5imw

Trapped Toxin

Method: X-RAY DIFFRACTION

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

Intermedilysin

Streptococcus intermedius

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	No other associated polymer	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	No other associated polymer	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9LCB8_STRIT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–471； UniProt 57–527 Author chain B； PDBConstruct 1–471； UniProt 57–527

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	5imw
Deposition date deposition_date	2016-03-07
Structure title title	Trapped Toxin
Keywords keywords	Toxin, Locked; 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.

5imw__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

5imw__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5imw__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	32.27 Å
Rg (electron density)	32.42 Å
Total Rg	32.55 Å
Atom count	7128
Residues	462
Excluded volume	63445 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5imw__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5imw__assembly_2__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 (1)

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d5imwa1
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.69 — Perfringolysin N-terminal-like
Superfamily Superfamily superfamily	f.69.1 — Perfringolysin N-terminal-like
Family Family family	f.69.1.1 — Perfringolysin N-terminal-like

Domain ID domain_id	d5imwa2
Class class	b — All beta proteins
Fold Fold fold	b.183 — Perfringolysin C-terminal-like
Superfamily Superfamily superfamily	b.183.1 — Perfringolysin C-terminal-like
Family Family family	b.183.1.1 — Perfringolysin C-terminal-like

Domain ID domain_id	d5imwb1
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.69 — Perfringolysin N-terminal-like
Superfamily Superfamily superfamily	f.69.1 — Perfringolysin N-terminal-like
Family Family family	f.69.1.1 — Perfringolysin N-terminal-like

Domain ID domain_id	d5imwb2
Class class	b — All beta proteins
Fold Fold fold	b.183 — Perfringolysin C-terminal-like
Superfamily Superfamily superfamily	b.183.1 — Perfringolysin C-terminal-like
Family Family family	b.183.1.1 — Perfringolysin C-terminal-like

CATH v4.4 (8 domains)

Domain ID domain_id	5imwA01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	840 — HIV-1 Reverse Transcriptase; Chain A, domain 3
Homologous superfamily homologous superfamily	10 — Thiol-activated cytolysin superfamily/Thiol-activated cytolysin, alpha-beta domain

Domain ID domain_id	5imwA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1040 — Carboxypeptidase Inhibitor; Chain A
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	5imwA03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	30 — Glutaredoxin
Homologous superfamily homologous superfamily	40 — Perfringolysin

Domain ID domain_id	5imwA04
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1430 — Perfringolysin, domain 4

Domain ID domain_id	5imwB01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	840 — HIV-1 Reverse Transcriptase; Chain A, domain 3
Homologous superfamily homologous superfamily	10 — Thiol-activated cytolysin superfamily/Thiol-activated cytolysin, alpha-beta domain

Domain ID domain_id	5imwB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1040 — Carboxypeptidase Inhibitor; Chain A
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	5imwB03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	30 — Glutaredoxin
Homologous superfamily homologous superfamily	40 — Perfringolysin

Domain ID domain_id	5imwB04
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1430 — Perfringolysin, domain 4

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Unit-cell length a length_a	84.465 Å
Unit-cell length b length_b	101.565 Å
Unit-cell length c length_c	175.735 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 2 21
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.890 Å
Low-resolution limit resolution_low	48.135 Å
R factor r_factor	0.2603
R_work r_work	0.2584
R_free r_free	0.2950

Description description	Intermedilysin
Molecular weight formula_weight	51885.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	14175

Trapped Toxin

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

Intermedilysin

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

5imw__assembly_2__model_1

5imw__assembly_2__model_1 | I(q)

5imw__assembly_2__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 (1)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Source organism organism	Streptococcus intermedius
NCBI taxonomy ID ncbi_taxonomy_id	1338
Host organism host_organism	Escherichia coli

Trapped Toxin

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

Intermedilysin

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

5imw__assembly_2__model_1

5imw__assembly_2__model_1 | I(q)

5imw__assembly_2__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 (1)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. Citations (1)