2hqs

Crystal structure of TolB/Pal complex

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	Peptidoglycan-associated lipoprotein × 1 （P0A912） ACETATE ION × 2 SULFATE ION × 1 GLYCEROL × 2 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Peptidoglycan-associated lipoprotein × 1 （P0A912） ACETATE ION × 2 SULFATE ION × 1 GLYCEROL × 2 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Peptidoglycan-associated lipoprotein × 1 （P0A912） ACETATE ION × 1 SULFATE ION × 1 GLYCEROL × 1 water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	Peptidoglycan-associated lipoprotein × 1 （P0A912） ACETATE ION × 2 SULFATE ION × 3 GLYCEROL × 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 2–409； UniProt 23–430 Author chain B； PDBConstruct 2–409； UniProt 23–430 Author chain D； PDBConstruct 2–409； UniProt 23–430 Author chain F； PDBConstruct 2–409； UniProt 23–430

Peptidoglycan-associated lipoprotein

Escherichia coli

UniProt P0A912

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） ACETATE ION × 2 SULFATE ION × 1 GLYCEROL × 2 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Protein tolB × 1 （P0A855） ACETATE ION × 2 SULFATE ION × 1 GLYCEROL × 2 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Protein tolB × 1 （P0A855） ACETATE ION × 1 SULFATE ION × 1 GLYCEROL × 1 water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	Protein tolB × 1 （P0A855） ACETATE ION × 2 SULFATE ION × 3 GLYCEROL × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PAL_ECOLI
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 2–110； UniProt 65–173 Author chain E； PDBConstruct 2–110； UniProt 65–173 Author chain G； PDBConstruct 2–110； UniProt 65–173 Author chain H； PDBConstruct 2–110； UniProt 65–173

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	2hqs
Deposition date deposition_date	2006-07-19
Structure title title	Crystal structure of TolB/Pal complex
Keywords keywords	TolB, Pal, Tol, TRANSPORT PROTEIN-LIPOPROTEIN COMPLEX; TRANSPORT PROTEIN/LIPOPROTEIN
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.

2hqs__assembly_2__model_1

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

Download this curve (.dat)

2hqs__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2hqs__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	26.19 Å
Rg (electron density)	25.65 Å
Total Rg	26.28 Å
Atom count	3964
Residues	517
Excluded volume	69663 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2hqs__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2hqs__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2hqs__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`2hqs__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 (6)

Entity 1 Entity 1 polymer

Description description	Protein tolB
Molecular weight formula_weight	44468.3 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,D,F
Atom count atom_count	18839

MVRIVIDSGVDSGRPIGVVPFQWAGPGAAPEDIGGIVAADLRNSGKFNPLDRARLPQQPGSAQEVQPAAWSALGIDAVVVGQVTPNPDGSYNVAYQLVDTGGAPGTVLAQNSYKVNKQWLRYAGHTASDEVFEKLTGIKGAFRTRIAYVVQTNGGQFPYELRVSDYDGYNQFVVHRSPQPLMSPAWSPDGSKLAYVTFESGRSALVIQTLANGAVRQVASFPRHNGAPAFSPDGSKLAFALSKTGSLNLYVMDLASGQIRQVTDGRSNNTEPTWFPDSQNLAFTSDQAGRPQVYKVNINGGAPQRITWEGSQNQDADVSSDGKFMVMVSSNGGQQHIAKQDLATGGVQVLSSTFLDETPSLAPNGTMVIYSSSQGMGSVLNLVSTDGRFKARLPATDGQVKFPAWSPYLHHHHHH

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	Peptidoglycan-associated lipoprotein
Molecular weight formula_weight	13518.1 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

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

MLQQNNIVYFDLDKYDIRSDFAQMLDAHANFLRSNPSYKVTVEGHADERGTPEYNISLGERRANAVKMYLQGKGVSADQISIVSYGKEKPAVLGHDEAAYSKNRRAVLVYLEHHHHHH

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

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	7

Entity 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 5 Entity 5 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	2812

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6. Fold Classification (SCOP + CATH) 32 domains

SCOP 2.08 (20 domains)

Domain ID domain_id	d2hqsa1
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	d2hqsa2
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	d2hqsa3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2hqsb1
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	d2hqsb2
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	d2hqsb3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2hqsc2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.79 — Bacillus chorismate mutase-like
Superfamily Superfamily superfamily	d.79.7 — OmpA-like
Family Family family	d.79.7.1 — OmpA-like

Domain ID domain_id	d2hqsc3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2hqsd1
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	d2hqsd2
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	d2hqsd3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2hqse2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.79 — Bacillus chorismate mutase-like
Superfamily Superfamily superfamily	d.79.7 — OmpA-like
Family Family family	d.79.7.1 — OmpA-like

Domain ID domain_id	d2hqse3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2hqsf1
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	d2hqsf2
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	d2hqsf3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2hqsg2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.79 — Bacillus chorismate mutase-like
Superfamily Superfamily superfamily	d.79.7 — OmpA-like
Family Family family	d.79.7.1 — OmpA-like

Domain ID domain_id	d2hqsg3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2hqsh2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.79 — Bacillus chorismate mutase-like
Superfamily Superfamily superfamily	d.79.7 — OmpA-like
Family Family family	d.79.7.1 — OmpA-like

Domain ID domain_id	d2hqsh3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (12 domains)

Domain ID domain_id	2hqsA01
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	2hqsA02
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	2hqsB01
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	2hqsB02
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	2hqsC00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily	60 — OmpA-like domain

Domain ID domain_id	2hqsD01
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	2hqsD02
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	2hqsE00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily	60 — OmpA-like domain

Domain ID domain_id	2hqsF01
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	2hqsF02
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	2hqsG00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily	60 — OmpA-like domain

Domain ID domain_id	2hqsH00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily	60 — OmpA-like domain

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Unit-cell length a length_a	74.847 Å
Unit-cell length b length_b	89.049 Å
Unit-cell length c length_c	91.051 Å
Unit-cell angle α angle_alpha	87.15 °
Unit-cell angle β angle_beta	89.62 °
Unit-cell angle γ angle_gamma	68.81 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	1.500 Å
Low-resolution limit resolution_low	38.320 Å
R factor r_factor	0.1820
R_work r_work	0.1804
R_free r_free	0.2127

Crystal structure of TolB/Pal complex

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

Peptidoglycan-associated lipoprotein

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

2hqs__assembly_2__model_1

2hqs__assembly_2__model_1 | I(q)

2hqs__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 32 domains

SCOP 2.08 (20 domains)

CATH v4.4 (12 domains)

7. Citations (1)

Crystal structure of TolB/Pal complex

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

Peptidoglycan-associated lipoprotein

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

2hqs__assembly_2__model_1

2hqs__assembly_2__model_1 | I(q)

2hqs__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 32 domains

SCOP 2.08 (20 domains)

CATH v4.4 (12 domains)

7. Citations (1)