2q41

Ensemble refinement of the protein crystal structure of spermidine synthase from Arabidopsis thaliana gene At1g23820

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 4	water × 4	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 2–334； UniProt 2–334 Author chain B； PDBConstruct 2–334； UniProt 2–334 Author chain C； PDBConstruct 2–334； UniProt 2–334 Author chain D； PDBConstruct 2–334； UniProt 2–334

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	2q41
Deposition date deposition_date	2007-05-31
Structure title title	Ensemble refinement of the protein crystal structure of spermidine synthase from Arabidopsis thaliana gene At1g23820
Keywords keywords	;Ensemble Refinement, Refinement Methodology Development, AT1G23820, PUTRESCINE AMINOPROPYL TRANSFERASE, SPERMIDINE SYNTHASE, SPDS1, POLYAMINE, Structural Genomics, Protein Structure Initiative, PSI, Center for Eukaryotic Structural Genomics, CESG, 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.

2q41__assembly_1__model_7

Assembly 1 · Model 7 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2q41__assembly_1__model_7 | I(q)

100 plotted points; both axes use logarithmic scales.

2q41__assembly_1__model_7 | P(r) · Pending

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

Rg（Guinier）	36.28 Å
Rg (electron density)	35.85 Å
Total Rg	36.12 Å
Atom count	8864
Residues	1122
Excluded volume	159280 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2q41__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	2	`2q41__assembly_1__model_2`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	3	`2q41__assembly_1__model_3`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	4	`2q41__assembly_1__model_4`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	5	`2q41__assembly_1__model_5`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	6	`2q41__assembly_1__model_6`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	7	`2q41__assembly_1__model_7`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	8	`2q41__assembly_1__model_8`	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 (2)

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2q41a_
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	d2q41b_
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	d2q41c_
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	d2q41d_
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	2q41A01
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	2q41A02
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	2q41B01
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	2q41B02
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	2q41C01
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	2q41C02
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	2q41D01
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	2q41D02
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	88.814 Å
Unit-cell length b length_b	95.207 Å
Unit-cell length c length_c	89.164 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	104.96 °
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	2.700 Å
Low-resolution limit resolution_low	26.290 Å
R factor r_factor	0.1640
R_work r_work	0.1640
R_free r_free	0.2490

Description description	Spermidine synthase 1
Molecular weight formula_weight	36921.4 kDa
EC 编号 ec_number	2.5.1.16
Source method src_method	man
Copy count entity_count	4

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	75520

Ensemble refinement of the protein crystal structure of spermidine synthase from Arabidopsis thaliana gene At1g23820

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

2q41__assembly_1__model_7

2q41__assembly_1__model_7 | I(q)

2q41__assembly_1__model_7 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

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) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Source organism organism	Arabidopsis thaliana
Common name common_name	thale cress
NCBI taxonomy ID ncbi_taxonomy_id	3702
Host organism host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	576

Ensemble refinement of the protein crystal structure of spermidine synthase from Arabidopsis thaliana gene At1g23820

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

2q41__assembly_1__model_7

2q41__assembly_1__model_7 | I(q)

2q41__assembly_1__model_7 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

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) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. Citations (1)