SAXSdb — 1qm6

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

PHOSPHOLIPASE C

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 × 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
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 29–398	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

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 1QM6	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CA1 ALPHA-TOXIN FROM CLOSTRIDIUM PERFRINGENS Deposited 1998-04-22	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 × 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
1CA1 ALPHA-TOXIN FROM CLOSTRIDIUM PERFRINGENS Deposited 1998-04-22	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 29–398（370 aa）	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
1CA1 ALPHA-TOXIN FROM CLOSTRIDIUM PERFRINGENS Deposited 1998-04-22	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 29–398（370 aa）	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
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 Different structure-quality metrics	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 Different structure-quality metrics	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
1QMD calcium bound closed form alpha-toxin from Clostridium perfringens Deposited 1999-09-27	Different ligand/ion 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 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 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PHLC_CLOPE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–370； UniProt 29–398 Author chain B； 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	1qm6
Deposition date deposition_date	1999-09-21
Structure title title	Closed form of Clostridium perfringens alpha-toxin strain NCTC8237
Keywords keywords	HYDROLASE, ZINC PHOSPHOLIPASE C, GANGRENE DETERMINANT, C2 DOMAIN, CA AND MEMBRANE BINDING.; 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	31.13 Å
Radius of gyration Rg (electron density) rg_electron	30.61 Å
Forward intensity I(0) i0	120942000.00
Molecular weight molecular_weight	85283.0 kDa
Excluded volume excluded_volume	105550 Å³
Envelope volume envelope_volume	133640 Å³
Hydration-shell volume shell_volume	36327 Å³
Envelope diameter envelope_diameter	104.4 Å
Shell Rg shell_rg	37.60 Å
Envelope Rg envelope_rg	30.30 Å
Shape Rg shape_rg	30.58 Å
Total Rg total_rg	31.34 Å
Total atoms total_atoms	6016
Residues n_residues	740
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	98.0 Å
Rg (real space) rg_real	31.12 Å
Rg uncertainty (real space) rg_real_error	0.74 Å
I(0) (real space) i0_real	1.2090e+08
I(0) uncertainty (real space) i0_real_error	1.8420e+06
Rg (reciprocal space) rg_reciprocal	31.13 Å
I(0) (reciprocal space) i0_reciprocal	120900000.0000
Solution quality estimate total_estimate	0.9022
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	34.6 Å
Skewness Skewness skewness	0.291
Kurtosis Kurtosis kurtosis	-0.517
Angular range angular_range	— – 0.2550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	17390000.0000
Real-space data points n_real_points	52
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.954; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.984; Smooth: 0.877

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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	PHOSPHOLIPASE C
Molecular weight formula_weight	42577.8 kDa
EC 编号 ec_number	3.1.4.3
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	6105

WDGKIDGTGTHAMIVTQGVSILENDLSKNEPESVRKNLEILKENMHELQLGSTYPDYDKNAYDLYQDHFWDPDTDNNFSKDNSWYLAYSIPDTGESQIRKFSALARYEWQRGNYKQATFYLGEAMHYFGDIDTPYHPANVTAVDSAGHVKFETFAEERKEQYKINTAGCKTNEAFYTDILKNKDFNAWSKEYARGFAKTGKSIYYSHASMSHSWDDWDYAAKVTLANSQKGTAGYIYRFLHDVSEGNDPSVGKNVKELVAYISTSGEKDAGTDDYMYFGIKTKDGKTQEWEMDNPGNDFMTGSKDTYTFKLKDENLKIDDIQNMWIRKRKYTAFSDAYKPENIKIIANGKVVVDKDINEWISGNSTYNIK

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	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	89

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1qm6a1
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	d1qm6a2
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

Domain ID domain_id	d1qm6b1
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	d1qm6b2
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 (4 domains)

Domain ID domain_id	1qm6A01
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	1qm6A02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	60 — Lipoxygenase-1
Homologous superfamily homologous superfamily	20 — PLAT/LH2 domain

Domain ID domain_id	1qm6B01
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	1qm6B02
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 (3)

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Unit-cell length a length_a	149.540 Å
Unit-cell length b length_b	149.540 Å
Unit-cell length c length_c	193.830 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	36

Space group space_group	H 3 2
Space-group number int_tables_number	155
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2200
R_work r_work	0.2200
R_free r_free	0.2470

fit	/app/data/saxs_computation/qm/1qm6/1qm6.fit
pddf	/app/data/pr_computation/qm/1qm6/1qm6.pr.out
profile	/app/data/saxs_computation/qm/1qm6/1qm6.dat

Closed form of Clostridium perfringens alpha-toxin strain NCTC8237

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

PHOSPHOLIPASE C

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