SAXSdb — 9p6c

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

Hemolysin

Bordetella pertussis

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1529–1680	Mutation：D1533N, A1542N, D1560N, S1569N, D1587N, H1598N, H1608N	CA CALCIUM ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.5；289 K；Buffer: 0.1 M MES, 0.1 M imidazole, pH 6.5 Precipitant: 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD; 0.02 M of each amino acid (L-glutamate, DL-alanine, glycine, DL-lysine, and DL-serine) Protein solution: 50 mM Tris, 150 mM NaCl, 10 mM CaCl2, pH 8	Resolution 1.99 Å R-free 0.292
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1529–1680	Mutation：D1533N, A1542N, D1560N, S1569N, D1587N, H1598N, H1608N	CA CALCIUM ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.5；289 K；Buffer: 0.1 M MES, 0.1 M imidazole, pH 6.5 Precipitant: 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD; 0.02 M of each amino acid (L-glutamate, DL-alanine, glycine, DL-lysine, and DL-serine) Protein solution: 50 mM Tris, 150 mM NaCl, 10 mM CaCl2, pH 8	Resolution 1.99 Å R-free 0.292

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 9P6C	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5CXL CRYSTAL STRUCTURE OF RTX DOMAIN BLOCK V OF ADENYLATE CYCLASE TOXIN FROM BORDETELLA PERTUSSIS Deposited 2015-07-29	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1529–1681（153 aa） Fragment：BLOCK V OF RTX DOMAIN (UNP RESISDUES 1529-1681)	Not recorded	CA CALCIUM ION × 8 NO3 NITRATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291.15 K；BUFFER COMPOSITION: 5 mM TRIS-HCL PH=7.4, 150 mM NaCl, 10 mM CaCl2. PRECIPITANT COMPOSITION: 0.2 M MAGNESIUM NITRATE, 20% V/V PEG 3350,	Resolution 1.45 Å R-free 0.207
5CXL CRYSTAL STRUCTURE OF RTX DOMAIN BLOCK V OF ADENYLATE CYCLASE TOXIN FROM BORDETELLA PERTUSSIS Deposited 2015-07-29	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1529–1681（153 aa） Fragment：BLOCK V OF RTX DOMAIN (UNP RESISDUES 1529-1681)	Not recorded	CA CALCIUM ION × 8 NO3 NITRATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291.15 K；BUFFER COMPOSITION: 5 mM TRIS-HCL PH=7.4, 150 mM NaCl, 10 mM CaCl2. PRECIPITANT COMPOSITION: 0.2 M MAGNESIUM NITRATE, 20% V/V PEG 3350,	Resolution 1.45 Å R-free 0.207
6SUS Crystal structure of RTX domain blocks IV and V of adenylate cyclase toxin from Bordetella pertussis Deposited 2019-09-16	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1371–1690（320 aa）	Not recorded	CA CALCIUM ION × 15 PGE TRIETHYLENE GLYCOL × 2 GOL GLYCEROL × 2 NO3 NITRATE ION × 1 EDO 1,2-ETHANEDIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.2 M NH4NO3 20% w/v PEG 3350	Resolution 1.76 Å R-free 0.201
9P0C Crystal structure of Ca2+-bound RTX domain block V of adenylate cyclase toxin from Bordetella pertussis Deposited 2025-06-06	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1529–1680（152 aa）	Not recorded	CA CALCIUM ION × 8 ZN ZINC ION × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；289.15 K；Buffer: 40 mM polyamines, 100 mM glycylglycine and 2-Amino-2-methyl-1,3-propanediol (AMPD), pH 8.5. Precipitant: 31% v/v of 10% w/v PEG 20k, 50% w/v trimethylpropane (TMP), 2% w/v NDSB-195.	Resolution 1.70 Å R-free 0.208
9P0C Crystal structure of Ca2+-bound RTX domain block V of adenylate cyclase toxin from Bordetella pertussis Deposited 2025-06-06	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1529–1680（152 aa）	Not recorded	CA CALCIUM ION × 8 ZN ZINC ION × 3 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；289.15 K；Buffer: 40 mM polyamines, 100 mM glycylglycine and 2-Amino-2-methyl-1,3-propanediol (AMPD), pH 8.5. Precipitant: 31% v/v of 10% w/v PEG 20k, 50% w/v trimethylpropane (TMP), 2% w/v NDSB-195.	Resolution 1.70 Å R-free 0.208
9P0D Crystal structure of Sr2+-bound RTX domain block V of adenylate cyclase toxin from Bordetella pertussis Deposited 2025-06-06	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1529–1680（152 aa）	Not recorded	SR STRONTIUM ION × 8 CL CHLORIDE ION × 1 NA SODIUM ION × 1 FOR FORMYL GROUP × 2 GOL GLYCEROL × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；289 K；Buffer: 100 mM amino acids, 100 mM imidazole, 100 mM 2-(N-morpholino)ethanesulfonic acid (MES), pH 6.5. Precipitant: 37.5% v/v of 25% v/v 2-Methyl-2,4-pentanediol (MPD), 25% w/v PEG 1000, 25% w/v PEG 3350	Resolution 1.50 Å R-free 0.201

4 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9p6c
Deposition date deposition_date	2025-06-18
最后修订 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

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	20.87 Å
Radius of gyration Rg (electron density) rg_electron	20.54 Å
Forward intensity I(0) i0	21726600.00
Molecular weight molecular_weight	32872.0 kDa
Excluded volume excluded_volume	39834 Å³
Envelope volume envelope_volume	45606 Å³
Hydration-shell volume shell_volume	19261 Å³
Envelope diameter envelope_diameter	79.1 Å
Shell Rg shell_rg	26.79 Å
Envelope Rg envelope_rg	21.34 Å
Shape Rg shape_rg	20.58 Å
Total Rg total_rg	21.19 Å
Total atoms total_atoms	2292
Residues n_residues	310
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	77.8 Å
Rg (real space) rg_real	21.00 Å
Rg uncertainty (real space) rg_real_error	0.58 Å
I(0) (real space) i0_real	2.1730e+07
I(0) uncertainty (real space) i0_real_error	2.8470e+05
Rg (reciprocal space) rg_reciprocal	20.97 Å
I(0) (reciprocal space) i0_reciprocal	21730000.0000
Solution quality estimate total_estimate	0.7911
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.7 Å
Skewness Skewness skewness	0.624
Kurtosis Kurtosis kurtosis	0.299
Angular range angular_range	— – 0.3800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2757000.0000
Real-space data points n_real_points	70
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.484; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.882; Smooth: 0.947

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. 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

来源 Source

来源生物 organism	Bordetella pertussis
NCBI Class编号 ncbi_taxonomy_id	520
宿主生物 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

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8. Citations (1)

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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

fit	/app/data/saxs_computation/p6/9p6c/9p6c.fit
pddf	/app/data/pr_computation/p6/9p6c/9p6c.pr.out
profile	/app/data/saxs_computation/p6/9p6c/9p6c.dat

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

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction