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1qmd

calcium bound closed form alpha-toxin from Clostridium perfringens

Method: X-RAY DIFFRACTION Dmax: 100.1 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

PHOSPHOLIPASE C

CLOSTRIDIUM PERFRINGENS

UniProt P15310

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 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
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 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

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 1QMD 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
1QM6 Closed form of Clostridium perfringens alpha-toxin strain NCTC8237 Deposited 1999-09-21 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 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 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

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.

SAXS scattering curve SAXS Profile

SAXS profile for 1qmd

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1qmd
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1qmd
Deposition date deposition_date1999-09-27
Structure title titlecalcium bound closed form alpha-toxin from Clostridium perfringens
Keywords keywordsHYDROLASE, ZINC PHOSPHOLIPASE C, GANGRENE DETERMINANT, C2 DOMAIN, CA AND MEMBRANE BINDING.; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier31.03 Å
Radius of gyration Rg (electron density) rg_electron30.52 Å
Forward intensity I(0) i0121256000.00
Molecular weight molecular_weight85524.0 kDa
Excluded volume excluded_volume105860 ų
Envelope volume envelope_volume132590 ų
Hydration-shell volume shell_volume36102 ų
Envelope diameter envelope_diameter106.5 Å
Shell Rg shell_rg37.53 Å
Envelope Rg envelope_rg30.27 Å
Shape Rg shape_rg30.49 Å
Total Rg total_rg31.20 Å
Total atoms total_atoms6022
Residues n_residues740
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax100.1 Å
Rg (real space) rg_real31.03 Å
Rg uncertainty (real space) rg_real_error0.82 Å
I(0) (real space) i0_real1.2130e+08
I(0) uncertainty (real space) i0_real_error1.7910e+06
Rg (reciprocal space) rg_reciprocal31.03 Å
I(0) (reciprocal space) i0_reciprocal121300000.0000
Solution quality estimate total_estimate0.9014
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary35.3 Å
Skewness Skewness skewness0.294
Kurtosis Kurtosis kurtosis-0.512
Angular range angular_range— – 0.2550 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha17330000.0000
Real-space data points n_real_points52
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.932; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.974; Smooth: 0.944
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd1qmda1
Class classa — All alpha proteins
Fold Fold folda.124 — Phospholipase C/P1 nuclease
Superfamily Superfamily superfamilya.124.1 — Phospholipase C/P1 nuclease
Family Family familya.124.1.1 — Phospholipase C
Domain ID domain_idd1qmda2
Class classb — All beta proteins
Fold Fold foldb.12 — Lipase/lipooxygenase domain (PLAT/LH2 domain)
Superfamily Superfamily superfamilyb.12.1 — Lipase/lipooxygenase domain (PLAT/LH2 domain)
Family Family familyb.12.1.3 — Alpha-toxin, C-terminal domain
Domain ID domain_idd1qmdb1
Class classa — All alpha proteins
Fold Fold folda.124 — Phospholipase C/P1 nuclease
Superfamily Superfamily superfamilya.124.1 — Phospholipase C/P1 nuclease
Family Family familya.124.1.1 — Phospholipase C
Domain ID domain_idd1qmdb2
Class classb — All beta proteins
Fold Fold foldb.12 — Lipase/lipooxygenase domain (PLAT/LH2 domain)
Superfamily Superfamily superfamilyb.12.1 — Lipase/lipooxygenase domain (PLAT/LH2 domain)
Family Family familyb.12.1.3 — Alpha-toxin, C-terminal domain

CATH v4.4 (4 domains)

Domain ID domain_id1qmdA01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology575 — P1 Nuclease
Homologous superfamily homologous superfamily10 — P1 Nuclease
Domain ID domain_id1qmdA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology60 — Lipoxygenase-1
Homologous superfamily homologous superfamily20 — PLAT/LH2 domain
Domain ID domain_id1qmdB01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology575 — P1 Nuclease
Homologous superfamily homologous superfamily10 — P1 Nuclease
Domain ID domain_id1qmdB02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology60 — Lipoxygenase-1
Homologous superfamily homologous superfamily20 — PLAT/LH2 domain
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8. Citations (3)

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9. Files and Curves (10)