1u0u

An Aldol Switch Discovered in Stilbene Synthases Mediates Cyclization Specificity of Type III Polyketide Synthases: Pine stilbene synthase structure

Method: X-RAY DIFFRACTION

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

Dihydropinosylvin synthase

Pinus sylvestris

State in the Current Structure

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

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DPSS_PINSY
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–397； UniProt 1–393 Author chain B； PDBConstruct 5–397； UniProt 1–393 Author chain C； PDBConstruct 5–397； UniProt 1–393 Author chain D； PDBConstruct 5–397； UniProt 1–393 Author chain E； PDBConstruct 5–397； UniProt 1–393 Author chain F； PDBConstruct 5–397； UniProt 1–393

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	1u0u
Deposition date deposition_date	2004-07-14
Structure title title	An Aldol Switch Discovered in Stilbene Synthases Mediates Cyclization Specificity of Type III Polyketide Synthases: Pine stilbene synthase structure
Keywords keywords	;PKS, type III polyketide synthase, condensing enzyme, thiolase fold, alpha-beta-alpha-beta-alpha fold, aldol switch, catalytic triad, TRANSFERASE ;; TRANSFERASE
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.

1u0u__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1u0u__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1u0u__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	27.12 Å
Rg (electron density)	25.97 Å
Total Rg	26.80 Å
Atom count	5958
Residues	778
Excluded volume	106450 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1u0u__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1u0u__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1u0u__assembly_3__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 (2)

Entity 1 Entity 1 polymer

Description description	Dihydropinosylvin synthase
Molecular weight formula_weight	43122.3 kDa
EC 编号 ec_number	2.3.1.-
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	19745

GSHGMGGVDFEGFRKLQRADGFASILAIGTANPPNAVDQSTYPDFYFRITGNEHNTELKDKFKRICERSAIKQRYMYLTEEILKKNPDVCAFVEVPSLDARQAMLAMEVPRLAKEAAEKAIQEWGQSKSGITHLIFCSTTTPDLPGADFEVAKLLGLHPSVKRVGVFQHGCFAGGTVLRMAKDLAENNRGARVLVICSETTAVTFRGPSETHLDSLVGQALFGDGASALIVGADPIPQVEKACFEIVWTAQTVVPNSEGAIGGKVREVGLTFQLKGAVPDLISANIENCMVEAFSQFKISDWNKLFWVVHPGGRAILDRVEAKLNLDPTKLIPTRHVMSEYGNMSSACVHFILDQTRKASLQNGCSTTGEGLEMGVLFGFGPGLTIETVVLKSVPIQ

Source Source

Source organism organism	Pinus sylvestris
Common name common_name	Scots pine
NCBI taxonomy ID ncbi_taxonomy_id	3349
Host organism host_organism	Escherichia coli BL21

Entity 2 Entity 2 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1871

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6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d1u0ua1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.95 — Thiolase-like
Superfamily Superfamily superfamily	c.95.1 — Thiolase-like
Family Family family	c.95.1.2 — Chalcone synthase-like

Domain ID domain_id	d1u0ua2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.95 — Thiolase-like
Superfamily Superfamily superfamily	c.95.1 — Thiolase-like
Family Family family	c.95.1.2 — Chalcone synthase-like

Domain ID domain_id	d1u0ub1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.95 — Thiolase-like
Superfamily Superfamily superfamily	c.95.1 — Thiolase-like
Family Family family	c.95.1.2 — Chalcone synthase-like

Domain ID domain_id	d1u0ub2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.95 — Thiolase-like
Superfamily Superfamily superfamily	c.95.1 — Thiolase-like
Family Family family	c.95.1.2 — Chalcone synthase-like

Domain ID domain_id	d1u0uc1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.95 — Thiolase-like
Superfamily Superfamily superfamily	c.95.1 — Thiolase-like
Family Family family	c.95.1.2 — Chalcone synthase-like

Domain ID domain_id	d1u0uc2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.95 — Thiolase-like
Superfamily Superfamily superfamily	c.95.1 — Thiolase-like
Family Family family	c.95.1.2 — Chalcone synthase-like

Domain ID domain_id	d1u0ud1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.95 — Thiolase-like
Superfamily Superfamily superfamily	c.95.1 — Thiolase-like
Family Family family	c.95.1.2 — Chalcone synthase-like

Domain ID domain_id	d1u0ud2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.95 — Thiolase-like
Superfamily Superfamily superfamily	c.95.1 — Thiolase-like
Family Family family	c.95.1.2 — Chalcone synthase-like

Domain ID domain_id	d1u0ue1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.95 — Thiolase-like
Superfamily Superfamily superfamily	c.95.1 — Thiolase-like
Family Family family	c.95.1.2 — Chalcone synthase-like

Domain ID domain_id	d1u0ue2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.95 — Thiolase-like
Superfamily Superfamily superfamily	c.95.1 — Thiolase-like
Family Family family	c.95.1.2 — Chalcone synthase-like

Domain ID domain_id	d1u0uf1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.95 — Thiolase-like
Superfamily Superfamily superfamily	c.95.1 — Thiolase-like
Family Family family	c.95.1.2 — Chalcone synthase-like

Domain ID domain_id	d1u0uf2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.95 — Thiolase-like
Superfamily Superfamily superfamily	c.95.1 — Thiolase-like
Family Family family	c.95.1.2 — Chalcone synthase-like

CATH v4.4 (12 domains)

Domain ID domain_id	1u0uA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	47 — Peroxisomal Thiolase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Thiolase/Chalcone synthase

Domain ID domain_id	1u0uA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	47 — Peroxisomal Thiolase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Thiolase/Chalcone synthase

Domain ID domain_id	1u0uB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	47 — Peroxisomal Thiolase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Thiolase/Chalcone synthase

Domain ID domain_id	1u0uB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	47 — Peroxisomal Thiolase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Thiolase/Chalcone synthase

Domain ID domain_id	1u0uC01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	47 — Peroxisomal Thiolase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Thiolase/Chalcone synthase

Domain ID domain_id	1u0uC02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	47 — Peroxisomal Thiolase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Thiolase/Chalcone synthase

Domain ID domain_id	1u0uD01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	47 — Peroxisomal Thiolase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Thiolase/Chalcone synthase

Domain ID domain_id	1u0uD02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	47 — Peroxisomal Thiolase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Thiolase/Chalcone synthase

Domain ID domain_id	1u0uE01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	47 — Peroxisomal Thiolase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Thiolase/Chalcone synthase

Domain ID domain_id	1u0uE02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	47 — Peroxisomal Thiolase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Thiolase/Chalcone synthase

Domain ID domain_id	1u0uF01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	47 — Peroxisomal Thiolase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Thiolase/Chalcone synthase

Domain ID domain_id	1u0uF02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	47 — Peroxisomal Thiolase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Thiolase/Chalcone synthase

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Unit-cell length a length_a	57.221 Å
Unit-cell length b length_b	361.291 Å
Unit-cell length c length_c	57.317 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	98.39 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

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

Resolution resolution	2.110 Å
Low-resolution limit resolution_low	54.100 Å
R factor r_factor	0.2250
R_work r_work	0.2250
R_free r_free	0.2890

An Aldol Switch Discovered in Stilbene Synthases Mediates Cyclization Specificity of Type III Polyketide Synthases: Pine stilbene synthase structure

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

Dihydropinosylvin 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

1u0u__assembly_3__model_1

1u0u__assembly_3__model_1 | I(q)

1u0u__assembly_3__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

7. Citations (1)

An Aldol Switch Discovered in Stilbene Synthases Mediates Cyclization Specificity of Type III Polyketide Synthases: Pine stilbene synthase structure

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

Dihydropinosylvin 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

1u0u__assembly_3__model_1

1u0u__assembly_3__model_1 | I(q)

1u0u__assembly_3__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

7. Citations (1)