SAXSdb — 6b21

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

Ammonia channel

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 3	;[(2R,5R,11R,14S,24E)-14-[(acetyloxy)methyl]-8-{[5-(3,5-dimethyl-1H-pyrrol-2-yl-kappaN)-5-(3,5-dimethyl-2H-pyrrol-2-ylidene-kappaN)pentanoyl]oxy}-5,11-dihydroxy-2-{[(9E)-octadec-9-enoyl]oxy}-5,11,16-trioxo-4,6,10,12,15-pentaoxa-5lambda~5~,11lambda~5~-diphosphatritriacont-24-en-1-yl (9E)-octadec-9-enoatato](difluoro)boron ; × 3 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	AMTB_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–406； UniProt 26–428

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	6b21
Deposition date deposition_date	2017-09-19
Structure title title	Crystal structure of AmtB from E. coli bound to TopFluor cardiolipin
Keywords keywords	ammonia channel, AmtB, cardiolipin, transporter, MEMBRANE PROTEIN; MEMBRANE 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.

6b21__assembly_1__model_1

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

Download this curve (.dat)

6b21__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6b21__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	29.09 Å
Rg (electron density)	28.34 Å
Total Rg	29.34 Å
Atom count	8265
Residues	1107
Excluded volume	152030 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6b21__assembly_1__model_1`	trimeric （3）	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 (3)

Entity 1 Entity 1 polymer

Description description	Ammonia channel
Molecular weight formula_weight	42303.5 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	2832

GASVADKADNAFMMICTALVLFMTIPGIALFYGGLIRGKNVLSMLTQVTVTFALVCILWVVYGYSLAFGEGNNFFGNINWLMLKNIELTAVMGSIYQYIHVAFQGSFACITVGLIVGALAERIRFSAVLIFVVVWLTLSYIPIAHMVWGGGLLASHGALDFAGGTVVHINAAIAGLVGAYLIGKRVGFGKEAFKPHNLPMVFTGTAILYIGWFGFNAGSAGTANEIAALAFVNTVVATAAAILGWIFGEWALRGKPSLLGACSGAIAGLVGVTPACGYIGVGGALIIGVVAGLAGLWGVTMLKRLLRVDDPCDVFGVHGVCGIVGCIMTGIFAASSLGGVGFAEGVTMGHQLLVQLESIAITIVWSGVVAFIGYKLADLTVGLRVPEEQEREGLDVNSHGENAYNA

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	;[(2R,5R,11R,14S,24E)-14-[(acetyloxy)methyl]-8-{[5-(3,5-dimethyl-1H-pyrrol-2-yl-kappaN)-5-(3,5-dimethyl-2H-pyrrol-2-ylidene-kappaN)pentanoyl]oxy}-5,11-dihydroxy-2-{[(9E)-octadec-9-enoyl]oxy}-5,11,16-trioxo-4,6,10,12,15-pentaoxa-5lambda~5~,11lambda~5~-diphosphatritriacont-24-en-1-yl (9E)-octadec-9-enoatato](difluoro)boron ;
Molecular weight formula_weight	1551.7 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	77

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6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d6b21a1
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.44 — Ammonium transporter
Superfamily Superfamily superfamily	f.44.1 — Ammonium transporter
Family Family family	f.44.1.0 — automated matches

Domain ID domain_id	d6b21a2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id	6b21A00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3430 — Ammonium transporter fold
Homologous superfamily homologous superfamily	10 — Ammonium transporter AmtB like domains

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Unit-cell length a length_a	138.780 Å
Unit-cell length b length_b	138.780 Å
Unit-cell length c length_c	159.140 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	18

Space group space_group	H 3 2
Space-group number int_tables_number	155
Crystal system crystal_system	—

Resolution resolution	2.450 Å
Low-resolution limit resolution_low	56.219 Å
R factor r_factor	0.1719
R_work r_work	0.1699
R_free r_free	0.2125

Crystal structure of AmtB from E. coli bound to TopFluor cardiolipin

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

Ammonia channel

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

6b21__assembly_1__model_1

6b21__assembly_1__model_1 | I(q)

6b21__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

CATH v4.4 (1 domains)

7. Citations (1)

Crystal structure of AmtB from E. coli bound to TopFluor cardiolipin

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

Ammonia channel

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

6b21__assembly_1__model_1

6b21__assembly_1__model_1 | I(q)

6b21__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

CATH v4.4 (1 domains)

7. Citations (1)