SAXSdb — 9p6c

▼

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

Hemolysin

Bordetella pertussis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	CALCIUM ION × 8 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	CALCIUM ION × 8 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CYAA_BORPE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 20–171； UniProt 1529–1680 Author chain B； PDBConstruct 20–171； UniProt 1529–1680

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	9p6c
Deposition date deposition_date	2025-06-18
Last revision last_revision	2025-12-24
Structure title title	RTX domain block V of adenylate cyclase toxin with mutations D1533N, A1542N, D1560N, S1569N, D1587N, H1598N, H1608N
Keywords keywords	Calcium binding, Repeats-In-Toxin, beta roll, TOXIN; TOXIN
Experimental Method method	X-RAY DIFFRACTION

▼

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.

9p6c__assembly_1__model_1

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

Download this curve (.dat)

9p6c__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9p6c__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	16.21 Å
Rg (electron density)	15.20 Å
Total Rg	16.14 Å
Atom count	1173
Residues	158
Excluded volume	20384 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9p6c__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`9p6c__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Hemolysin
Molecular weight formula_weight	19141.5 kDa
Mutation mutation	D1533N, A1542N, D1560N, S1569N, D1587N, H1598N, H1608N
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2331

MRGSHHHHHHGSHMELGASGSARNDVLIGDAGNNVLNGLAGNDVLSGGAGNDVLLGDEGNDLLSGDAGNDDLFGGQGNDTYLFGVGYGNDTIYESGGGNDTIRINAGADQLWFARQGNDLEIRILGTDDALTVHDWYRDADHRVEIIHAANQAVDQAGIEKLVEAMAQYPDEFTSLEKLN

Source Source

Source organism organism	Bordetella pertussis
NCBI taxonomy ID ncbi_taxonomy_id	520
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	16

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	39

▶

Unit-cell length a length_a	33.305 Å
Unit-cell length b length_b	38.003 Å
Unit-cell length c length_c	57.016 Å
Unit-cell angle α angle_alpha	84.13 °
Unit-cell angle β angle_beta	81.47 °
Unit-cell angle γ angle_gamma	67.61 °
Molecules per unit cell Z z_pdb	2

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

Resolution resolution	1.990 Å
Low-resolution limit resolution_low	30.580 Å
R factor r_factor	0.2316
R_work r_work	0.2285
R_free r_free	0.2923

RTX domain block V of adenylate cyclase toxin with mutations D1533N, A1542N, D1560N, S1569N, D1587N, H1598N, H1608N

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

Hemolysin

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

9p6c__assembly_1__model_1

9p6c__assembly_1__model_1 | I(q)

9p6c__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 non-polymer

Entity 3 Entity 3 water

7. Citations (1)

RTX domain block V of adenylate cyclase toxin with mutations D1533N, A1542N, D1560N, S1569N, D1587N, H1598N, H1608N

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

Hemolysin

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

9p6c__assembly_1__model_1

9p6c__assembly_1__model_1 | I(q)

9p6c__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 non-polymer

Entity 3 Entity 3 water

7. Citations (1)