SAXSdb — 1mjf

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

spermidine synthase

Pyrococcus furiosus

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

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SPEE_PYRFU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–281； UniProt 1–281 Author chain B； PDBConstruct 1–281； UniProt 1–281

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	1mjf
Deposition date deposition_date	2002-08-27
Structure title title	PUTATIVE SPERMIDINE SYNTHETASE FROM PYROCOCCUS FURIOSUS PFU-132382
Keywords keywords	;Pyrococcus furiosus, spermidine synthetase, structural genomics, PSI, Protein Structure Initiative, Southeast Collaboratory for Structural Genomics, SECSG, 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.

1mjf__assembly_1__model_1

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

Download this curve (.dat)

1mjf__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1mjf__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.59 Å
Rg (electron density)	24.40 Å
Total Rg	25.47 Å
Atom count	4326
Residues	540
Excluded volume	77934 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1mjf__assembly_1__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)

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1mjfa_
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	d1mjfb_
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 (4 domains)

Domain ID domain_id	1mjfA01
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	1mjfA02
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	1mjfB01
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	1mjfB02
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	95.639 Å
Unit-cell length b length_b	110.821 Å
Unit-cell length c length_c	49.256 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.798 Å
Low-resolution limit resolution_low	72.550 Å
R factor r_factor	0.2066
R_work r_work	0.2048
R_free r_free	0.2416

Description description	spermidine synthase
Molecular weight formula_weight	32377.3 kDa
EC 编号 ec_number	2.5.1.16
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	4527

PUTATIVE SPERMIDINE SYNTHETASE FROM PYROCOCCUS FURIOSUS PFU-132382

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

spermidine 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

1mjf__assembly_1__model_1

1mjf__assembly_1__model_1 | I(q)

1mjf__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Source organism organism	Pyrococcus furiosus
NCBI taxonomy ID ncbi_taxonomy_id	2261
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	201

PUTATIVE SPERMIDINE SYNTHETASE FROM PYROCOCCUS FURIOSUS PFU-132382

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

spermidine 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

1mjf__assembly_1__model_1

1mjf__assembly_1__model_1 | I(q)

1mjf__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)