2pt7

Crystal structure of Cag VirB11 (HP0525) and an inhibitory protein (HP1451)

Method: X-RAY DIFFRACTION

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

Cag-alfa

Helicobacter pylori

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	Hypothetical protein × 2 （O25990） water × 8	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q7BK04_HELPY
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–330； UniProt 1–330 Author chain B； PDBConstruct 1–330； UniProt 1–330 Author chain C； PDBConstruct 1–330； UniProt 1–330 Author chain D； PDBConstruct 1–330； UniProt 1–330 Author chain E； PDBConstruct 1–330； UniProt 1–330 Author chain F； PDBConstruct 1–330； UniProt 1–330

Hypothetical protein

Helicobacter pylori

UniProt O25990

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	Cag-alfa × 6 （Q7BK04） water × 8	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O25990_HELPY
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain G； PDBConstruct 1–152； UniProt 113–264 Author chain H； PDBConstruct 1–152； UniProt 113–264

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	2pt7
Deposition date deposition_date	2007-05-08
Structure title title	Crystal structure of Cag VirB11 (HP0525) and an inhibitory protein (HP1451)
Keywords keywords	ATPase, Protein-Protein complex, Type IV secretion, hydrolase-protein binding COMPLEX; hydrolase/protein binding
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.

2pt7__assembly_1__model_1

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

Download this curve (.dat)

2pt7__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2pt7__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	40.60 Å
Rg (electron density)	39.92 Å
Total Rg	40.27 Å
Atom count	17207
Residues	2166
Excluded volume	306960 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2pt7__assembly_1__model_1`	octameric （8）	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 (3)

Entity 1 Entity 1 polymer

Description description	Cag-alfa
Molecular weight formula_weight	37632.9 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	17894

MTEDRLSAEDKKFLEVERALKEAALNPLRHATEELFGDFLKMENITEICYNGNKVVWVLKNNGEWQPFDVRDRKAFSLSRLMHFARCCASFKKKTIDNYENPILSSNLANGERVQIVLSPVTVNDETISISIRIPSKTTYPHSFFEEQGFYNLLDNKEQAISAIKDGIAIGKNVIVCGGTGSGKTTYIKSIMEFIPKEERIISIEDTEEIVFKHHKNYTQLFFGGNITSADCLKSCLRMRPDRIILGELRSSEAYDFYNVLCSGHKGTLTTLHAGSSEEAFIRLANMSSSNSAARNIKFESLIEGFKDLIDMIVHINHHKQCDEFYIKHR

Source Source

Source organism organism	Helicobacter pylori
NCBI taxonomy ID ncbi_taxonomy_id	85962
Host organism host_organism	Escherichia coli BL21

Entity 2 Entity 2 polymer

Description description	Hypothetical protein
Molecular weight formula_weight	17578.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

GDKLHEIKQELKDLFSHLPYKINKVEVSLYEPGVLLIDIDGEDSALLIGEKGYRYKALSYLLFNWIHPTYGYSIRLEISTFLQNQEKVMDTQLQSVIMTVHEVGKGQMKAPDGVLTYIALKKLRKAFPNKYVSIKTNLNDEKYIVINDFNNE

Source Source

Source organism organism	Helicobacter pylori
NCBI taxonomy ID ncbi_taxonomy_id	85962
Host organism host_organism	Escherichia coli BL21

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	687

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6. Fold Classification (SCOP + CATH) 22 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d2pt7a_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.11 — RecA protein-like (ATPase-domain)

Domain ID domain_id	d2pt7b_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.11 — RecA protein-like (ATPase-domain)

Domain ID domain_id	d2pt7c_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.11 — RecA protein-like (ATPase-domain)

Domain ID domain_id	d2pt7d_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.11 — RecA protein-like (ATPase-domain)

Domain ID domain_id	d2pt7e_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.11 — RecA protein-like (ATPase-domain)

Domain ID domain_id	d2pt7f_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.11 — RecA protein-like (ATPase-domain)

CATH v4.4 (16 domains)

Domain ID domain_id	2pt7A01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	450 — Beta-Lactamase
Homologous superfamily homologous superfamily	90 —

Domain ID domain_id	2pt7A02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	2pt7B01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	450 — Beta-Lactamase
Homologous superfamily homologous superfamily	90 —

Domain ID domain_id	2pt7B02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	2pt7C01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	450 — Beta-Lactamase
Homologous superfamily homologous superfamily	90 —

Domain ID domain_id	2pt7C02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	2pt7D01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	450 — Beta-Lactamase
Homologous superfamily homologous superfamily	90 —

Domain ID domain_id	2pt7D02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	2pt7E01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	450 — Beta-Lactamase
Homologous superfamily homologous superfamily	90 —

Domain ID domain_id	2pt7E02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	2pt7F01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	450 — Beta-Lactamase
Homologous superfamily homologous superfamily	90 —

Domain ID domain_id	2pt7F02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	2pt7G01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	300 — GMP Synthetase; Chain A, domain 3
Homologous superfamily homologous superfamily	20 — K homology (KH) domain

Domain ID domain_id	2pt7G02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1370 — Ribosomal Protein S8; Chain: A, domain 1
Homologous superfamily homologous superfamily	180 —

Domain ID domain_id	2pt7H01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	300 — GMP Synthetase; Chain A, domain 3
Homologous superfamily homologous superfamily	20 — K homology (KH) domain

Domain ID domain_id	2pt7H02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1370 — Ribosomal Protein S8; Chain: A, domain 1
Homologous superfamily homologous superfamily	180 —

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Unit-cell length a length_a	86.851 Å
Unit-cell length b length_b	86.900 Å
Unit-cell length c length_c	104.129 Å
Unit-cell angle α angle_alpha	111.04 °
Unit-cell angle β angle_beta	95.98 °
Unit-cell angle γ angle_gamma	104.94 °
Molecules per unit cell Z z_pdb	6

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

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	40.000 Å
R factor r_factor	0.2319
R_work r_work	0.2299
R_free r_free	0.2697

Crystal structure of Cag VirB11 (HP0525) and an inhibitory protein (HP1451)

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

Cag-alfa

State in the Current Structure

Other States of the Same Protein in the Database

Hypothetical protein

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

2pt7__assembly_1__model_1

2pt7__assembly_1__model_1 | I(q)

2pt7__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 22 domains

SCOP 2.08 (6 domains)

CATH v4.4 (16 domains)

7. Citations (1)

Crystal structure of Cag VirB11 (HP0525) and an inhibitory protein (HP1451)

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

Cag-alfa

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Hypothetical protein

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

2pt7__assembly_1__model_1

2pt7__assembly_1__model_1 | I(q)

2pt7__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 22 domains

SCOP 2.08 (6 domains)

CATH v4.4 (16 domains)

7. Citations (1)