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- PDB-1ca1: ALPHA-TOXIN FROM CLOSTRIDIUM PERFRINGENS -

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Basic information

Entry
Database: PDB / ID: 1ca1
TitleALPHA-TOXIN FROM CLOSTRIDIUM PERFRINGENS
ComponentsALPHA-TOXIN
KeywordsHYDROLASE / ZINC PHOSPHOLIPASE C / GANGRENE DETERMINANT / C2 DOMAIN / CA AND MEMBRANE BINDING
Function / homology
Function and homology information


calcium-dependent phospholipase C activity / phospholipase C / phosphatidylcholine phospholipase C activity / hemolysis in another organism / toxin activity / killing of cells of another organism / extracellular region / zinc ion binding
Similarity search - Function
Zinc-dependent phospholipase C / Phospholipase C/D / Zinc dependent phospholipase C / Prokaryotic zinc-dependent phospholipase C signature. / Prokaryotic zinc-dependent phospholipase C domain profile. / Zinc dependent phospholipase C (alpha toxin) / P1 Nuclease / P1 Nuclease / Phospholipase C/P1 nuclease domain superfamily / PLAT/LH2 domain ...Zinc-dependent phospholipase C / Phospholipase C/D / Zinc dependent phospholipase C / Prokaryotic zinc-dependent phospholipase C signature. / Prokaryotic zinc-dependent phospholipase C domain profile. / Zinc dependent phospholipase C (alpha toxin) / P1 Nuclease / P1 Nuclease / Phospholipase C/P1 nuclease domain superfamily / PLAT/LH2 domain / Lipoxygenase-1 / PLAT/LH2 domain / PLAT/LH2 domain superfamily / PLAT/LH2 domain / PLAT domain profile. / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
: / Phospholipase C / Phospholipase C
Similarity search - Component
Biological speciesClostridium perfringens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIR, MOLECULAR REPLACEMENT, CROSS-CRYSTAL AVERAGING / Resolution: 1.9 Å
AuthorsNaylor, C.E. / Basak, A.K. / Titball, R.W.
Citation
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Crystallization and Preliminary X-Ray Diffraction Studies of Alpha-Toxin from Two Different Strains (Nctc8237 and Cer89L43) of Clostridium Perfringens
Authors: Basak, A.K. / Howells, A. / Eaton, J.T. / Moss, D.S. / Naylor, C.E. / Miller, J. / Titball, R.W.
History
DepositionApr 22, 1998Processing site: BNL
Revision 1.0May 4, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Dec 21, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ALPHA-TOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,03014
Polymers42,6161
Non-polymers1,41413
Water3,117173
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: ALPHA-TOXIN
hetero molecules

A: ALPHA-TOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,06028
Polymers85,2322
Non-polymers2,82926
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area5100 Å2
ΔGint-228 kcal/mol
Surface area29140 Å2
MethodPISA, PQS
3
A: ALPHA-TOXIN
hetero molecules

A: ALPHA-TOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,06028
Polymers85,2322
Non-polymers2,82926
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
Buried area3200 Å2
ΔGint-228 kcal/mol
Surface area31050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.300, 177.300, 79.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-381-

CD

21A-382-

CD

31A-407-

HOH

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Components

#1: Protein ALPHA-TOXIN / PHOSPHOLIPASE C


Mass: 42615.863 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium perfringens (bacteria) / Strain: CER89L43 / Gene: CPA / Plasmid: PUC18 / Cellular location (production host): PERIPLASMIC / Gene (production host): CPA / Production host: Escherichia coli (E. coli) / Strain (production host): JM109
References: UniProt: P15310, UniProt: P0C216*PLUS, phospholipase C
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cd
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 5

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50 %
Description: EARLIER MODEL WILL BE DEPOSITED AFTER FULL REFINEMENT. SIR CARRIED OUT ON ALTERNATE CRYSTAL FORM WHICH WILL ALSO BE DEPOSITED IN NEAR FUTURE.
Crystal growpH: 7.5 / Details: pH 7.5
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.05 M1dropCdSO4
20.1 MNa-HEPES1drop
31 Msodium acetate1reservoir

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.5
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Aug 1, 1995 / Details: MIRRORS
RadiationMonochromator: SI CRYSTAL OR NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.9→40 Å / Num. obs: 30175 / % possible obs: 87.5 % / Observed criterion σ(I): -3 / Redundancy: 5.26 % / Biso Wilson estimate: 32.8 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 13.5
Reflection shellResolution: 1.9→1.96 Å / Rmerge(I) obs: 0.157 / Mean I/σ(I) obs: 4.3 / % possible all: 73.8
Reflection
*PLUS
% possible obs: 91 % / Num. measured all: 202958

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: SIR, MOLECULAR REPLACEMENT, CROSS-CRYSTAL AVERAGING
Starting model: INCOMPLETE EARLIER CHAIN TRACE OF ALTERNATE STRAIN

Resolution: 1.9→25 Å / Isotropic thermal model: INDIVIDUAL RESTRAINED B-F / Cross valid method: USED THROUGHOUT REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.254 1636 5.4 %RANDOM
Rwork0.208 ---
obs0.208 30150 87.5 %-
Displacement parametersBiso mean: 29.2 Å2
Refine analyzeLuzzati d res low obs: 25 Å / Luzzati sigma a obs: 0.28 Å
Refinement stepCycle: LAST / Resolution: 1.9→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3009 0 13 173 3195
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.117
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.26
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.625
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it0.7883
X-RAY DIFFRACTIONx_mcangle_it0.7624
X-RAY DIFFRACTIONx_scbond_it0.7883
X-RAY DIFFRACTIONx_scangle_it0.7624
LS refinement shellResolution: 1.9→1.97 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.333 147 5.8 %
Rwork0.323 2379 -
obs--73.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLPARAM19.SOL
X-RAY DIFFRACTION3PARAM19.IONPARAM19.ION
X-RAY DIFFRACTION4PARAM_ALPHA_SUBMISSION.CDTOP_ALPHA_SUBMISSION.CD
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.262
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.625

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