SAXSdb — 5i8s

▼

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

1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase

Mus musculus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	NICKEL (II) ION × 1 PENTANOIC ACID × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MTND_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–179； UniProt 1–179

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	5i8s
Deposition date deposition_date	2016-02-19
Structure title title	Structure of Mouse Acireductone dioxygenase with Ni2+ ion and pentanoic acid in the active site
Keywords keywords	Product analog, off-pathway chemistry, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method method	X-RAY DIFFRACTION

▼

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.

5i8s__assembly_1__model_1

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

Download this curve (.dat)

5i8s__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5i8s__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	17.02 Å
Rg (electron density)	15.77 Å
Total Rg	16.84 Å
Atom count	1499
Residues	179
Excluded volume	26489 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5i8s__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase
Molecular weight formula_weight	21554.6 kDa
EC 编号 ec_number	1.13.11.54
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1826

MVQAWYMDESTADPRKPHRAQPDRPVSLEQLRTLGVLYWKLDADKYENDPELEKIRKMRNYSWMDIITICKDTLPNYEEKIKMFFEEHLHLDEEIRYILEGSGYFDVRDKEDKWIRISMEKGDMITLPAGIYHRFTLDEKNYVKAMRLFVGEPVWTPYNRPADHFDARVQYMSFLEGTA

Source Source

Source organism organism	Mus musculus
Common name common_name	Mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	NICKEL (II) ION
Molecular weight formula_weight	58.7 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	PENTANOIC ACID
Molecular weight formula_weight	102.1 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	271

▼

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d5i8sa_
Class class	b — All beta proteins
Fold Fold fold	b.82 — Double-stranded beta-helix
Superfamily Superfamily superfamily	b.82.1 — RmlC-like cupins
Family Family family	b.82.1.6 — Acireductone dioxygenase

CATH v4.4 (1 domains)

Domain ID domain_id	5i8sA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	10 — Jelly Rolls

▶

Unit-cell length a length_a	79.090 Å
Unit-cell length b length_b	79.090 Å
Unit-cell length c length_c	115.355 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 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	1.890 Å
Low-resolution limit resolution_low	27.151 Å
R factor r_factor	0.1740
R_work r_work	0.1726
R_free r_free	0.2004

Structure of Mouse Acireductone dioxygenase with Ni2+ ion and pentanoic acid in the active site

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

1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase

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

5i8s__assembly_1__model_1

5i8s__assembly_1__model_1 | I(q)

5i8s__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 (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) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)

Structure of Mouse Acireductone dioxygenase with Ni2+ ion and pentanoic acid in the active site

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

1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase

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

5i8s__assembly_1__model_1

5i8s__assembly_1__model_1 | I(q)

5i8s__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 (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) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)