1xet

Crystal structure of stilbene synthase from Pinus sylvestris, complexed with methylmalonyl CoA

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	3-(1H-INDOL-3-YL)-2-OXOPROPANOIC ACID × 1 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	3-(1H-INDOL-3-YL)-2-OXOPROPANOIC ACID × 2 METHYLMALONYL-COENZYME A × 1 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 21–413； UniProt 1–393 Author chain B； PDBConstruct 21–413； UniProt 1–393 Author chain C； PDBConstruct 21–413； UniProt 1–393 Author chain D； PDBConstruct 21–413； 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	1xet
Deposition date deposition_date	2004-09-12
Structure title title	Crystal structure of stilbene synthase from Pinus sylvestris, complexed with methylmalonyl CoA
Keywords keywords	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.

1xet__assembly_2__model_1

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

Download this curve (.dat)

1xet__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1xet__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	26.86 Å
Rg (electron density)	25.58 Å
Total Rg	26.40 Å
Atom count	5795
Residues	766
Excluded volume	103180 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1xet__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1xet__assembly_2__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 (4)

Entity 1 Entity 1 polymer

Description description	Dihydropinosylvin synthase
Molecular weight formula_weight	44954.3 kDa
EC 编号 ec_number	2.3.1.-
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	12508

MGSSHHHHHHSSGLVPRGSHMGGVDFEGFRKLQRADGFASILAIGTANPPNAVDQSTYPDFYFRITGNEHNTELKDKFKRICERSAIKQRYMYLTEEILKKNPDVCAFVEVPSLDARQAMLAMEVPRLAKEAAEKAIQEWGQSKSGITHLIFCSTTTPDLPGADFEVAKLLGLHPSVKRVGVFQHGCFAGGTVLRMAKDLAENNRGARVLVICSETTAVTFRGPSETHLDSLVGQALFGDGASALIVGADPIPQVEKACFEIVWTAQTVVPNSEGAIGGKVREVGLTFQLKGAVPDLISANIENCMVEAFSQFKISDWNKLFWVVHPGGRAILDRVEAKLNLDPTKLIPTRHVMSEYGNMSSACVHFILDQTRKASLQNGCSTTGEGLEMGVLFGFGPGLTIETVVLKSVPIQ

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(DE3)

Entity 2 Entity 2 non-polymer

Description description	3-(1H-INDOL-3-YL)-2-OXOPROPANOIC ACID
Molecular weight formula_weight	203.2 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

Description description	METHYLMALONYL-COENZYME A
Molecular weight formula_weight	867.6 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	854

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d1xeta1
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.95.1.0 — automated matches

Domain ID domain_id	d1xeta2
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.95.1.0 — automated matches

Domain ID domain_id	d1xetb1
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.95.1.0 — automated matches

Domain ID domain_id	d1xetb2
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.95.1.0 — automated matches

Domain ID domain_id	d1xetc1
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.95.1.0 — automated matches

Domain ID domain_id	d1xetc2
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.95.1.0 — automated matches

Domain ID domain_id	d1xetd1
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.95.1.0 — automated matches

Domain ID domain_id	d1xetd2
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.95.1.0 — automated matches

CATH v4.4 (8 domains)

Domain ID domain_id	1xetA01
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	1xetA02
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	1xetB01
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	1xetB02
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	1xetC01
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	1xetC02
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	1xetD01
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	1xetD02
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	54.465 Å
Unit-cell length b length_b	111.190 Å
Unit-cell length c length_c	132.015 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	93.13 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	22.580 Å
R factor r_factor	0.1950
R_work r_work	0.1950
R_free r_free	0.2230

Crystal structure of stilbene synthase from Pinus sylvestris, complexed with methylmalonyl CoA

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

1xet__assembly_2__model_1

1xet__assembly_2__model_1 | I(q)

1xet__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Crystal structure of stilbene synthase from Pinus sylvestris, complexed with methylmalonyl CoA

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

1xet__assembly_2__model_1

1xet__assembly_2__model_1 | I(q)

1xet__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)