SAXSdb — 3gf3

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

Glutaconyl-CoA decarboxylase subunit A

Clostridium symbiosum

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	CROTONYL COENZYME A × 4 CHLORIDE ION × 4 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	B7TVP1_CLOSY
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–588； UniProt 1–588

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	3gf3
Deposition date deposition_date	2009-02-26
Structure title title	Glutaconyl-coA decarboxylase A subunit from Clostridium symbiosum co-crystallized with glutaconyl-coA
Keywords keywords	glutaconyl-CoA decarboxylase, sodium ion transport, biotin, glutamate fermentation, LYASE; LYASE
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.

3gf3__assembly_1__model_1

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

Download this curve (.dat)

3gf3__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3gf3__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	37.58 Å
Rg (electron density)	36.53 Å
Total Rg	37.18 Å
Atom count	17600
Residues	2252
Excluded volume	313330 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3gf3__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 (4)

Entity 1 Entity 1 polymer

Description description	Glutaconyl-CoA decarboxylase subunit A
Molecular weight formula_weight	65024.0 kDa
EC 编号 ec_number	4.1.1.70
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	4865

MNMYSMPGYFQNMPTIGKELVNPNPENEQEIKAVESDIHESIKKALDAGITSEEKLNERGQLSAMQRINALIDPGTWCPLNSLFNPENNKFGTTNIVNGLGRVDGKWVYIVASDNKKMAGAWVPGQAENLIRCSDAAKMMHLPLIYLLNCSGVEFPNQDKVYPNRRGGGTPFFRNSELNQLGIPVIVGIYGTNPAGGGYHSISPTILIAHQDANMAVGGAGILSGMNPKGYIDDEAAEQIIAAQIENSKLKVPAPGSVPIHYDETGFFREVYQNDLGVIDGIKKYISYLPAYNLEFFRVDTPKAPQLPAEDLYSIIPMNQKRPYDIYEVIARLFDNSEFSEYKKGYGPEMVTGLAKVNGLLVGVIANVQGLLMNYPEYKQNSVGIGGKLYRQGLIKMNEFVTLCARDRIPLIWLQDTTGIDVGDEAEKAELLGLGQSLIYSIENSKLPSLEITIRKASAAAHYVLGGPQGNNTNVFSIGTGACEYYVMPGETAANAMYSRKLVKAKKAGEDLQPIIGKMNDMIQMYTDKSRPKYCTEKGMVDEIVDMTEVRPYIQAFTEAAYQNPQSICPMHQMLTPRSTREFETFGK

Source Source

Source organism organism	Clostridium symbiosum
NCBI taxonomy ID ncbi_taxonomy_id	1512
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	CROTONYL COENZYME A
Molecular weight formula_weight	835.6 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	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	465

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6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3gf3a1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.14 — ClpP/crotonase
Superfamily Superfamily superfamily	c.14.1 — ClpP/crotonase
Family Family family	c.14.1.4 — Biotin dependent carboxylase carboxyltransferase domain

Domain ID domain_id	d3gf3a2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.14 — ClpP/crotonase
Superfamily Superfamily superfamily	c.14.1 — ClpP/crotonase
Family Family family	c.14.1.4 — Biotin dependent carboxylase carboxyltransferase domain

CATH v4.4 (3 domains)

Domain ID domain_id	3gf3A01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	680 — Single Helix bin

Domain ID domain_id	3gf3A02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — 2-enoyl-CoA Hydratase; Chain A, domain 1

Domain ID domain_id	3gf3A03
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — 2-enoyl-CoA Hydratase; Chain A, domain 1

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Unit-cell length a length_a	102.360 Å
Unit-cell length b length_b	144.360 Å
Unit-cell length c length_c	167.150 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	16

Space group space_group	F 2 2 2
Space-group number int_tables_number	22
Crystal system crystal_system	—

Resolution resolution	1.750 Å
Low-resolution limit resolution_low	36.150 Å
R factor r_factor	0.1630
R_work r_work	0.1630
R_free r_free	0.1760

Glutaconyl-coA decarboxylase A subunit from Clostridium symbiosum co-crystallized with glutaconyl-coA

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

Glutaconyl-CoA decarboxylase subunit A

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

3gf3__assembly_1__model_1

3gf3__assembly_1__model_1 | I(q)

3gf3__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) 5 domains

SCOP 2.08 (2 domains)

CATH v4.4 (3 domains)

7. Citations (1)

Glutaconyl-coA decarboxylase A subunit from Clostridium symbiosum co-crystallized with glutaconyl-coA

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

Glutaconyl-CoA decarboxylase 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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3gf3__assembly_1__model_1

3gf3__assembly_1__model_1 | I(q)

3gf3__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) 5 domains

SCOP 2.08 (2 domains)

CATH v4.4 (3 domains)

7. Citations (1)