SAXSdb — 3dy5

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

Allene oxide synthase-lipoxygenase protein

Plexaura homomalla

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	FE (II) ION × 1 PROTOPORPHYRIN IX CONTAINING FE × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	FE (II) ION × 1 PROTOPORPHYRIN IX CONTAINING FE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	AOSL_PLEHO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–1066； UniProt 1–1066 Author chain C； PDBConstruct 1–1066； UniProt 1–1066

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	3dy5
Deposition date deposition_date	2008-07-25
Structure title title	Allene oxide synthase 8R-lipoxygenase from Plexaura homomalla
Keywords keywords	;fusion protein, bi-functional enzyme, Dioxygenase, Fatty acid biosynthesis, Heme, Iron, Lipid synthesis, Lyase, Membrane, Metal-binding, Multifunctional enzyme, Oxidoreductase, Oxylipin biosynthesis ;; LYASE, 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.

3dy5__assembly_1__model_1

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

Download this curve (.dat)

3dy5__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3dy5__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	35.32 Å
Rg (electron density)	34.75 Å
Total Rg	35.24 Å
Atom count	8109
Residues	1002
Excluded volume	143730 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3dy5__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3dy5__assembly_2__model_1`	monomeric （1）	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	Allene oxide synthase-lipoxygenase protein
Molecular weight formula_weight	121969.9 kDa
EC 编号 ec_number	4.2.1.92, 1.13.11.40
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	16218

MTWKNFGFEIFGEKYGQEELEKRIKDEHTPPPDSPVFGGLKLKLKKEKFKTLFTLGTTLKGFRRATHTVGTGGIGEITIVNDPKFPEHEFFTAGRTFPARLRHANLKYPDDAGADARSFSIKFADSDSDGPLDIVMNTGEANIFWNSPSLEDFVPVEEGDAAEEYVYKNPYYYYNLVEALRRAPDTFAHLYYYSQVTMPFKAKDGKVRYCRYRALPGDVDIKEEDESGRLTEEEQRKIWIFSRHENEKRPDDYLRKEYVERLQKGPVNYRLQIQIHEASPDDTATIFHAGILWDKETHPWFDLAKVSIKTPLSPDVLEKTAFNIANQPASLGLLEAKSPEDYNSIGELRVAVYTWVQHLRKLKIGSLVPAGQNAIYNVEVETGDREHAGTDATITIRITGAKGRTDYLKLDKWFHNDFEAGSKEQYTVQGFDVGDIQLIELHSDGGGYWSGDPDWFVNRVIIISSTQDRVYSFPCFRWVIKDMVLFPGEATLPFNEVPAIVSEQRQKELEQRKLTYQWDYVSDDMPGNIKAKTHDDLPRDVQFTDEKSRSYQESRKAALVNLGIGSLFTMFENWDSYDDYHILYRNWILGGTPNMADRWHEDRWFGYQFLNGANPVILTRCDALPSNFPVTNEHVNASLDRGKNLDEEIKDGHIYIVDFKVLVGAKSYGGPVLEDIGYKVPDHLKHDEADIRYCAAPLALFYVNKLGHLMPIAIQINQEPGPENPIWTPHEENEHDWMMAKFWLGVAESNFHQLNTHLLRTHLTTESFALSTWRNLASAHPIFKLLQPHIYGVLAIDTIGRKELIGSGGIVDQSLSLGGGGHVTFMEKCFKEVNLQDYHLPNALKKRGVDDPSKLPGFYYRDDGLALWEAIETFIGEIIAIFYKNDDDVKRDNEIQSWIYDVHKNGWRVNPGHQDHGVPASFESREQLKEVLTSLVFTFSCQHAAVNFSQKDHYGFTPNAPAILRHPPPKKKGEATLQSILSTLPSKSQAAKAIATVYILTKFSEDERYLGNYSATAWEDKDALDAINRFQDKLEDISKKIKQRNENLEVPYIYLLPERIPNGTAI

Source Source

Source organism organism	Plexaura homomalla
Common name common_name	Black sea rod
NCBI taxonomy ID ncbi_taxonomy_id	47982
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	FE (II) ION
Molecular weight formula_weight	55.8 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	PROTOPORPHYRIN IX CONTAINING FE
Molecular weight formula_weight	616.5 kDa
Source method src_method	syn
Copy count entity_count	2

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6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	3dy5A01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	180 — Catalase HpII, Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Catalase core domain

Domain ID domain_id	3dy5A02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	245 — Lipoxygenase-1; domain 5
Homologous superfamily homologous superfamily	10 — Lipoxygenase-1; Domain 5

Domain ID domain_id	3dy5A03
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	60 —

Domain ID domain_id	3dy5C01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	180 — Catalase HpII, Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Catalase core domain

Domain ID domain_id	3dy5C02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	245 — Lipoxygenase-1; domain 5
Homologous superfamily homologous superfamily	10 — Lipoxygenase-1; Domain 5

Domain ID domain_id	3dy5C03
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	60 —

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Unit-cell length a length_a	235.520 Å
Unit-cell length b length_b	77.493 Å
Unit-cell length c length_c	157.966 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	112.45 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	3.510 Å
Low-resolution limit resolution_low	20.860 Å
R factor r_factor	0.2751
R_work r_work	0.2726
R_free r_free	0.3219

Allene oxide synthase 8R-lipoxygenase from Plexaura homomalla

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

Allene oxide synthase-lipoxygenase protein

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

3dy5__assembly_1__model_1

3dy5__assembly_1__model_1 | I(q)

3dy5__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 non-polymer

Entity 3 Entity 3 non-polymer

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)

Allene oxide synthase 8R-lipoxygenase from Plexaura homomalla

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

Allene oxide synthase-lipoxygenase protein

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

3dy5__assembly_1__model_1

3dy5__assembly_1__model_1 | I(q)

3dy5__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 non-polymer

Entity 3 Entity 3 non-polymer

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)