5dbn

Crystal structure of AtoDA complex

Method: X-RAY DIFFRACTION

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

Acetate CoA-transferase subunit alpha

Escherichia coli DH5[alpha]

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Acetate CoA-transferase subunit beta × 2 （P76459） PHOSPHATE ION × 2 DI(HYDROXYETHYL)ETHER × 3 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Acetate CoA-transferase subunit beta × 2 （P76459） PHOSPHATE ION × 3 DI(HYDROXYETHYL)ETHER × 2 CHLORIDE ION × 1 GLYCEROL × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ATOD_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–221； UniProt 1–220 Author chain C； PDBConstruct 2–221； UniProt 1–220 Author chain E； PDBConstruct 2–221； UniProt 1–220 Author chain G； PDBConstruct 2–221； UniProt 1–220

Acetate CoA-transferase subunit beta

Escherichia coli DH5[alpha]

UniProt P76459

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Acetate CoA-transferase subunit alpha × 2 （P76458） PHOSPHATE ION × 2 DI(HYDROXYETHYL)ETHER × 3 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Acetate CoA-transferase subunit alpha × 2 （P76458） PHOSPHATE ION × 3 DI(HYDROXYETHYL)ETHER × 2 CHLORIDE ION × 1 GLYCEROL × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ATOA_ECOLI
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–216； UniProt 1–216 Author chain D； PDBConstruct 1–216； UniProt 1–216 Author chain F； PDBConstruct 1–216； UniProt 1–216 Author chain H； PDBConstruct 1–216； UniProt 1–216

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	5dbn
Deposition date deposition_date	2015-08-21
Structure title title	Crystal structure of AtoDA complex
Keywords keywords	protein complex, acetoacetyl-CoA transferase, protein binding, TRANSFERASE; TRANSFERASE
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.

5dbn__assembly_1__model_1

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

Download this curve (.dat)

5dbn__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5dbn__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	29.50 Å
Rg (electron density)	28.63 Å
Total Rg	29.36 Å
Atom count	12723
Residues	855
Excluded volume	113120 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5dbn__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5dbn__assembly_2__model_1`	tetrameric （4）	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 (7)

Entity 1 Entity 1 polymer

Description description	Acetate CoA-transferase subunit alpha
Molecular weight formula_weight	23636.2 kDa
EC 编号 ec_number	2.8.3.8
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E,G
Atom count atom_count	25941

SMKTKLMTLQDATGFFRDGMTIMVGGFMGIGTPSRLVEALLESGVRDLTLIANDTAFVDTGIGPLIVNGRVRKVIASHIGTNPETGRRMISGEMDVVLVPQGTLIEQIRCGGAGLGGFLTPTGVGTVVEEGKQTLTLDGKTWLLERPLRADLALIRAHRCDTLGNLTYQLSARNFNPLIALAADITLVEPDELVETGELQPDHIVTPGAVIDHIIVSQESK

Source Source

Source organism organism	Escherichia coli DH5[alpha]
NCBI taxonomy ID ncbi_taxonomy_id	668369
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Acetate CoA-transferase subunit beta
Molecular weight formula_weight	23914.6 kDa
EC 编号 ec_number	2.8.3.8
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D,F,H

MDAKQRIARRVAQELRDGDIVNLGIGLPTMVANYLPEGIHITLQSENGFLGLGPVTTAHPDLVNAGGQPCGVLPGAAMFDSAMSFALIRGGHIDACVLGGLQVDEEANLANWVVPGKMVPGMGGAMDLVTGSRKVIIAMEHCAKDGSAKILRRCTMPLTAQHAVHMLVTELAVFRFIDGKMWLTEIADGCDLATVRAKTEARFEVAADLNTQRGDLTHHHHHH

Source Source

Source organism organism	Escherichia coli DH5[alpha]
NCBI taxonomy ID ncbi_taxonomy_id	668369
Host organism host_organism	Escherichia coli BL21

Entity 3 Entity 3 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 4 Entity 4 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 5 Entity 5 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	457

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d5dbna_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.124 — NagB/RpiA/CoA transferase-like
Superfamily Superfamily superfamily	c.124.1 — NagB/RpiA/CoA transferase-like
Family Family family	c.124.1.0 — automated matches

Domain ID domain_id	d5dbnc_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.124 — NagB/RpiA/CoA transferase-like
Superfamily Superfamily superfamily	c.124.1 — NagB/RpiA/CoA transferase-like
Family Family family	c.124.1.0 — automated matches

Domain ID domain_id	d5dbne_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.124 — NagB/RpiA/CoA transferase-like
Superfamily Superfamily superfamily	c.124.1 — NagB/RpiA/CoA transferase-like
Family Family family	c.124.1.0 — automated matches

Domain ID domain_id	d5dbng_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.124 — NagB/RpiA/CoA transferase-like
Superfamily Superfamily superfamily	c.124.1 — NagB/RpiA/CoA transferase-like
Family Family family	c.124.1.0 — automated matches

CATH v4.4 (8 domains)

Domain ID domain_id	5dbnA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1080 — Glutaconate Coenzyme A-transferase
Homologous superfamily homologous superfamily	10 — Glutaconate Coenzyme A-transferase

Domain ID domain_id	5dbnB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1080 — Glutaconate Coenzyme A-transferase
Homologous superfamily homologous superfamily	10 — Glutaconate Coenzyme A-transferase

Domain ID domain_id	5dbnC00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1080 — Glutaconate Coenzyme A-transferase
Homologous superfamily homologous superfamily	10 — Glutaconate Coenzyme A-transferase

Domain ID domain_id	5dbnD00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1080 — Glutaconate Coenzyme A-transferase
Homologous superfamily homologous superfamily	10 — Glutaconate Coenzyme A-transferase

Domain ID domain_id	5dbnE00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1080 — Glutaconate Coenzyme A-transferase
Homologous superfamily homologous superfamily	10 — Glutaconate Coenzyme A-transferase

Domain ID domain_id	5dbnF00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1080 — Glutaconate Coenzyme A-transferase
Homologous superfamily homologous superfamily	10 — Glutaconate Coenzyme A-transferase

Domain ID domain_id	5dbnG00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1080 — Glutaconate Coenzyme A-transferase
Homologous superfamily homologous superfamily	10 — Glutaconate Coenzyme A-transferase

Domain ID domain_id	5dbnH00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1080 — Glutaconate Coenzyme A-transferase
Homologous superfamily homologous superfamily	10 — Glutaconate Coenzyme A-transferase

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Unit-cell length a length_a	73.680 Å
Unit-cell length b length_b	175.680 Å
Unit-cell length c length_c	76.160 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	113.01 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	2.549 Å
Low-resolution limit resolution_low	44.323 Å
R factor r_factor	0.1894
R_work r_work	0.1877
R_free r_free	0.2206

Crystal structure of AtoDA complex

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

Acetate CoA-transferase subunit alpha

State in the Current Structure

Other States of the Same Protein in the Database

Acetate CoA-transferase subunit beta

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

5dbn__assembly_1__model_1

5dbn__assembly_1__model_1 | I(q)

5dbn__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Crystal structure of AtoDA complex

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

Acetate CoA-transferase subunit alpha

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Acetate CoA-transferase subunit beta

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

5dbn__assembly_1__model_1

5dbn__assembly_1__model_1 | I(q)

5dbn__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. Citations (1)