2ivz

Structure of TolB in complex with a peptide of the colicin E9 T- domain

Method: X-RAY DIFFRACTION

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

PROTEIN TOLB

ESCHERICHIA COLI

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	COLICIN-E9 × 1 （P09883） CALCIUM ION × 2 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	COLICIN-E9 × 1 （P09883） CALCIUM ION × 1 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	COLICIN-E9 × 1 （P09883） CALCIUM ION × 2 water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	COLICIN-E9 × 1 （P09883） CALCIUM ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TOLB_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–431； UniProt 1–430 Author chain B； PDBConstruct 2–431； UniProt 1–430 Author chain C； PDBConstruct 2–431； UniProt 1–430 Author chain D； PDBConstruct 2–431； UniProt 1–430

COLICIN-E9

OrganismNot specified

UniProt P09883

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	PROTEIN TOLB × 1 （P0A855） CALCIUM ION × 2 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	PROTEIN TOLB × 1 （P0A855） CALCIUM ION × 1 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	PROTEIN TOLB × 1 （P0A855） CALCIUM ION × 2 water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	PROTEIN TOLB × 1 （P0A855） CALCIUM ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CEA9_ECOLI
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain E； PDBConstruct 1–16； UniProt 32–47 Author chain F； PDBConstruct 1–16； UniProt 32–47 Author chain G； PDBConstruct 1–16； UniProt 32–47 Author chain H； PDBConstruct 1–16； UniProt 32–47

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	2ivz
Deposition date deposition_date	2006-06-23
Structure title title	Structure of TolB in complex with a peptide of the colicin E9 T- domain
Keywords keywords	;PROTEIN TRANSPORT/HYDROLASE, PROTEIN-PROTEIN INTERACTION, PROTEIN TRANSPORT, BACTERIOCIN TRANSPORT, TOLB, COLICIN, PLASMID, NUCLEASE, HYDROLASE, TRANSPORT, ANTIBIOTIC, PERIPLASMIC, BACTERIOCIN, NATIVELY DISORDERED PROTEINS, PROTEIN TRANSPORT-HYDROLASE COMPLEX, ENDONUCLEASE, ANTIMICROBIAL, TRANSLOCATION ;; PROTEIN TRANSPORT/HYDROLASE
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.

2ivz__assembly_1__model_1

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

Download this curve (.dat)

2ivz__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2ivz__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	23.40 Å
Rg (electron density)	22.46 Å
Total Rg	23.24 Å
Atom count	3076
Residues	407
Excluded volume	54015 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2ivz__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2ivz__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2ivz__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`2ivz__assembly_4__model_1`	dimeric （2）	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	PROTEIN TOLB
Molecular weight formula_weight	47196.6 kDa
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	13614

MMKQALRVAFGFLILWASVLHAEVRIVIDSGVDSGRPIGVVPFQWAGPGAAPEDIGGIVAADLRNSGKFNPLDRARLPQQPGSAQEVQPAAWSALGIDAVVVGQVTPNPDGSYNVAYQLVDTGGAPGTVLAQNSYKVNKQWLRYAGHTASDEVFEKLTGIKGAFRTRIAYVVQTNGGQFPYELRVSDYDGYNQFVVHRSPQPLMSPAWSPDGSKLAYVTFESGRSALVIQTLANGAVRQVASFPRHNGAPAFSPDGSKLAFALSKTGSLNLYVMDLASGQIRQVTDGRSNNTEPTWFPDSQNLAFTSDQAGRPQVYKVNINGGAPQRITWEGSQNQDADVSSDGKFMVMVSSNGGQQHIAKQDLATGGVQVLSSTFLDETPSLAPNGTMVIYSSSQGMGSVLNLVSTDGRFKARLPATDGQVKFPAWSPYLLEHHHHHH

Source Source

Source organism organism	ESCHERICHIA COLI
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 polymer

Description description	COLICIN-E9
Molecular weight formula_weight	1607.6 kDa
EC 编号 ec_number	3.1.-.-
Source method src_method	syn
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,F,G,H

GASDGSGWSSENNPWG

Entity 3 Entity 3 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1242

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d2ivza1
Class class	b — All beta proteins
Fold Fold fold	b.68 — 6-bladed beta-propeller
Superfamily Superfamily superfamily	b.68.4 — TolB, C-terminal domain
Family Family family	b.68.4.1 — TolB, C-terminal domain

Domain ID domain_id	d2ivza2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.51 — Anticodon-binding domain-like
Superfamily Superfamily superfamily	c.51.2 — TolB, N-terminal domain
Family Family family	c.51.2.1 — TolB, N-terminal domain

Domain ID domain_id	d2ivzb1
Class class	b — All beta proteins
Fold Fold fold	b.68 — 6-bladed beta-propeller
Superfamily Superfamily superfamily	b.68.4 — TolB, C-terminal domain
Family Family family	b.68.4.1 — TolB, C-terminal domain

Domain ID domain_id	d2ivzb2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.51 — Anticodon-binding domain-like
Superfamily Superfamily superfamily	c.51.2 — TolB, N-terminal domain
Family Family family	c.51.2.1 — TolB, N-terminal domain

Domain ID domain_id	d2ivzc1
Class class	b — All beta proteins
Fold Fold fold	b.68 — 6-bladed beta-propeller
Superfamily Superfamily superfamily	b.68.4 — TolB, C-terminal domain
Family Family family	b.68.4.1 — TolB, C-terminal domain

Domain ID domain_id	d2ivzc2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.51 — Anticodon-binding domain-like
Superfamily Superfamily superfamily	c.51.2 — TolB, N-terminal domain
Family Family family	c.51.2.1 — TolB, N-terminal domain

Domain ID domain_id	d2ivzd1
Class class	b — All beta proteins
Fold Fold fold	b.68 — 6-bladed beta-propeller
Superfamily Superfamily superfamily	b.68.4 — TolB, C-terminal domain
Family Family family	b.68.4.1 — TolB, C-terminal domain

Domain ID domain_id	d2ivzd2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.51 — Anticodon-binding domain-like
Superfamily Superfamily superfamily	c.51.2 — TolB, N-terminal domain
Family Family family	c.51.2.1 — TolB, N-terminal domain

CATH v4.4 (8 domains)

Domain ID domain_id	2ivzA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10070 — TolB, N-terminal domain

Domain ID domain_id	2ivzA02
Class class	2 — Mainly Beta
Architecture architecture	120 — 6 Propeller
Topology topology	10 — Neuraminidase
Homologous superfamily homologous superfamily	30 — TolB, C-terminal domain

Domain ID domain_id	2ivzB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10070 — TolB, N-terminal domain

Domain ID domain_id	2ivzB02
Class class	2 — Mainly Beta
Architecture architecture	120 — 6 Propeller
Topology topology	10 — Neuraminidase
Homologous superfamily homologous superfamily	30 — TolB, C-terminal domain

Domain ID domain_id	2ivzC01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10070 — TolB, N-terminal domain

Domain ID domain_id	2ivzC02
Class class	2 — Mainly Beta
Architecture architecture	120 — 6 Propeller
Topology topology	10 — Neuraminidase
Homologous superfamily homologous superfamily	30 — TolB, C-terminal domain

Domain ID domain_id	2ivzD01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10070 — TolB, N-terminal domain

Domain ID domain_id	2ivzD02
Class class	2 — Mainly Beta
Architecture architecture	120 — 6 Propeller
Topology topology	10 — Neuraminidase
Homologous superfamily homologous superfamily	30 — TolB, C-terminal domain

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Unit-cell length a length_a	130.092 Å
Unit-cell length b length_b	39.933 Å
Unit-cell length c length_c	154.848 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	110.62 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	144.340 Å
R factor r_factor	0.1700
R_work r_work	0.1680
R_free r_free	0.2220

Structure of TolB in complex with a peptide of the colicin E9 T- domain

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

PROTEIN TOLB

State in the Current Structure

Other States of the Same Protein in the Database

COLICIN-E9

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

2ivz__assembly_1__model_1

2ivz__assembly_1__model_1 | I(q)

2ivz__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (3)

Structure of TolB in complex with a peptide of the colicin E9 T- domain

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

PROTEIN TOLB

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

COLICIN-E9

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

2ivz__assembly_1__model_1

2ivz__assembly_1__model_1 | I(q)

2ivz__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (3)