1o9i

Crystal structure of the Y42F mutant of manganese catalase from Lactobacillus plantarum at 1.33A resolution

Method: X-RAY DIFFRACTION

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

Manganese catalase

Lactobacillus plantarum

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 6	MANGANESE (III) ION × 12 CALCIUM ION × 6 OXYGEN ATOM × 6 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 5 SODIUM ION × 2 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MCAT_LACPN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–266； UniProt 1–266 Author chain B； PDBConstruct 1–266； UniProt 1–266 Author chain C； PDBConstruct 1–266； UniProt 1–266 Author chain D； PDBConstruct 1–266； UniProt 1–266 Author chain E； PDBConstruct 1–266； UniProt 1–266 Author chain F； PDBConstruct 1–266； UniProt 1–266

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	1o9i
Deposition date deposition_date	2002-12-13
Structure title title	Crystal structure of the Y42F mutant of manganese catalase from Lactobacillus plantarum at 1.33A resolution
Keywords keywords	OXIDOREDUCTASE, HEXAMER, DIMANGANESE CATALASE, METALLOENZYME, PREOXIDASE; 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.

1o9i__assembly_1__model_1

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

Download this curve (.dat)

1o9i__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1o9i__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	31.72 Å
Rg (electron density)	30.73 Å
Total Rg	31.51 Å
Atom count	12584
Residues	1596
Excluded volume	221410 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1o9i__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 (7)

Entity 1 Entity 1 polymer

Description description	Manganese catalase
Molecular weight formula_weight	29763.4 kDa
EC 编号 ec_number	1.11.1.6
Mutation mutation	YES
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	14325

MFKHTRKLQYNAKPDRSDPIMARRLQESLGGQWGETTGMMSFLSQGWASTGAEKYKDLLLDTGTEEMAHVEMISTMIGYLLEDAPFGPEDLKRDPSLATTMAGMDPEHSLVHGLNASLNNPNGAAWNAGYVTSSGNLVADMRFNVVRESEARLQVSRLYSMTEDEGVRDMLKFLLARETQHQLQFMKAQEELEEKYGIIVPGDMKEIEHSEFSHVLMNFSDGDGSKAFEGQVAKDGEKFTYQENPEAMGGIPHIKPGDPRLHNHQG

Source Source

Source organism organism	Lactobacillus plantarum
NCBI taxonomy ID ncbi_taxonomy_id	1590
Host organism host_organism	LACTOBACILLUS PLANTARUM

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	12

Entity 3 Entity 3 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 non-polymer

Description description	OXYGEN ATOM
Molecular weight formula_weight	16.0 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 5 Entity 5 non-polymer

Description description	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
Molecular weight formula_weight	195.2 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 6 Entity 6 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1459

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6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1o9ia_
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	d1o9ib_
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	d1o9ic_
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	d1o9id_
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	d1o9ie_
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	d1o9if_
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 (12 domains)

Domain ID domain_id	1o9iA01
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	1o9iA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1530 — manganese catalase, domain 2, chain A
Homologous superfamily homologous superfamily	10 — manganese catalase, domain 2, chain A

Domain ID domain_id	1o9iB01
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	1o9iB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1530 — manganese catalase, domain 2, chain A
Homologous superfamily homologous superfamily	10 — manganese catalase, domain 2, chain A

Domain ID domain_id	1o9iC01
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	1o9iC02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1530 — manganese catalase, domain 2, chain A
Homologous superfamily homologous superfamily	10 — manganese catalase, domain 2, chain A

Domain ID domain_id	1o9iD01
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	1o9iD02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1530 — manganese catalase, domain 2, chain A
Homologous superfamily homologous superfamily	10 — manganese catalase, domain 2, chain A

Domain ID domain_id	1o9iE01
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	1o9iE02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1530 — manganese catalase, domain 2, chain A
Homologous superfamily homologous superfamily	10 — manganese catalase, domain 2, chain A

Domain ID domain_id	1o9iF01
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	1o9iF02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1530 — manganese catalase, domain 2, chain A
Homologous superfamily homologous superfamily	10 — manganese catalase, domain 2, chain A

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Unit-cell length a length_a	73.490 Å
Unit-cell length b length_b	95.270 Å
Unit-cell length c length_c	105.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	106.55 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.330 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.1170
R_work r_work	0.1150
R_free r_free	0.1450

Crystal structure of the Y42F mutant of manganese catalase from Lactobacillus plantarum at 1.33A resolution

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

Manganese catalase

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

1o9i__assembly_1__model_1

1o9i__assembly_1__model_1 | I(q)

1o9i__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 (7)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (6 domains)

CATH v4.4 (12 domains)

7. Citations (2)

Crystal structure of the Y42F mutant of manganese catalase from Lactobacillus plantarum at 1.33A resolution

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

Manganese catalase

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

1o9i__assembly_1__model_1

1o9i__assembly_1__model_1 | I(q)

1o9i__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 (7)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (6 domains)

CATH v4.4 (12 domains)

7. Citations (2)