SAXSdb — 3bfr

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

Superoxide dismutase [Mn]

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	MANGANESE (III) ION × 4 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SODM_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 9–215； UniProt 27–233

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	3bfr
Deposition date deposition_date	2007-11-23
Structure title title	The crystal structure of Sod2 from Saccharomyces cerevisiae
Keywords keywords	alpha/beta fold, Manganese, Metal-binding, Mitochondrion, Oxidoreductase, Transit peptide; OXIDOREDUCTASE
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.

3bfr__assembly_1__model_1

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

Download this curve (.dat)

3bfr__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3bfr__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	28.22 Å
Rg (electron density)	27.06 Å
Total Rg	27.95 Å
Atom count	6440
Residues	820
Excluded volume	114070 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3bfr__assembly_1__model_1`	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 (3)

Entity 1 Entity 1 polymer

Description description	Superoxide dismutase [Mn]
Molecular weight formula_weight	24125.1 kDa
EC 编号 ec_number	1.15.1.1
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	1752

MGHHHHHHKVTLPDLKWDFGALEPYISGQINELHYTKHHQTYVNGFNTAVDQFQELSDLLAKEPSPANARKMIAIQQNIKFHGGGFTNHCLFWENLAPESQGGGEPPTGALAKAIDEQFGSLDELIKLTNTKLAGVQGSGWAFIVKNLSNGGKLDVVQTYNQDTVTGPLVPLVAIDAWEHAYYLQYQNKKADYFKAIWNVVNWKEASRRFDAGKI

Source Source

Source organism organism	Saccharomyces cerevisiae
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	MANGANESE (III) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	122

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3bfra1
Class class	a — All alpha proteins
Fold Fold fold	a.2 — Long alpha-hairpin
Superfamily Superfamily superfamily	a.2.11 — Fe,Mn superoxide dismutase (SOD), N-terminal domain
Family Family family	a.2.11.1 — Fe,Mn superoxide dismutase (SOD), N-terminal domain

Domain ID domain_id	d3bfra2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.44 — Fe,Mn superoxide dismutase (SOD), C-terminal domain
Superfamily Superfamily superfamily	d.44.1 — Fe,Mn superoxide dismutase (SOD), C-terminal domain
Family Family family	d.44.1.1 — Fe,Mn superoxide dismutase (SOD), C-terminal domain

CATH v4.4 (2 domains)

Domain ID domain_id	3bfrA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	990 — Fe,Mn superoxide dismutase (SOD) domain

Domain ID domain_id	3bfrA02
Class class	3 — Alpha Beta
Architecture architecture	55 — 3-Layer(bab) Sandwich
Topology topology	40 — minor pseudopilin epsh fold
Homologous superfamily homologous superfamily	20 — Iron/manganese superoxide dismutase, C-terminal domain

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Unit-cell length a length_a	92.740 Å
Unit-cell length b length_b	92.740 Å
Unit-cell length c length_c	92.740 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	12

Space group space_group	P 2 3
Space-group number int_tables_number	195
Crystal system crystal_system	—

Resolution resolution	2.050 Å
Low-resolution limit resolution_low	15.000 Å
R factor r_factor	0.1967
R_work r_work	0.1948
R_free r_free	0.2336

The crystal structure of Sod2 from Saccharomyces cerevisiae

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

Superoxide dismutase [Mn]

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

3bfr__assembly_1__model_1

3bfr__assembly_1__model_1 | I(q)

3bfr__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

The crystal structure of Sod2 from Saccharomyces cerevisiae

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

Superoxide dismutase [Mn]

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

3bfr__assembly_1__model_1

3bfr__assembly_1__model_1 | I(q)

3bfr__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)