2isa

Crystal Structure of Vibrio salmonicida catalase

Method: X-RAY DIFFRACTION

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

Catalase

Vibrio salmonicida

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	PROTOPORPHYRIN IX CONTAINING FE × 4 GLYCEROL × 4 CHLORIDE ION × 2 water × 4	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 4	PROTOPORPHYRIN IX CONTAINING FE × 4 GLYCEROL × 4 CHLORIDE ION × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q3LSM1_9VIBR
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–483； UniProt 1–483 Author chain B； PDBConstruct 1–483； UniProt 1–483 Author chain C； PDBConstruct 1–483； UniProt 1–483 Author chain D； PDBConstruct 1–483； UniProt 1–483 Author chain E； PDBConstruct 1–483； UniProt 1–483 Author chain F； PDBConstruct 1–483； UniProt 1–483 Author chain G； PDBConstruct 1–483； UniProt 1–483 Author chain H； PDBConstruct 1–483； UniProt 1–483

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	2isa
Deposition date deposition_date	2006-10-17
Structure title title	Crystal Structure of Vibrio salmonicida catalase
Keywords keywords	Peroxidase, Heme, Oxidoreductase, Iron, Hydrogen peroxide; 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.

2isa__assembly_1__model_1

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

Download this curve (.dat)

2isa__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2isa__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	36.32 Å
Rg (electron density)	35.80 Å
Total Rg	36.34 Å
Atom count	15658
Residues	1924
Excluded volume	274110 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2isa__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2isa__assembly_2__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 (5)

Entity 1 Entity 1 polymer

Description description	Catalase
Molecular weight formula_weight	54844.9 kDa
EC 编号 ec_number	1.11.1.6
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H
Atom count atom_count	35944

MSKKLTTAAGCPVAHNQNVQTAGKRGPQLLQDVWFLEKLAHFDREVIPERRMHAKGSGAYGTFTVTHDITKYTKAKIFSDIGKKTDMFARFSTVAGERGAADAERDIRGFSLKFYTEEGNWDLAGNNTPVFFLRDPLKFPDLNHAVKRDPRTNMRSAKNNWDFWTSLPEALHQVTIVMSDRGIPATYRHMHGFGSHTFSFINSDNERYWVKFHFVSQQGIKNLSDAEAGELVGNDRESHQRDLLDSIDNQDFPKWTLKVQIMPEADAATVPYNPFDLTKVWPHKDYPLIEVGEFELNRNPQNYFAEVEQAAFNPANVVPGISFSPDKMLQGRLFAYGDAQRYRLGVNHQHIPVNAPRCPVHSYHRDGAMRVDGNFGSTLGYEPNDQGQWAEQPDFSEPPLNLDGAAAHWDHREDEDYFSQPGDLFGLMTAEKQAILFDNTARNLNGVPKEIQLRHVTHCYKADPAYGEGIGKLLGFDISEYNS

Source Source

Source organism organism	Vibrio salmonicida
NCBI taxonomy ID ncbi_taxonomy_id	316275
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	PROTOPORPHYRIN IX CONTAINING FE
Molecular weight formula_weight	616.5 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 4 Entity 4 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	4594

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d2isaa_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.5 — Heme-dependent catalase-like
Superfamily Superfamily superfamily	e.5.1 — Heme-dependent catalase-like
Family Family family	e.5.1.1 — Heme-dependent catalases

Domain ID domain_id	d2isab_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.5 — Heme-dependent catalase-like
Superfamily Superfamily superfamily	e.5.1 — Heme-dependent catalase-like
Family Family family	e.5.1.1 — Heme-dependent catalases

Domain ID domain_id	d2isac_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.5 — Heme-dependent catalase-like
Superfamily Superfamily superfamily	e.5.1 — Heme-dependent catalase-like
Family Family family	e.5.1.1 — Heme-dependent catalases

Domain ID domain_id	d2isad_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.5 — Heme-dependent catalase-like
Superfamily Superfamily superfamily	e.5.1 — Heme-dependent catalase-like
Family Family family	e.5.1.1 — Heme-dependent catalases

Domain ID domain_id	d2isae_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.5 — Heme-dependent catalase-like
Superfamily Superfamily superfamily	e.5.1 — Heme-dependent catalase-like
Family Family family	e.5.1.1 — Heme-dependent catalases

Domain ID domain_id	d2isaf_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.5 — Heme-dependent catalase-like
Superfamily Superfamily superfamily	e.5.1 — Heme-dependent catalase-like
Family Family family	e.5.1.1 — Heme-dependent catalases

Domain ID domain_id	d2isag_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.5 — Heme-dependent catalase-like
Superfamily Superfamily superfamily	e.5.1 — Heme-dependent catalase-like
Family Family family	e.5.1.1 — Heme-dependent catalases

Domain ID domain_id	d2isah_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.5 — Heme-dependent catalase-like
Superfamily Superfamily superfamily	e.5.1 — Heme-dependent catalase-like
Family Family family	e.5.1.1 — Heme-dependent catalases

CATH v4.4 (8 domains)

Domain ID domain_id	2isaA00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	180 — Catalase HpII, Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Catalase core domain

Domain ID domain_id	2isaB00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	180 — Catalase HpII, Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Catalase core domain

Domain ID domain_id	2isaC00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	180 — Catalase HpII, Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Catalase core domain

Domain ID domain_id	2isaD00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	180 — Catalase HpII, Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Catalase core domain

Domain ID domain_id	2isaE00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	180 — Catalase HpII, Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Catalase core domain

Domain ID domain_id	2isaF00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	180 — Catalase HpII, Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Catalase core domain

Domain ID domain_id	2isaG00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	180 — Catalase HpII, Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Catalase core domain

Domain ID domain_id	2isaH00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	180 — Catalase HpII, Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Catalase core domain

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Unit-cell length a length_a	98.150 Å
Unit-cell length b length_b	217.760 Å
Unit-cell length c length_c	99.280 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	110.48 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

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

Resolution resolution	1.970 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.1508
R_work r_work	0.1482
R_free r_free	0.2003

Crystal Structure of Vibrio salmonicida catalase

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

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

2isa__assembly_1__model_1

2isa__assembly_1__model_1 | I(q)

2isa__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Crystal Structure of Vibrio salmonicida catalase

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

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

2isa__assembly_1__model_1

2isa__assembly_1__model_1 | I(q)

2isa__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)