SAXSdb — 5imi

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

Aristolochene synthase

Aspergillus terreus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	PYROPHOSPHATE 2- × 2 MAGNESIUM ION × 6 (1S,5S,8S,9aR)-1,9a-dimethyl-8-(prop-1-en-2-yl)octahydro-2H-quinolizinium × 2 GLYCEROL × 1 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	PYROPHOSPHATE 2- × 2 MAGNESIUM ION × 6 (1S,5S,8S,9aR)-1,9a-dimethyl-8-(prop-1-en-2-yl)octahydro-2H-quinolizinium × 2 water × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 4	PYROPHOSPHATE 2- × 4 MAGNESIUM ION × 12 (1S,5S,8S,9aR)-1,9a-dimethyl-8-(prop-1-en-2-yl)octahydro-2H-quinolizinium × 4 GLYCEROL × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ARIS_ASPTE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 8–314； UniProt 14–320 Author chain B； PDBConstruct 8–314； UniProt 14–320 Author chain C； PDBConstruct 8–314； UniProt 14–320 Author chain D； PDBConstruct 8–314； UniProt 14–320

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	5imi
Deposition date deposition_date	2016-03-06
Structure title title	Crystal structure of S303A Aspergillus terreus aristolochene synthase complexed with (1S,8S,9aR)-1,9a-dimethyl-8-(prop-1-en-2-yl)decahydroquinolizin-5-ium
Keywords keywords	Lyase, terpene cyclases, LYASE-LYASE INHIBITOR complex; LYASE/LYASE INHIBITOR
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.

5imi__assembly_1__model_1

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

Download this curve (.dat)

5imi__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5imi__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	30.00 Å
Rg (electron density)	29.75 Å
Total Rg	30.16 Å
Atom count	4997
Residues	612
Excluded volume	89298 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5imi__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5imi__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`5imi__assembly_3__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 (6)

Entity 1 Entity 1 polymer

Description description	Aristolochene synthase
Molecular weight formula_weight	36205.4 kDa
EC 编号 ec_number	4.2.3.9
Mutation mutation	S303A
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	10599

MHHHHHHLEPPPSTFQPLCHPLVEEVSKEVDGYFLQHWNFPNEKARKKFVAAGFSRVTCLYFPKALDDRIHFACRLLTVLFLIDDLLEYMSFEEGSAYNEKLIPISRGDVLPDRSIPVEYIIYDLWESMRAHDREMADEILEPVFLFMRAQTDRTRARPMGLGGYLEYRERDVGKELLAALMRFSMGLKLSPSELQRVREIDANCSKHLSVVNDIYSYEKELYTSKTAHSEGGILCTSVQILAQEADVTAEAAKRVLFVMCREWELRHQLLVARLSAEGLETPGLAAYVEGLEYQMSGNELWAQTTLRYSVVVD

Source Source

Source organism organism	Aspergillus terreus
NCBI taxonomy ID ncbi_taxonomy_id	33178
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	PYROPHOSPHATE 2-
Molecular weight formula_weight	176.0 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 4 Entity 4 non-polymer

Description description	(1S,5S,8S,9aR)-1,9a-dimethyl-8-(prop-1-en-2-yl)octahydro-2H-quinolizinium
Molecular weight formula_weight	208.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	602

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6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (5 domains)

Domain ID domain_id	d5imia_
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.128.1.4 — Aristolochene/pentalenene synthase

Domain ID domain_id	d5imib1
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.128.1.4 — Aristolochene/pentalenene synthase

Domain ID domain_id	d5imib2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d5imic_
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.128.1.4 — Aristolochene/pentalenene synthase

Domain ID domain_id	d5imid_
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.128.1.4 — Aristolochene/pentalenene synthase

CATH v4.4 (4 domains)

Domain ID domain_id	5imiA00
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	5imiB00
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	5imiC00
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	5imiD00
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	124.127 Å
Unit-cell length b length_b	124.127 Å
Unit-cell length c length_c	203.411 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	24

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

Resolution resolution	2.462 Å
Low-resolution limit resolution_low	47.521 Å
R factor r_factor	0.2134
R_work r_work	0.2122
R_free r_free	0.2505

Crystal structure of S303A Aspergillus terreus aristolochene synthase complexed with (1S,8S,9aR)-1,9a-dimethyl-8-(prop-1-en-2-yl)decahydroquinolizin-5-ium

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

Aristolochene 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

5imi__assembly_1__model_1

5imi__assembly_1__model_1 | I(q)

5imi__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 (6)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (5 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of S303A Aspergillus terreus aristolochene synthase complexed with (1S,8S,9aR)-1,9a-dimethyl-8-(prop-1-en-2-yl)decahydroquinolizin-5-ium

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

Aristolochene 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

5imi__assembly_1__model_1

5imi__assembly_1__model_1 | I(q)

5imi__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 (6)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (5 domains)

CATH v4.4 (4 domains)

7. Citations (1)