5tr0

Lipoxygenase-1 (soybean) L754A mutant at 293K

Method: X-RAY DIFFRACTION

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

Seed linoleate 13S-lipoxygenase-1

Glycine max

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 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	FE (II) ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LOX1_SOYBN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–839； UniProt 1–839 Author chain B； PDBConstruct 1–839； UniProt 1–839

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	5tr0
Deposition date deposition_date	2016-10-24
Structure title title	Lipoxygenase-1 (soybean) L754A mutant at 293K
Keywords keywords	lipoxygenase, hydrogen tunneling, OXIDOREDUCTASE; 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.

5tr0__assembly_2__model_1

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

Download this curve (.dat)

5tr0__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5tr0__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	29.06 Å
Rg (electron density)	28.16 Å
Total Rg	29.01 Å
Atom count	12886
Residues	815
Excluded volume	115810 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5tr0__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5tr0__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	Seed linoleate 13S-lipoxygenase-1
Molecular weight formula_weight	94480.1 kDa
EC 编号 ec_number	1.13.11.12
Mutation mutation	L754A
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	42779

MFSAGHKIKGTVVLMPKNELEVNPDGSAVDNLNAFLGRSVSLQLISATKADAHGKGKVGKDTFLEGINTSLPTLGAGESAFNIHFEWDGSMGIPGAFYIKNYMQVEFFLKSLTLEAISNQGTIRFVCNSWVYNTKLYKSVRIFFANHTYVPSETPAPLVEYREEELKSLRGNGTGERKEYDRIYDYDVYNDLGNPDKSEKLARPVLGGSSTFPYPRRGRTGRGPTVTDPNTEKQGEVFYVPRDENLGHLKSKDALEIGTKSLSQIVQPAFESAFDLKSTPIEFHSFQDVHDLYEGGIKLPRDVISTIIPLPVIKELYRTDGQHILKFPQPHVVQVSQSAWMTDEEFAREMIAGVNPCVIRGLEEFPPKSNLDPAIYGDQSSKITADSLDLDGYTMDEALGSRRLFMLDYHDIFMPYVRQINQLNSAKTYATRTILFLREDGTLKPVAIELSLPHSAGDLSAAVSQVVLPAKEGVESTIWLLAKAYVIVNDSCYHQLMSHWLNTHAAMEPFVIATHRHLSVLHPIYKLLTPHYRNNMNINALARQSLINANGIIETTFLPSKYSVEMSSAVYKNWVFTDQALPADLIKRGVAIKDPSTPHGVRLLIEDYPYAADGLEIWAAIKTWVQEYVPLYYARDDDVKNDSELQHWWKEAVEKGHGDLKDKPWWPKLQTLEDLVEVCLIIIWIASALHAAVNFGQYPYGGLIMNRPTASRRLLPEKGTPEYEEMINNHEKAYLRTITSKLPTLISLSVIEIASTHASDEVYLGQRDNPHWTSDSKALQAFQKFGNKLKEIEEKLVRRNNDPSLQGNRLGPVQLPYTLLYPSSEEGLTFRGIPNSISI

Source Source

Source organism organism	Glycine max
Common name common_name	Soybean
NCBI taxonomy ID ncbi_taxonomy_id	3847
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 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	689

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6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d5tr0a1
Class class	b — All beta proteins
Fold Fold fold	b.12 — Lipase/lipooxygenase domain (PLAT/LH2 domain)
Superfamily Superfamily superfamily	b.12.1 — Lipase/lipooxygenase domain (PLAT/LH2 domain)
Family Family family	b.12.1.1 — Lipoxigenase N-terminal domain

Domain ID domain_id	d5tr0a2
Class class	a — All alpha proteins
Fold Fold fold	a.119 — Lipoxigenase
Superfamily Superfamily superfamily	a.119.1 — Lipoxigenase
Family Family family	a.119.1.1 — Plant lipoxigenases

Domain ID domain_id	d5tr0b1
Class class	b — All beta proteins
Fold Fold fold	b.12 — Lipase/lipooxygenase domain (PLAT/LH2 domain)
Superfamily Superfamily superfamily	b.12.1 — Lipase/lipooxygenase domain (PLAT/LH2 domain)
Family Family family	b.12.1.1 — Lipoxigenase N-terminal domain

Domain ID domain_id	d5tr0b2
Class class	a — All alpha proteins
Fold Fold fold	a.119 — Lipoxigenase
Superfamily Superfamily superfamily	a.119.1 — Lipoxigenase
Family Family family	a.119.1.1 — Plant lipoxigenases

CATH v4.4 (10 domains)

Domain ID domain_id	5tr0A01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	60 — Lipoxygenase-1
Homologous superfamily homologous superfamily	20 — PLAT/LH2 domain

Domain ID domain_id	5tr0A02
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	375 — Lipoxygenase-1; domain 2
Homologous superfamily homologous superfamily	10 — Lipoxygenase-1; Domain 2

Domain ID domain_id	5tr0A03
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	372 — Lipoxygenase-1; domain 3
Homologous superfamily homologous superfamily	10 — Lipoxygenase-1; Domain 3

Domain ID domain_id	5tr0A04
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	5tr0A05
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	5tr0B01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	60 — Lipoxygenase-1
Homologous superfamily homologous superfamily	20 — PLAT/LH2 domain

Domain ID domain_id	5tr0B02
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	375 — Lipoxygenase-1; domain 2
Homologous superfamily homologous superfamily	10 — Lipoxygenase-1; Domain 2

Domain ID domain_id	5tr0B03
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	372 — Lipoxygenase-1; domain 3
Homologous superfamily homologous superfamily	10 — Lipoxygenase-1; Domain 3

Domain ID domain_id	5tr0B04
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	5tr0B05
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

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Unit-cell length a length_a	91.452 Å
Unit-cell length b length_b	92.652 Å
Unit-cell length c length_c	100.722 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	93.39 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.850 Å
Low-resolution limit resolution_low	45.646 Å
R factor r_factor	0.1414
R_work r_work	0.1399
R_free r_free	0.1695

Lipoxygenase-1 (soybean) L754A mutant at 293K

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

Seed linoleate 13S-lipoxygenase-1

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

5tr0__assembly_2__model_1

5tr0__assembly_2__model_1 | I(q)

5tr0__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 (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) 14 domains

SCOP 2.08 (4 domains)

CATH v4.4 (10 domains)

7. Citations (1)

Lipoxygenase-1 (soybean) L754A mutant at 293K

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

Seed linoleate 13S-lipoxygenase-1

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

5tr0__assembly_2__model_1

5tr0__assembly_2__model_1 | I(q)

5tr0__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 (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) 14 domains

SCOP 2.08 (4 domains)

CATH v4.4 (10 domains)

7. Citations (1)