2cdy

Manganese Superoxide Dismutase (Mn-SOD) from Deinococcus radiodurans

Method: X-RAY DIFFRACTION

▼

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

SUPEROXIDE DISMUTASE [MN]

DEINOCOCCUS RADIODURANS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	MANGANESE (II) ION × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	MANGANESE (II) ION × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	MANGANESE (II) ION × 1 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	MANGANESE (II) ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SODM_DEIRA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 22–231； UniProt 1–210 Author chain B； PDBConstruct 22–231； UniProt 1–210 Author chain C； PDBConstruct 22–231； UniProt 1–210 Author chain D； PDBConstruct 22–231； UniProt 1–210

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	2cdy
Deposition date deposition_date	2006-01-31
Structure title title	Manganese Superoxide Dismutase (Mn-SOD) from Deinococcus radiodurans
Keywords keywords	MANGANESE SUPEROXIDE DISMUTASE, DEINOCOCCUS RADIODURANS, RADIATION RESISTANCE, 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.

2cdy__assembly_4__model_1

Assembly 4 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2cdy__assembly_4__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2cdy__assembly_4__model_1 | P(r) · Pending

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

Rg（Guinier）	17.58 Å
Rg (electron density)	16.42 Å
Total Rg	17.46 Å
Atom count	1623
Residues	207
Excluded volume	28471 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2cdy__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2cdy__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2cdy__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`2cdy__assembly_4__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 (3)

Entity 1 Entity 1 polymer

Description description	SUPEROXIDE DISMUTASE [MN]
Molecular weight formula_weight	25982.9 kDa
EC 编号 ec_number	1.15.1.1
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	7049

MSYYHHHHHHLESTSLYKKALAYTLPQLPYAYDALEPHIDARTMEIHHTKHHQTYVDNANKALEGTEFADLPVEQLIQQLDRVPADKKGALRNNAGGHANHSMFWQIMGQGQGQNGANQPSGELLDAINSAFGSFDAFKQKFEDAAKTRFGSGWAWLVVKDGKLDVVSTANQDNPLMGEAIAGVSGTPILGVDVWEHAYYLNYQNRRPDYLAAFWNVVNWDEVSKRYAAAK

Source Source

Source organism organism	DEINOCOCCUS RADIODURANS
NCBI taxonomy ID ncbi_taxonomy_id	243230
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	567

▼

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d2cdya1
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.2.11.0 — automated matches

Domain ID domain_id	d2cdya2
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

Domain ID domain_id	d2cdyb1
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.2.11.0 — automated matches

Domain ID domain_id	d2cdyb2
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

Domain ID domain_id	d2cdyc1
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.2.11.0 — automated matches

Domain ID domain_id	d2cdyc2
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

Domain ID domain_id	d2cdyd1
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.2.11.0 — automated matches

Domain ID domain_id	d2cdyd2
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 (8 domains)

Domain ID domain_id	2cdyA01
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	2cdyA02
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

Domain ID domain_id	2cdyB01
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	2cdyB02
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

Domain ID domain_id	2cdyC01
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	2cdyC02
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

Domain ID domain_id	2cdyD01
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	2cdyD02
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

▶

Unit-cell length a length_a	43.577 Å
Unit-cell length b length_b	87.100 Å
Unit-cell length c length_c	116.418 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	92.10 °
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	2.000 Å
Low-resolution limit resolution_low	41.200 Å
R factor r_factor	0.1760
R_work r_work	0.1730
R_free r_free	0.2210

Manganese Superoxide Dismutase (Mn-SOD) from Deinococcus radiodurans

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

2cdy__assembly_4__model_1

2cdy__assembly_4__model_1 | I(q)

2cdy__assembly_4__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) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Manganese Superoxide Dismutase (Mn-SOD) from Deinococcus radiodurans

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

2cdy__assembly_4__model_1

2cdy__assembly_4__model_1 | I(q)

2cdy__assembly_4__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) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)