SAXSdb — 1ca1

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

ALPHA-TOXIN

Clostridium perfringens

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 29–398	Not recorded	ZN ZINC ION × 1 CD CADMIUM ION × 12	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；pH 7.5	Resolution 1.90 Å R-free 0.254
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 29–398	Not recorded	ZN ZINC ION × 2 CD CADMIUM ION × 24	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；pH 7.5	Resolution 1.90 Å R-free 0.254
3	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 29–398	Not recorded	ZN ZINC ION × 2 CD CADMIUM ION × 24	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；pH 7.5	Resolution 1.90 Å R-free 0.254

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 1CA1	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1GYG R32 CLOSED FORM OF ALPHA-TOXIN FROM CLOSTRIDIUM PERFRINGENS STRAIN CER89L43 Deposited 2002-04-23	Different oligomeric state Different ligand/ion Different experimental conditions	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 29–398（370 aa）	Not recorded	ZN ZINC ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；10 MG/ML PH 7.5, AGAINST 1.7M NACL PH 4.6	Resolution 1.90 Å R-free 0.254
1GYG R32 CLOSED FORM OF ALPHA-TOXIN FROM CLOSTRIDIUM PERFRINGENS STRAIN CER89L43 Deposited 2002-04-23	Different oligomeric state Different ligand/ion Different experimental conditions	Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain B 29–398（370 aa）	Not recorded	ZN ZINC ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；10 MG/ML PH 7.5, AGAINST 1.7M NACL PH 4.6	Resolution 1.90 Å R-free 0.254
1QM6 Closed form of Clostridium perfringens alpha-toxin strain NCTC8237 Deposited 1999-09-21	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 29–398（370 aa）	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.7；PROTEIN WAS CRYSTALLISED BY HANGING DROP FROM 1.8-2.0 M NACL IN 0.1 M NA ACETATE, PH 4.7 OR 4.8	Resolution 2.50 Å R-free 0.247
1QM6 Closed form of Clostridium perfringens alpha-toxin strain NCTC8237 Deposited 1999-09-21	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 29–398（370 aa）	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.7；PROTEIN WAS CRYSTALLISED BY HANGING DROP FROM 1.8-2.0 M NACL IN 0.1 M NA ACETATE, PH 4.7 OR 4.8	Resolution 2.50 Å R-free 0.247
1QMD calcium bound closed form alpha-toxin from Clostridium perfringens Deposited 1999-09-27	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 29–398（370 aa）	Not recorded	ZN ZINC ION × 2 CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.7；PROTEIN WAS CRYSTALLISED BY HANGING DROP FROM 1.8-2.0 M NACL IN 0.1 M NA ACETATE, PH 4.7 OR 4.8	Resolution 2.20 Å R-free 0.235
1QMD calcium bound closed form alpha-toxin from Clostridium perfringens Deposited 1999-09-27	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 29–398（370 aa）	Not recorded	ZN ZINC ION × 2 CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.7；PROTEIN WAS CRYSTALLISED BY HANGING DROP FROM 1.8-2.0 M NACL IN 0.1 M NA ACETATE, PH 4.7 OR 4.8	Resolution 2.20 Å R-free 0.235

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

View Construct and Data Evidence

UniProt name	PHLC1_CLOPE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–370； UniProt 29–398

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	1ca1
Deposition date deposition_date	1998-04-22
Structure title title	ALPHA-TOXIN FROM CLOSTRIDIUM PERFRINGENS
Keywords keywords	ZINC PHOSPHOLIPASE C, GANGRENE DETERMINANT, C2 DOMAIN, CA AND MEMBRANE BINDING, HYDROLASE; HYDROLASE
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	22.31 Å
Radius of gyration Rg (electron density) rg_electron	21.35 Å
Forward intensity I(0) i0	36733900.00
Molecular weight molecular_weight	43962.0 kDa
Excluded volume excluded_volume	53316 Å³
Envelope volume envelope_volume	61020 Å³
Hydration-shell volume shell_volume	23919 Å³
Envelope diameter envelope_diameter	77.2 Å
Shell Rg shell_rg	28.04 Å
Envelope Rg envelope_rg	21.49 Å
Shape Rg shape_rg	21.23 Å
Total Rg total_rg	22.43 Å
Total atoms total_atoms	3022
Residues n_residues	370
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	72.5 Å
Rg (real space) rg_real	22.24 Å
Rg uncertainty (real space) rg_real_error	0.36 Å
I(0) (real space) i0_real	3.6730e+07
I(0) uncertainty (real space) i0_real_error	4.5960e+05
Rg (reciprocal space) rg_reciprocal	22.26 Å
I(0) (reciprocal space) i0_reciprocal	36730000.0000
Solution quality estimate total_estimate	0.8954
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	27.5 Å
Skewness Skewness skewness	0.263
Kurtosis Kurtosis kurtosis	-0.373
Angular range angular_range	— – 0.3550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6066000.0000
Real-space data points n_real_points	67
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.879; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.999

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	ALPHA-TOXIN
Molecular weight formula_weight	42615.9 kDa
EC 编号 ec_number	3.1.4.3
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3195

WDGKIDGTGTHAMIVTQGVSILENDLSKNEPESVRKNLEILKENMHELQLGSTYPDYDKNAYDLYQDHFWDPDTDNNFSKDNSWYLAYSIPDTGESQIRKFSALARYEWQRGNYKQATFYLGEAMHYFGDIDTPYHPANVTAVDSAGHVKFETFAEERKEQYKINTVGCKTNEDFYADILKNKDFNAWSKEYARGFAKTGKSIYYSHASMSHSWDDWDYAAKVTLANSQKGTAGYIYRFLHDVSEGNDPSVGKNVKELVAYISTSGEKDAGTDDYMYFGIKTKDGKTQEWEMDNPGNDFMTGSKDTYTFKLKDENLKIDDIQNMWIRKRKYTAFPDAYKPENIKVIANGKVVVDKDINEWISGNSTYNIK

来源 Source

来源生物 organism	Clostridium perfringens
NCBI Class编号 ncbi_taxonomy_id	1502
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	CADMIUM ION
Molecular weight formula_weight	112.4 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	173

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1ca1a1
Class class	a — All alpha proteins
Fold Fold fold	a.124 — Phospholipase C/P1 nuclease
Superfamily Superfamily superfamily	a.124.1 — Phospholipase C/P1 nuclease
Family Family family	a.124.1.1 — Phospholipase C

Domain ID domain_id	d1ca1a2
Class class	b — All beta proteins
Fold Fold fold	b.12 — Lipase/lipooxygenase domain (PLAT/LH2 domain)
Superfamily Superfamily superfamily	b.12.1 — Lipase/lipooxygenase domain (PLAT/LH2 domain)
Family Family family	b.12.1.3 — Alpha-toxin, C-terminal domain

CATH v4.4 (2 domains)

Domain ID domain_id	1ca1A01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	575 — P1 Nuclease
Homologous superfamily homologous superfamily	10 — P1 Nuclease

Domain ID domain_id	1ca1A02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	60 — Lipoxygenase-1
Homologous superfamily homologous superfamily	20 — PLAT/LH2 domain

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8. Citations (2)

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Unit-cell length a length_a	61.300 Å
Unit-cell length b length_b	177.300 Å
Unit-cell length c length_c	79.100 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	25.000 Å
R factor r_factor	0.2080
R_work r_work	0.2080
R_free r_free	0.2540

fit	/app/data/saxs_computation/ca/1ca1/1ca1.fit
pddf	/app/data/pr_computation/ca/1ca1/1ca1.pr.out
profile	/app/data/saxs_computation/ca/1ca1/1ca1.dat

ALPHA-TOXIN FROM CLOSTRIDIUM PERFRINGENS

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

ALPHA-TOXIN

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