6o63

Crystal Structure of Arabidopsis thaliana Spermidine Synthase isoform 1 (AtSPDS1)

Method: X-RAY DIFFRACTION

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

Spermidine synthase 1

Arabidopsis thaliana

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	DI(HYDROXYETHYL)ETHER × 2 GLYCEROL × 2 SULFATE ION × 1 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	DI(HYDROXYETHYL)ETHER × 2 GLYCEROL × 2 SULFATE ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SPD1_ARATH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–337； UniProt 1–334 Author chain B； PDBConstruct 4–337； UniProt 1–334 Author chain C； PDBConstruct 4–337； UniProt 1–334 Author chain D； PDBConstruct 4–337； UniProt 1–334

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	6o63
Deposition date deposition_date	2019-03-05
Structure title title	Crystal Structure of Arabidopsis thaliana Spermidine Synthase isoform 1 (AtSPDS1)
Keywords keywords	Polyamine metabolism, Putrescine Biosynthesis, Transferase, dc-SAM, MTA; 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.

6o63__assembly_1__model_1

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

Download this curve (.dat)

6o63__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6o63__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.24 Å
Rg (electron density)	24.20 Å
Total Rg	25.13 Å
Atom count	4482
Residues	577
Excluded volume	80317 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6o63__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6o63__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 (5)

Entity 1 Entity 1 polymer

Description description	Spermidine synthase 1
Molecular weight formula_weight	36862.6 kDa
EC 编号 ec_number	2.5.1.16
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	9923

SNAMDAKETSATDLKRPREEDDNGGAATMETENGDQKKEPACFSTVIPGWFSEMSPMWPGEAHSLKVEKVLFQGKSDYQDVIVFQSATYGKVLVLDGVIQLTERDECAYQEMITHLPLCSIPNPKKVLVIGGGDGGVLREVARHASIEQIDMCEIDKMVVDVSKQFFPDVAIGYEDPRVNLVIGDGVAFLKNAAEGSYDAVIVDSSDPIGPAKELFEKPFFQSVARALRPGGVVCTQAESLWLHMDIIEDIVSNCREIFKGSVNYAWTSVPTYPSGVIGFMLCSTEGPDVDFKHPLNPIDESSSKSNGPLKFYNAEIHSAAFCLPSFAKKVIESKAN

Source Source

Source organism organism	Arabidopsis thaliana
Common name common_name	Mouse-ear cress
NCBI taxonomy ID ncbi_taxonomy_id	3702
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	986

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d6o63a_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.66 — S-adenosyl-L-methionine-dependent methyltransferases
Superfamily Superfamily superfamily	c.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
Family Family family	c.66.1.17 — Spermidine synthase

Domain ID domain_id	d6o63b_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.66 — S-adenosyl-L-methionine-dependent methyltransferases
Superfamily Superfamily superfamily	c.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
Family Family family	c.66.1.17 — Spermidine synthase

Domain ID domain_id	d6o63c_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.66 — S-adenosyl-L-methionine-dependent methyltransferases
Superfamily Superfamily superfamily	c.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
Family Family family	c.66.1.17 — Spermidine synthase

Domain ID domain_id	d6o63d_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.66 — S-adenosyl-L-methionine-dependent methyltransferases
Superfamily Superfamily superfamily	c.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
Family Family family	c.66.1.17 — Spermidine synthase

CATH v4.4 (8 domains)

Domain ID domain_id	6o63A01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	140 — Spermidine Synthase; Chain: A, domain 2
Homologous superfamily homologous superfamily	10 — Spermidine synthase, tetramerisation domain

Domain ID domain_id	6o63A02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	150 — Vaccinia Virus protein VP39

Domain ID domain_id	6o63B01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	140 — Spermidine Synthase; Chain: A, domain 2
Homologous superfamily homologous superfamily	10 — Spermidine synthase, tetramerisation domain

Domain ID domain_id	6o63B02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	150 — Vaccinia Virus protein VP39

Domain ID domain_id	6o63C01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	140 — Spermidine Synthase; Chain: A, domain 2
Homologous superfamily homologous superfamily	10 — Spermidine synthase, tetramerisation domain

Domain ID domain_id	6o63C02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	150 — Vaccinia Virus protein VP39

Domain ID domain_id	6o63D01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	140 — Spermidine Synthase; Chain: A, domain 2
Homologous superfamily homologous superfamily	10 — Spermidine synthase, tetramerisation domain

Domain ID domain_id	6o63D02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	150 — Vaccinia Virus protein VP39

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Unit-cell length a length_a	89.536 Å
Unit-cell length b length_b	76.338 Å
Unit-cell length c length_c	90.192 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	104.68 °
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	1.800 Å
Low-resolution limit resolution_low	43.460 Å
R factor r_factor	0.1658
R_work r_work	0.1652
R_free r_free	0.2221

Crystal Structure of Arabidopsis thaliana Spermidine Synthase isoform 1 (AtSPDS1)

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

Spermidine synthase 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

6o63__assembly_1__model_1

6o63__assembly_1__model_1 | I(q)

6o63__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Crystal Structure of Arabidopsis thaliana Spermidine Synthase isoform 1 (AtSPDS1)

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

Spermidine synthase 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

6o63__assembly_1__model_1

6o63__assembly_1__model_1 | I(q)

6o63__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. Citations (1)