SAXSdb — 2v8u

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

MANGANESE-CONTAINING PSEUDOCATALASE

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 6	OXYGEN ATOM × 30 MANGANESE (II) ION × 12 LITHIUM ION × 15 SULFATE ION × 21 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q84DB4_THETH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–302； UniProt 1–302 Author chain B； PDBConstruct 1–302； UniProt 1–302

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	2v8u
Deposition date deposition_date	2007-08-14
Structure title title	Atomic resolution structure of Mn catalase from Thermus Thermophilus
Keywords keywords	MANGANESE CATALASE, OXIDOREDUCTASE; 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.

2v8u__assembly_1__model_1

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

Download this curve (.dat)

2v8u__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2v8u__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	33.56 Å
Rg (electron density)	32.64 Å
Total Rg	33.39 Å
Atom count	14238
Residues	1812
Excluded volume	253810 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2v8u__assembly_1__model_1`	hexameric （6）	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 (6)

Entity 1 Entity 1 polymer

Description description	MANGANESE-CONTAINING PSEUDOCATALASE
Molecular weight formula_weight	33345.1 kDa
EC 编号 ec_number	1.11.1.6
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	6092

MFLRIDRLQIELPMPKEQDPNAAAAVQALLGGRFGEMSTLMNYMYQSFNFRGKKALKPYYDLIANIATEELGHIELVAATINSLLAKNPGKDLEEGVDPASTPLGFAKDVRNAAHFIAGGANSLVMGAMGEHWNGEYVFTSGNLILDLLHNFFLEVAARTHKLRVYEMTDNPVAREMIGYLLVRGGVHAAAYGKALESLTGVEMTKMLPIPKIDNSKIPEAKKYMDLGFHRNLYRFSPEDYRDLGLIWKGASPEDGTEVVVVDGPPTGGPVFDAGHDAAEFAPEFHPGELYEIAKKLYEKAK

Entity 2 Entity 2 non-polymer

Description description	OXYGEN ATOM
Molecular weight formula_weight	16.0 kDa
Source method src_method	syn
Copy count entity_count	10

Entity 3 Entity 3 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 4 Entity 4 non-polymer

Description description	LITHIUM ION
Molecular weight formula_weight	6.9 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 5 Entity 5 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1077

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2v8ua_
Class class	a — All alpha proteins
Fold Fold fold	a.25 — Ferritin-like
Superfamily Superfamily superfamily	a.25.1 — Ferritin-like
Family Family family	a.25.1.3 — Manganese catalase (T-catalase)

Domain ID domain_id	d2v8ub_
Class class	a — All alpha proteins
Fold Fold fold	a.25 — Ferritin-like
Superfamily Superfamily superfamily	a.25.1 — Ferritin-like
Family Family family	a.25.1.3 — Manganese catalase (T-catalase)

CATH v4.4 (2 domains)

Domain ID domain_id	2v8uA01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1260 — Ferritin
Homologous superfamily homologous superfamily	10 — Ferritin, core subunit, four-helix bundle

Domain ID domain_id	2v8uB01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1260 — Ferritin
Homologous superfamily homologous superfamily	10 — Ferritin, core subunit, four-helix bundle

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Unit-cell length a length_a	132.300 Å
Unit-cell length b length_b	132.300 Å
Unit-cell length c length_c	132.300 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	24

Space group space_group	P 21 3
Space-group number int_tables_number	198
Crystal system crystal_system	—

Resolution resolution	1.050 Å
Low-resolution limit resolution_low	95.350 Å
R factor r_factor	0.1060
R_work r_work	0.1060
R_free r_free	0.1210

Atomic resolution structure of Mn catalase from Thermus Thermophilus

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

MANGANESE-CONTAINING PSEUDOCATALASE

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

2v8u__assembly_1__model_1

2v8u__assembly_1__model_1 | I(q)

2v8u__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Atomic resolution structure of Mn catalase from Thermus Thermophilus

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

MANGANESE-CONTAINING PSEUDOCATALASE

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

2v8u__assembly_1__model_1

2v8u__assembly_1__model_1 | I(q)

2v8u__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)