SAXSdb — 1pix

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

Glutaconyl-CoA decarboxylase A subunit

Acidaminococcus fermentans

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	SULFATE ION × 5 FORMIC ACID × 4 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 4	SULFATE ION × 10 FORMIC ACID × 8 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GCDA_ACIFE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–587； UniProt 1–587 Author chain B； PDBConstruct 1–587； UniProt 1–587

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	1pix
Deposition date deposition_date	2003-05-30
Structure title title	Crystal structure of the carboxyltransferase subunit of the bacterial ion pump glutaconyl-coenzyme A decarboxylase
Keywords keywords	decarboxylase, biotin-dependent ion pump, carboxyltransferase, 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.

1pix__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1pix__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1pix__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	38.50 Å
Rg (electron density)	37.46 Å
Total Rg	38.13 Å
Atom count	18112
Residues	2344
Excluded volume	322560 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1pix__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1pix__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 (4)

Entity 1 Entity 1 polymer

Description description	Glutaconyl-CoA decarboxylase A subunit
Molecular weight formula_weight	64423.5 kDa
EC 编号 ec_number	4.1.1.70
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	9717

MGFYSMPRYFQNMPQVGKPLKKADAANEEQLKKIEEEIHQLIKEAQEAGKADADVNKRGELTALQRIEKLVEPGSWRPLNTLFNPQGNKNGSVAIVKGLGRVNGKWCVVVASDNKKLAGAWVPGQAECLLRASDTAKTLHVPLVYVLNCSGVKFDEQEKVYPNRRGGGTPFFRNAELNQLGIPVIVGIYGTNPAGGGYHSISPTVIIAHEKANMAVGGAGIMGGMNPKGHVDLEYANEIADMVDRTGKTEPPGAVDIHYTETGFMREVYASEEGVLEGIKKYVGMLPKYDPEFFRVDDPKAPAFPADDLYSMVPLNDKRAYDIYNVIARLFDNSELHEYKKGYGPEMVTGLAKVNGLLVGVVANVQGLLMNYPEYKAAGSVGIGGKLYRQGLVKMNEFVTLCARDRLPIVWIQDTTGIDVGNDAEKAELLGLGQSLIYSIQTSHIPQFEITLRKGTAAAHYVLGGPQGNDTNAFSIGTAATEIAVMNGETAATAMYSRRLAKDRKAGKDLQPTIDKMNNLIQAFYTKSRPKVCAELGLVDEIVDMNKIRGYVEAFTEAAYQNPESICPFHQMILPRAIREFETFVKK

Source Source

Source organism organism	Acidaminococcus fermentans
NCBI taxonomy ID ncbi_taxonomy_id	905
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 3 Entity 3 non-polymer

Description description	FORMIC ACID
Molecular weight formula_weight	46.0 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	661

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6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1pixa2
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	d1pixa3
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	d1pixb2
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	d1pixb3
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 (6 domains)

Domain ID domain_id	1pixA01
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	1pixA02
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	1pixA03
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	1pixB01
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	1pixB02
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	1pixB03
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	151.869 Å
Unit-cell length b length_b	151.869 Å
Unit-cell length c length_c	163.000 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	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	—
R_work r_work	0.2010
R_free r_free	0.2270

Crystal structure of the carboxyltransferase subunit of the bacterial ion pump glutaconyl-coenzyme A decarboxylase

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

Glutaconyl-CoA decarboxylase A subunit

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

1pix__assembly_2__model_1

1pix__assembly_2__model_1 | I(q)

1pix__assembly_2__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) 10 domains

SCOP 2.08 (4 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Crystal structure of the carboxyltransferase subunit of the bacterial ion pump glutaconyl-coenzyme A decarboxylase

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

Glutaconyl-CoA decarboxylase A subunit

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

1pix__assembly_2__model_1

1pix__assembly_2__model_1 | I(q)

1pix__assembly_2__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) 10 domains

SCOP 2.08 (4 domains)

CATH v4.4 (6 domains)

7. Citations (1)