2fon

X-ray crystal structure of LeACX1, an acyl-CoA oxidase from Lycopersicon esculentum (tomato)

Method: X-RAY DIFFRACTION

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

peroxisomal acyl-CoA oxidase 1A

Solanum lycopersicum

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	FLAVIN-ADENINE DINUCLEOTIDE × 2 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	FLAVIN-ADENINE DINUCLEOTIDE × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q5D8D3_LYCES
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 20–683； UniProt 1–664 Author chain B； PDBConstruct 20–683； UniProt 1–664 Author chain C； PDBConstruct 20–683； UniProt 1–664

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	2fon
Deposition date deposition_date	2006-01-13
Structure title title	X-ray crystal structure of LeACX1, an acyl-CoA oxidase from Lycopersicon esculentum (tomato)
Keywords keywords	oxidoreductase, peroxisomal beta-oxidation, FAD cofactor; OXIDOREDUCTASE
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.

2fon__assembly_1__model_1

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

Download this curve (.dat)

2fon__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2fon__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	32.11 Å
Rg (electron density)	31.10 Å
Total Rg	31.76 Å
Atom count	10156
Residues	1310
Excluded volume	179780 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2fon__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2fon__assembly_2__model_1`	dimeric （2）	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	peroxisomal acyl-CoA oxidase 1A
Molecular weight formula_weight	76545.2 kDa
EC 编号 ec_number	1.3.3.6
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	14949

MRGSHHHHHHGSACELVREMEGVDYLADERKKAGFDVDEMKIVWAGSRHDFELTDRISKLVASDPGFSKEGRTMLPRKELFKNTLRKAAYAWKRIIELRLSQEEATMLRRYVDEPAFTDLHWGMFIPAIKGQGTDKQQEKWLPLAYKMQIIGCYAQTELGHGSNVQGLETTATFDPQTDEFVIHSPTLTSSKWWPGGLGKVSTHAVVYARLITDGKDYGVNGFIVQLRSLEDHKPLPGVTVGDIGMKFGNGAYNSMDNGVLSFDHVRIPRDQMLMRVSQVTKEGKYVQSDIPRQLLYGTMVYVRQSIVADASLAMSRAVCIATRYSAVRRQFGSQNGGQETQVIDYKTQQNRLFPLLASAYAFRFVGEWLKWLYTDVTQRLAANDFSTLPEAHACTAGLKSLTTSATADGIEECRKLCGGHGYLCSSGLPELFAVYVPACTYEGDNVVLQLQVARFLMKTISQLGTGKKPVGTVSYMGRIEHLMQCRSDVKQAEDWLKPSAVLEAFEARSARMSVACAKNLSKFENQEEGFAELAADLVEAAVAHCQLIVVSKYIEKLQQNIPGKGVKQQLEVLCGIYSLFILHKHQGDFLGTGYITSKQGSLANDQLRALYSQLRPNAVSLVDAFNYTDHYLGSILGRYDGNVYPKLYEAAWKDPLNKSDIADGFHEYIRPLLKQQLRTAKL

Source Source

Source organism organism	Solanum lycopersicum
NCBI taxonomy ID ncbi_taxonomy_id	4081
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	FLAVIN-ADENINE DINUCLEOTIDE
Molecular weight formula_weight	785.5 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	36

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6. Fold Classification (SCOP + CATH) 21 domains

SCOP 2.08 (9 domains)

Domain ID domain_id	d2fona1
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.6 — Acyl-CoA dehydrogenase NM domain-like
Superfamily Superfamily superfamily	e.6.1 — Acyl-CoA dehydrogenase NM domain-like
Family Family family	e.6.1.0 — automated matches

Domain ID domain_id	d2fona2
Class class	a — All alpha proteins
Fold Fold fold	a.29 — Bromodomain-like
Superfamily Superfamily superfamily	a.29.3 — Acyl-CoA dehydrogenase C-terminal domain-like
Family Family family	a.29.3.0 — automated matches

Domain ID domain_id	d2fona3
Class class	a — All alpha proteins
Fold Fold fold	a.29 — Bromodomain-like
Superfamily Superfamily superfamily	a.29.3 — Acyl-CoA dehydrogenase C-terminal domain-like
Family Family family	a.29.3.0 — automated matches

Domain ID domain_id	d2fonb1
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.6 — Acyl-CoA dehydrogenase NM domain-like
Superfamily Superfamily superfamily	e.6.1 — Acyl-CoA dehydrogenase NM domain-like
Family Family family	e.6.1.0 — automated matches

Domain ID domain_id	d2fonb2
Class class	a — All alpha proteins
Fold Fold fold	a.29 — Bromodomain-like
Superfamily Superfamily superfamily	a.29.3 — Acyl-CoA dehydrogenase C-terminal domain-like
Family Family family	a.29.3.0 — automated matches

Domain ID domain_id	d2fonb3
Class class	a — All alpha proteins
Fold Fold fold	a.29 — Bromodomain-like
Superfamily Superfamily superfamily	a.29.3 — Acyl-CoA dehydrogenase C-terminal domain-like
Family Family family	a.29.3.0 — automated matches

Domain ID domain_id	d2fonc1
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.6 — Acyl-CoA dehydrogenase NM domain-like
Superfamily Superfamily superfamily	e.6.1 — Acyl-CoA dehydrogenase NM domain-like
Family Family family	e.6.1.0 — automated matches

Domain ID domain_id	d2fonc2
Class class	a — All alpha proteins
Fold Fold fold	a.29 — Bromodomain-like
Superfamily Superfamily superfamily	a.29.3 — Acyl-CoA dehydrogenase C-terminal domain-like
Family Family family	a.29.3.0 — automated matches

Domain ID domain_id	d2fonc3
Class class	a — All alpha proteins
Fold Fold fold	a.29 — Bromodomain-like
Superfamily Superfamily superfamily	a.29.3 — Acyl-CoA dehydrogenase C-terminal domain-like
Family Family family	a.29.3.0 — automated matches

CATH v4.4 (12 domains)

Domain ID domain_id	2fonA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	540 — Butyryl-Coa Dehydrogenase, subunit A; domain 1
Homologous superfamily homologous superfamily	10 — Acyl-CoA dehydrogenase/oxidase, N-terminal domain

Domain ID domain_id	2fonA02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	110 — Butyryl-CoA Dehydrogenase, subunit A; domain 2
Homologous superfamily homologous superfamily	10 — Butyryl-CoA Dehydrogenase, subunit A, domain 2

Domain ID domain_id	2fonA03
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	140 — Butyryl-CoA Dehydrogenase, subunit A; domain 3
Homologous superfamily homologous superfamily	10 — Butyryl-CoA Dehydrogenase, subunit A, domain 3

Domain ID domain_id	2fonA04
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	140 — Butyryl-CoA Dehydrogenase, subunit A; domain 3
Homologous superfamily homologous superfamily	10 — Butyryl-CoA Dehydrogenase, subunit A, domain 3

Domain ID domain_id	2fonB01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	540 — Butyryl-Coa Dehydrogenase, subunit A; domain 1
Homologous superfamily homologous superfamily	10 — Acyl-CoA dehydrogenase/oxidase, N-terminal domain

Domain ID domain_id	2fonB02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	110 — Butyryl-CoA Dehydrogenase, subunit A; domain 2
Homologous superfamily homologous superfamily	10 — Butyryl-CoA Dehydrogenase, subunit A, domain 2

Domain ID domain_id	2fonB03
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	140 — Butyryl-CoA Dehydrogenase, subunit A; domain 3
Homologous superfamily homologous superfamily	10 — Butyryl-CoA Dehydrogenase, subunit A, domain 3

Domain ID domain_id	2fonB04
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	140 — Butyryl-CoA Dehydrogenase, subunit A; domain 3
Homologous superfamily homologous superfamily	10 — Butyryl-CoA Dehydrogenase, subunit A, domain 3

Domain ID domain_id	2fonC01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	540 — Butyryl-Coa Dehydrogenase, subunit A; domain 1
Homologous superfamily homologous superfamily	10 — Acyl-CoA dehydrogenase/oxidase, N-terminal domain

Domain ID domain_id	2fonC02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	110 — Butyryl-CoA Dehydrogenase, subunit A; domain 2
Homologous superfamily homologous superfamily	10 — Butyryl-CoA Dehydrogenase, subunit A, domain 2

Domain ID domain_id	2fonC03
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	140 — Butyryl-CoA Dehydrogenase, subunit A; domain 3
Homologous superfamily homologous superfamily	10 — Butyryl-CoA Dehydrogenase, subunit A, domain 3

Domain ID domain_id	2fonC04
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	140 — Butyryl-CoA Dehydrogenase, subunit A; domain 3
Homologous superfamily homologous superfamily	10 — Butyryl-CoA Dehydrogenase, subunit A, domain 3

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Unit-cell length a length_a	120.200 Å
Unit-cell length b length_b	240.330 Å
Unit-cell length c length_c	89.300 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	12

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.740 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	—
R_work r_work	0.2120
R_free r_free	0.2670

X-ray crystal structure of LeACX1, an acyl-CoA oxidase from Lycopersicon esculentum (tomato)

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

peroxisomal acyl-CoA oxidase 1A

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

2fon__assembly_1__model_1

2fon__assembly_1__model_1 | I(q)

2fon__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

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) 21 domains

SCOP 2.08 (9 domains)

CATH v4.4 (12 domains)

7. Citations (1)

X-ray crystal structure of LeACX1, an acyl-CoA oxidase from Lycopersicon esculentum (tomato)

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

peroxisomal acyl-CoA oxidase 1A

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

2fon__assembly_1__model_1

2fon__assembly_1__model_1 | I(q)

2fon__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

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) 21 domains

SCOP 2.08 (9 domains)

CATH v4.4 (12 domains)

7. Citations (1)