SAXSdb — 3cdk

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

Succinyl-CoA:3-ketoacid-coenzyme A transferase subunit A

Bacillus subtilis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Succinyl-CoA:3-ketoacid-coenzyme A transferase subunit B × 2 （P42316） water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SCOA_BACSU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–241； UniProt 1–238 Author chain C； PDBConstruct 4–241； UniProt 1–238

Succinyl-CoA:3-ketoacid-coenzyme A transferase subunit B

Bacillus subtilis

UniProt P42316

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Succinyl-CoA:3-ketoacid-coenzyme A transferase subunit A × 2 （P42315） water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SCOB_BACSU
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 4–219； UniProt 1–216 Author chain D； PDBConstruct 4–219； 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	3cdk
Deposition date deposition_date	2008-02-27
Structure title title	Crystal structure of the co-expressed succinyl-CoA transferase A and B complex from Bacillus subtilis
Keywords keywords	;CO-EXPRESSED COMPLEX, HETERO-TETRAMER, Structural Genomics, PSI-2, Protein Structure Initiative, Midwest Center for Structural Genomics, MCSG, 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.

3cdk__assembly_1__model_1

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

Download this curve (.dat)

3cdk__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3cdk__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	29.34 Å
Rg (electron density)	28.61 Å
Total Rg	29.43 Å
Atom count	6554
Residues	870
Excluded volume	117340 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3cdk__assembly_1__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 (3)

Entity 1 Entity 1 polymer

Description description	Succinyl-CoA:3-ketoacid-coenzyme A transferase subunit A
Molecular weight formula_weight	25704.4 kDa
EC 编号 ec_number	2.8.3.5
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	6720

SNAMGKVLSSSKEAAKLIHDGDTLIAGGFGLCGIPEQLILSIRDQGVKDLTVVSNNCGVDDWGLGLLLANKQIKKMIASYVGENKIFERQFLSGELEVELVPQGTLAERIRAGGAGIPGFYTATGVGTSIAEGKEHKTFGGRTYVLERGITGDVAIVKAWKADTMGNLIFRKTARNFNPIAAMAGKITIAEAEEIVEAGELDPDHIHTPGIYVQHVVLGASQEKRIEKRTVQQASGKGEAK

Source Source

Source organism organism	Bacillus subtilis
NCBI taxonomy ID ncbi_taxonomy_id	1423
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Succinyl-CoA:3-ketoacid-coenzyme A transferase subunit B
Molecular weight formula_weight	23629.1 kDa
EC 编号 ec_number	2.8.3.5
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

SNAMKEARKRMVKRAVQEIKDGMNVNLGIGMPTLVANEIPDGVHVMLQSENGLLGIGPYPLEGTEDADLINAGKETITEVTGASYFDSAESFAMIRGGHIDLAILGGMEVSEQGDLANWMIPGKMVKGMGGAMDLVNGAKRIVVIMEHVNKHGESKVKKTCSLPLTGQKVVHRLITDLAVFDFVNGRMTLTELQDGVTIEEVYEKTEADFAVSQSVLNS

Source Source

Source organism organism	Bacillus subtilis
NCBI taxonomy ID ncbi_taxonomy_id	1423
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	115

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3cdka_
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	d3cdkc_
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 (4 domains)

Domain ID domain_id	3cdkA01
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	3cdkB00
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	3cdkC01
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	3cdkD00
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	69.337 Å
Unit-cell length b length_b	70.404 Å
Unit-cell length c length_c	97.996 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	106.31 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 2 1
Space-group number int_tables_number	3
Crystal system crystal_system	—

Resolution resolution	2.590 Å
Low-resolution limit resolution_low	48.300 Å
R factor r_factor	0.1956
R_work r_work	0.1926
R_free r_free	0.2528

Crystal structure of the co-expressed succinyl-CoA transferase A and B complex from Bacillus subtilis

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

Succinyl-CoA:3-ketoacid-coenzyme A transferase subunit A

State in the Current Structure

Other States of the Same Protein in the Database

Succinyl-CoA:3-ketoacid-coenzyme A transferase subunit B

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

3cdk__assembly_1__model_1

3cdk__assembly_1__model_1 | I(q)

3cdk__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of the co-expressed succinyl-CoA transferase A and B complex from Bacillus subtilis

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

Succinyl-CoA:3-ketoacid-coenzyme A transferase subunit A

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Succinyl-CoA:3-ketoacid-coenzyme A transferase subunit B

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

3cdk__assembly_1__model_1

3cdk__assembly_1__model_1 | I(q)

3cdk__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)