SAXSdb — 4phq

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

Hemolysin E, chromosomal

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	GLYCEROL × 3 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	GLYCEROL × 3 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	GLYCEROL × 6 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	GLYCEROL × 1 ACETATE ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HLYE_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–298； UniProt 6–303 Author chain B； PDBConstruct 1–298； UniProt 6–303 Author chain C； PDBConstruct 1–298； UniProt 6–303 Author chain D； PDBConstruct 1–298； UniProt 6–303

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	4phq
Deposition date deposition_date	2014-05-06
Structure title title	ClyA CC6/264 ox (6-303)
Keywords keywords	alpha pore-forming toxin, intramolecular disulfide bond, toxin; TOXIN
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.

4phq__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

4phq__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4phq__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	28.00 Å
Rg (electron density)	28.56 Å
Total Rg	28.85 Å
Atom count	2371
Residues	298
Excluded volume	42695 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4phq__assembly_1__model_1`	Monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4phq__assembly_2__model_1`	Monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`4phq__assembly_3__model_1`	Monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`4phq__assembly_4__model_1`	Monomeric （1）	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 (4)

Entity 1 Entity 1 polymer

Description description	Hemolysin E, chromosomal
Molecular weight formula_weight	33193.7 kDa
Mutation mutation	delta 1-5, A6C, V264C, C87A, C285A
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	9910

CDKTVEVVKNAIETADGALDLYNKYLDQVIPWQTFDETIKELSRFKQEYSQAASVLVGDIKTLLMDSQDKYFEATQTVYEWAGVATQLLAAYILLFDEYNEKKASAQKDILIKVLDDGITKLNEAQKSLLVSSQSFNNASGKLLALDSQLTNDFSEKSSYFQSQVDKIRKEAYAGAAAGVVAGPFGLIISYSIAAGVVEGKLIPELKNKLKSVQNFFTTLSNTVKQANKDIDAAKLKLTTEIAAIGEIKTETETTRFYCDYDDLMLSLLKEAAKKMINTANEYQKRHGKKTLFEVPEV

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	13

Entity 3 Entity 3 non-polymer

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

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	630

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d4phqa_
Class class	h — Coiled coil proteins
Fold Fold fold	h.4 — Antiparallel coiled-coil
Superfamily Superfamily superfamily	h.4.4 — Bacterial hemolysins
Family Family family	h.4.4.1 — Hemolysin E (HlyE, ClyA, SheA)

Domain ID domain_id	d4phqb_
Class class	h — Coiled coil proteins
Fold Fold fold	h.4 — Antiparallel coiled-coil
Superfamily Superfamily superfamily	h.4.4 — Bacterial hemolysins
Family Family family	h.4.4.1 — Hemolysin E (HlyE, ClyA, SheA)

Domain ID domain_id	d4phqc_
Class class	h — Coiled coil proteins
Fold Fold fold	h.4 — Antiparallel coiled-coil
Superfamily Superfamily superfamily	h.4.4 — Bacterial hemolysins
Family Family family	h.4.4.1 — Hemolysin E (HlyE, ClyA, SheA)

Domain ID domain_id	d4phqd_
Class class	h — Coiled coil proteins
Fold Fold fold	h.4 — Antiparallel coiled-coil
Superfamily Superfamily superfamily	h.4.4 — Bacterial hemolysins
Family Family family	h.4.4.1 — Hemolysin E (HlyE, ClyA, SheA)

CATH v4.4 (4 domains)

Domain ID domain_id	4phqA00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1170 — Hemolysin E; Chain: A;
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	4phqB00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1170 — Hemolysin E; Chain: A;
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	4phqC00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1170 — Hemolysin E; Chain: A;
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	4phqD00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1170 — Hemolysin E; Chain: A;
Homologous superfamily homologous superfamily	10 —

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Unit-cell length a length_a	176.880 Å
Unit-cell length b length_b	48.440 Å
Unit-cell length c length_c	152.430 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	102.33 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.940 Å
Low-resolution limit resolution_low	38.540 Å
R factor r_factor	0.1731
R_work r_work	0.1721
R_free r_free	0.2137

ClyA CC6/264 ox (6-303)

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

Hemolysin E, chromosomal

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

4phq__assembly_3__model_1

4phq__assembly_3__model_1 | I(q)

4phq__assembly_3__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

ClyA CC6/264 ox (6-303)

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

Hemolysin E, chromosomal

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

4phq__assembly_3__model_1

4phq__assembly_3__model_1 | I(q)

4phq__assembly_3__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)