fold Fold fold	a.118 — alpha-alpha superhelix
Superfamily Superfamily superfamily	a.118.26 — MgtE N-terminal domain-like
Family Family family	a.118.26.1 — MgtE N-terminal domain-like

Domain ID domain_id	d2yvxc2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.37 — CBS-domain pair
Superfamily Superfamily superfamily	d.37.1 — CBS-domain pair
Family Family family	d.37.1.1 — CBS-domain pair

Domain ID domain_id	d2yvxc3
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.57 — MgtE membrane domain-like
Superfamily Superfamily superfamily	f.57.1 — MgtE membrane domain-like
Family Family family	f.57.1.1 — MgtE membrane domain-like

Domain ID domain_id	d2yvxd1
Class class	a — All alpha proteins
Fold Fold fold	a.118 — alpha-alpha superhelix
Superfamily Superfamily superfamily	a.118.26 — MgtE N-terminal domain-like
Family Family family	a.118.26.1 — MgtE N-terminal domain-like

Domain ID domain_id	d2yvxd2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.37 — CBS-domain pair
Superfamily Superfamily superfamily	d.37.1 — CBS-domain pair
Family Family family	d.37.1.1 — CBS-domain pair

Domain ID domain_id	d2yvxd3
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.57 — MgtE membrane domain-like
Superfamily Superfamily superfamily	f.57.1 — MgtE membrane domain-like
Family Family family	f.57.1.1 — MgtE membrane domain-like

CATH v4.4 (12 domains)

Domain ID domain_id	2yvxA01
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	60 — MgtE N-terminal fold
Homologous superfamily homologous superfamily	10 — MgtE N-terminal domain-like

Domain ID domain_id	2yvxA02
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	580 — CBS-domain
Homologous superfamily homologous superfamily	10 — CBS-domain

Domain ID domain_id	2yvxA03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	357 — Tetracycline Repressor; domain 2
Homologous superfamily homologous superfamily	20 — SLC41 divalent cation transporters, integral membrane domain

Domain ID domain_id	2yvxB01
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	60 — MgtE N-terminal fold
Homologous superfamily homologous superfamily	10 — MgtE N-terminal domain-like

Domain ID domain_id	2yvxB02
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	580 — CBS-domain
Homologous superfamily homologous superfamily	10 — CBS-domain

Domain ID domain_id	2yvxB03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	357 — Tetracycline Repressor; domain 2
Homologous superfamily homologous superfamily	20 — SLC41 divalent cation transporters, integral membrane domain

Domain ID domain_id	2yvxC01
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	60 — MgtE N-terminal fold
Homologous superfamily homologous superfamily	10 — MgtE N-terminal domain-like

Domain ID domain_id	2yvxC02
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	580 — CBS-domain
Homologous superfamily homologous superfamily	10 — CBS-domain

Domain ID domain_id	2yvxC03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	357 — Tetracycline Repressor; domain 2
Homologous superfamily homologous superfamily	20 — SLC41 divalent cation transporters, integral membrane domain

Domain ID domain_id	2yvxD01
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	60 — MgtE N-terminal fold
Homologous superfamily homologous superfamily	10 — MgtE N-terminal domain-like

Domain ID domain_id	2yvxD02
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	580 — CBS-domain
Homologous superfamily homologous superfamily	10 — CBS-domain

Domain ID domain_id	2yvxD03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	357 — Tetracycline Repressor; domain 2
Homologous superfamily homologous superfamily	20 — SLC41 divalent cation transporters, integral membrane domain

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Unit-cell length a length_a	118.314 Å
Unit-cell length b length_b	134.897 Å
Unit-cell length c length_c	366.252 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	32

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	3.500 Å
Low-resolution limit resolution_low	49.690 Å
R factor r_factor	0.2940
R_work r_work	0.2940
R_free r_free	0.3410

Crystal structure of magnesium transporter MgtE

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

Mg2+ transporter MgtE

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

2yvx__assembly_1__model_1

2yvx__assembly_1__model_1 | I(q)

2yvx__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

7. Citations (1)

Crystal structure of magnesium transporter MgtE

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

Mg2+ transporter MgtE

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

2yvx__assembly_1__model_1

2yvx__assembly_1__model_1 | I(q)

2yvx__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

7. Citations (1)