SAXSdb — 1yj4

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

Trichodiene synthase

Fusarium sporotrichioides

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	1,2-ETHANEDIOL × 4 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TRI5_FUSSP
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–374； UniProt 1–374 Author chain B； PDBConstruct 1–374； UniProt 1–374

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	1yj4
Deposition date deposition_date	2005-01-13
Structure title title	Y305F Trichodiene Synthase
Keywords keywords	terpenoid cyclase fold, site-directed mutant, 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.

1yj4__assembly_1__model_1

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

Download this curve (.dat)

1yj4__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1yj4__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.27 Å
Rg (electron density)	26.25 Å
Total Rg	27.12 Å
Atom count	5854
Residues	703
Excluded volume	103510 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1yj4__assembly_1__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	Trichodiene synthase
Molecular weight formula_weight	44034.6 kDa
EC 编号 ec_number	4.2.3.6
Mutation mutation	Y305F
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	6013

MENFPTEYFLNTTVRLLEYIRYRDSNYTREERIENLHYAYNKAAHHFAQPRQQQLLKVDPKRLQASLQTIVGMVVYSWAKVSKECMADLSIHYTYTLVLDDSKDDPYPTMVNYFDDLQAGREQAHPWWALVNEHFPNVLRHFGPFCSLNLIRSTLDFFEGCWIEQYNFGGFPGSHDYPQFLRRMNGLGHCVGASLWPKEQFNERSLFLEITSAIAQMENWMVWVNDLMSFYKEFDDERDQISLVKNYVVSDEISLHEALEKLTQDTLHSSKQMVAVFSDKDPQVMDTIECFMHGYVTWHLCDRRFRLSEIYEKVKEEKTEDAQKFCKFYEQAANVGAVSPSEWAYPPVAQLANVRSKDVKEVQKPFLSSIELVE

Source Source

Source organism organism	Fusarium sporotrichioides
NCBI taxonomy ID ncbi_taxonomy_id	5514
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	159

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1yj4a_
Class class	a — All alpha proteins
Fold Fold fold	a.128 — Terpenoid synthases
Superfamily Superfamily superfamily	a.128.1 — Terpenoid synthases
Family Family family	a.128.1.5 — Trichodiene synthase

Domain ID domain_id	d1yj4b_
Class class	a — All alpha proteins
Fold Fold fold	a.128 — Terpenoid synthases
Superfamily Superfamily superfamily	a.128.1 — Terpenoid synthases
Family Family family	a.128.1.5 — Trichodiene synthase

CATH v4.4 (2 domains)

Domain ID domain_id	1yj4A00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	600 — Farnesyl Diphosphate Synthase
Homologous superfamily homologous superfamily	10 — Farnesyl Diphosphate Synthase

Domain ID domain_id	1yj4B00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	600 — Farnesyl Diphosphate Synthase
Homologous superfamily homologous superfamily	10 — Farnesyl Diphosphate Synthase

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Unit-cell length a length_a	122.240 Å
Unit-cell length b length_b	122.240 Å
Unit-cell length c length_c	151.720 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	40.000 Å
R factor r_factor	—
R_work r_work	0.2440
R_free r_free	0.2750

Y305F Trichodiene Synthase

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

Trichodiene synthase

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

1yj4__assembly_1__model_1

1yj4__assembly_1__model_1 | I(q)

1yj4__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 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Y305F Trichodiene Synthase

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

Trichodiene synthase

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

1yj4__assembly_1__model_1

1yj4__assembly_1__model_1 | I(q)

1yj4__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 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)