SAXSdb — 2iqf

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

Catalase

Helicobacter pylori

State in the Current Structure

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

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CATA_HELPY
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–505； UniProt 1–505 Author chain B； PDBConstruct 1–505； UniProt 1–505

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	2iqf
Deposition date deposition_date	2006-10-13
Structure title title	Crystal structure of Helicobacter pylori catalase compound I
Keywords keywords	hydroxoferryl heme, beta barrel, 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.

2iqf__assembly_1__model_1

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

Download this curve (.dat)

2iqf__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2iqf__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	36.45 Å
Rg (electron density)	35.82 Å
Total Rg	36.51 Å
Atom count	16316
Residues	1948
Excluded volume	287830 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2iqf__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 (5)

Entity 1 Entity 1 polymer

Description description	Catalase
Molecular weight formula_weight	58794.0 kDa
EC 编号 ec_number	1.11.1.6
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	9111

MVNKDVKQTTAFGAPVWDDNNVITAGPRGPVLLQSTWFLEKLAAFDRERIPERVVHAKGSGAYGTFTVTKDITKYTKAKIFSKVGKKTECFFRFSTVAGERGSADAVRDPRGFAMKYYTEEGNWDLVGNNTPVFFIRDAIKFPDFIHTQKRDPQTNLPNHDMVWDFWSNVPESLYQVTWVMSDRGIPKSFRHMDGFGSHTFSLINAKGERFWVKFHFHTMQGVKHLTNEEAAEIRKHDPDSNQRDLFDAIARGDYPKWKLSIQVMPEEDAKKYRFHPFDVTKIWYTQDYPLMEVGIVELNKNPENYFAEVEQAAFTPANVVPGIGYSPDRMLQGRLFSYGDTHRYRLGVNYPQIPVNKPRCPFHSSSRDGYMQNGYYGSLQNYTPSSLPGYKEDKSARDPKFNLAHIEKEFEVWNWDYRADDSDYYTQPGDYYRSLPADEKERLHDTIGESLAHVTHKEIVDKQLEHFKKADPKYAEGVKKALEKHQKMMKDMHGKDMHHTKKKK

Source Source

Source organism organism	Helicobacter pylori
NCBI taxonomy ID ncbi_taxonomy_id	210
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	PROTOPORPHYRIN IX CONTAINING FE
Molecular weight formula_weight	616.5 kDa
Source method src_method	syn
Copy count entity_count	2

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	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	884

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2iqfa_
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	d2iqfb_
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 (2 domains)

Domain ID domain_id	2iqfA00
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	2iqfB00
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	64.385 Å
Unit-cell length b length_b	154.286 Å
Unit-cell length c length_c	95.808 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	8

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	1.860 Å
Low-resolution limit resolution_low	37.000 Å
R factor r_factor	0.1505
R_work r_work	0.1485
R_free r_free	0.1885

Crystal structure of Helicobacter pylori catalase compound I

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

2iqf__assembly_1__model_1

2iqf__assembly_1__model_1 | I(q)

2iqf__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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of Helicobacter pylori catalase compound I

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

2iqf__assembly_1__model_1

2iqf__assembly_1__model_1 | I(q)

2iqf__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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)