SAXSdb — 3mds

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

MANGANESE SUPEROXIDE DISMUTASE

Thermus thermophilus

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_THET8
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–203； UniProt 1–203 Author chain B； PDBConstruct 1–203； UniProt 1–203

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	3mds
Deposition date deposition_date	1993-10-20
Structure title title	MAGANESE SUPEROXIDE DISMUTASE FROM THERMUS THERMOPHILUS
Keywords keywords	OXIDOREDUCTASE, OXIDOREDUCTASE(SUPEROXIDE ACCEPTOR); OXIDOREDUCTASE(SUPEROXIDE ACCEPTOR)
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.

3mds__assembly_1__model_1

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

Download this curve (.dat)

3mds__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3mds__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	29.94 Å
Rg (electron density)	29.08 Å
Total Rg	29.91 Å
Atom count	6568
Residues	812
Excluded volume	116910 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3mds__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	MANGANESE SUPEROXIDE DISMUTASE
Molecular weight formula_weight	23129.3 kDa
EC 编号 ec_number	1.15.1.1
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3471

PYPFKLPDLGYPYEALEPHIDAKTMEIHHQKHHGAYVTNLNAALEKYPYLHGVEVEVLLRHLAALPQDIQTAVRNNGGGHLNHSLFWRLLTPGGAKEPVGELKKAIDEQFGGFQALKEKLTQAAMGRFGSGWAWLVKDPFGKLHVLSTPNQDNPVMEGFTPIVGIDVWEHAYYLKYQNRRADYLQAIWNVLNWDVAEEFFKKA

Source Source

Source organism organism	Thermus thermophilus
NCBI taxonomy ID ncbi_taxonomy_id	274

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	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	187

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d3mdsa1
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	d3mdsa2
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	d3mdsb1
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	d3mdsb2
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 (4 domains)

Domain ID domain_id	3mdsA01
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	3mdsA02
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	3mdsB01
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	3mdsB02
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	146.600 Å
Unit-cell length b length_b	146.600 Å
Unit-cell length c length_c	55.600 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	16

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.1900
R_work r_work	—
R_free r_free	—

MAGANESE SUPEROXIDE DISMUTASE FROM THERMUS THERMOPHILUS

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

MANGANESE SUPEROXIDE DISMUTASE

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

3mds__assembly_1__model_1

3mds__assembly_1__model_1 | I(q)

3mds__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

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) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (5)

MAGANESE SUPEROXIDE DISMUTASE FROM THERMUS THERMOPHILUS

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

MANGANESE SUPEROXIDE DISMUTASE

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

3mds__assembly_1__model_1

3mds__assembly_1__model_1 | I(q)

3mds__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

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) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (5)