6ztw

Crystal Structure of catalase HPII from Escherichia coli (serendipitously crystallized)

Method: X-RAY DIFFRACTION

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

Catalase HPII

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE × 4 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 4 GLYCEROL × 4 (4S)-2-METHYL-2,4-PENTANEDIOL × 1 1,2-ETHANEDIOL × 4 water × 4	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 4	CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE × 4 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 5 GLYCEROL × 2 1,2-ETHANEDIOL × 3 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CATE_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–753； UniProt 1–753 Author chain B； PDBConstruct 1–753； UniProt 1–753 Author chain C； PDBConstruct 1–753； UniProt 1–753 Author chain D； PDBConstruct 1–753； UniProt 1–753 Author chain E； PDBConstruct 1–753； UniProt 1–753 Author chain F； PDBConstruct 1–753； UniProt 1–753 Author chain G； PDBConstruct 1–753； UniProt 1–753 Author chain H； PDBConstruct 1–753； UniProt 1–753

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	6ztw
Deposition date deposition_date	2020-07-20
Structure title title	Crystal Structure of catalase HPII from Escherichia coli (serendipitously crystallized)
Keywords keywords	catalase, hydrogen-peroxide, heme, iron, oxidative stress, artifact crystallization, impurities, contaminations, 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.

6ztw__assembly_1__model_1

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

Download this curve (.dat)

6ztw__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6ztw__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	41.75 Å
Rg (electron density)	41.43 Å
Total Rg	42.03 Å
Atom count	23228
Residues	2900
Excluded volume	410220 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6ztw__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6ztw__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 (7)

Entity 1 Entity 1 polymer

Description description	Catalase HPII
Molecular weight formula_weight	84346.5 kDa
EC 编号 ec_number	1.11.1.6
Mutation mutation	S99N
Source method src_method	nat
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	51313

MSQHNEKNPHQHQSPLHDSSEAKPGMDSLAPEDGSHRPAAEPTPPGAQPTAPGSLKAPDTRNEKLNSLEDVRKGSENYALTTNQGVRIADDQNSLRAGNRGPTLLEDFILREKITHFDHERIPERIVHARGSAAHGYFQPYKSLSDITKADFLSDPNKITPVFVRFSTVQGGAGSADTVRDIRGFATKFYTEEGIFDLVGNNTPIFFIQDAHKFPDFVHAVKPEPHWAIPQGQSAHDTFWDYVSLQPETLHNVMWAMSDRGIPRSYRTMEGFGIHTFRLINAEGKATFVRFHWKPLAGKASLVWDEAQKLTGRDPDFHRRELWEAIEAGDFPEYELGFQLIPEEDEFKFDFDLLDPTKLIPEELVPVQRVGKMVLNRNPDNFFAENEQAAFHPGHIVPGLDFTNDPLLQGRLFSYTDTQISRLGGPNFHEIPINRPTCPYHNFQRDGMHRMGIDTNPANYEPNSINDNWPRETPPGPKRGGFESYQERVEGNKVRERSPSFGEYYSHPRLFWLSQTPFEQRHIVDGFSFELSKVVRPYIRERVVDQLAHIDLTLAQAVAKNLGIELTDDQLNITPPPDVNGLKKDPSLSLYAIPDGDVKGRVVAILLNDEVRSADLLAILKALKAKGVHAKLLYSRMGEVTADDGTVLPIAATFAGAPSLTVDAVIVPCGNIADIADNGDANYYLMEAYKHLKPIALAGDARKFKATIKIADQGEEGIVEADSADGSFMDELLTLMAAHRVWSRIPKIDKIPA

Entity 2 Entity 2 non-polymer

Description description	CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE
Molecular weight formula_weight	632.5 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 3 Entity 3 non-polymer

Description description	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Molecular weight formula_weight	122.1 kDa
Source method src_method	syn
Copy count entity_count	9

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 5 Entity 5 non-polymer

Description description	(4S)-2-METHYL-2,4-PENTANEDIOL
Molecular weight formula_weight	118.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	4695

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (16 domains)

Domain ID domain_id	d6ztwa1
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	d6ztwa2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.16 — Class I glutamine amidotransferase-like
Family Family family	c.23.16.0 — automated matches

Domain ID domain_id	d6ztwb1
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	d6ztwb2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.16 — Class I glutamine amidotransferase-like
Family Family family	c.23.16.0 — automated matches

Domain ID domain_id	d6ztwc1
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	d6ztwc2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.16 — Class I glutamine amidotransferase-like
Family Family family	c.23.16.0 — automated matches

Domain ID domain_id	d6ztwd1
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	d6ztwd2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.16 — Class I glutamine amidotransferase-like
Family Family family	c.23.16.0 — automated matches

Domain ID domain_id	d6ztwe1
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	d6ztwe2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.16 — Class I glutamine amidotransferase-like
Family Family family	c.23.16.0 — automated matches

Domain ID domain_id	d6ztwf1
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	d6ztwf2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.16 — Class I glutamine amidotransferase-like
Family Family family	c.23.16.0 — automated matches

Domain ID domain_id	d6ztwg1
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	d6ztwg2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.16 — Class I glutamine amidotransferase-like
Family Family family	c.23.16.0 — automated matches

Domain ID domain_id	d6ztwh1
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	d6ztwh2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.16 — Class I glutamine amidotransferase-like
Family Family family	c.23.16.0 — automated matches

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Unit-cell length a length_a	121.188 Å
Unit-cell length b length_b	168.071 Å
Unit-cell length c length_c	137.982 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	105.24 °
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	monoclinic

Resolution resolution	1.840 Å
Low-resolution limit resolution_low	78.250 Å
R factor r_factor	0.1445
R_work r_work	0.1443
R_free r_free	0.1839

Crystal Structure of catalase HPII from Escherichia coli (serendipitously crystallized)

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

Catalase HPII

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

6ztw__assembly_1__model_1

6ztw__assembly_1__model_1 | I(q)

6ztw__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

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) 16 domains

SCOP 2.08 (16 domains)

7. Citations (1)

Crystal Structure of catalase HPII from Escherichia coli (serendipitously crystallized)

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

Catalase HPII

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

6ztw__assembly_1__model_1

6ztw__assembly_1__model_1 | I(q)

6ztw__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

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) 16 domains

SCOP 2.08 (16 domains)

7. Citations (1)