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- PDB-2wxu: Clostridium perfringens alpha-toxin strain NCTC8237 mutant T74I -

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Basic information

Entry
Database: PDB / ID: 2wxu
TitleClostridium perfringens alpha-toxin strain NCTC8237 mutant T74I
ComponentsPHOSPHOLIPASE C
KeywordsHYDROLASE / CYTOLYSIS / HEMOLYSIS / MEMBRANE BINDING / VIRULENCE / GANGRENE DETERMINANT / C2 DOMAIN
Function / homology
Function and homology information


phospholipase C / phosphatidylcholine phospholipase C activity / hemolysis in another organism / symbiont-mediated killing of host cell / toxin activity / hydrolase activity / 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
Biological speciesCLOSTRIDIUM PERFRINGENS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsVachieri, S.G. / Naylor, C.E. / Basak, A.K.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2010
Title: Comparison of a Nontoxic Variant of Clostridium Perfringens [Alpha]-Toxin with the Toxic Wild-Type Strain
Authors: Vachieri, S.G. / Clark, G.C. / Alape-Giron, A. / Flores-Diaz, M. / Justin, N. / Naylor, C.E. / Titball, R.W. / Basak, A.K.
#1: Journal: Nat.Struct.Biol. / Year: 1998
Title: Structure of the Key Toxin in Gas Gangrene.
Authors: Naylor, C.E. / Eaton, J.T. / Howells, A. / Justin, N. / Moss, D.S. / Titball, R.W. / Basak, A.K.
#2: Journal: Microbiol.Immunol. / Year: 1996
Title: Threonine-74 is a Key Site for the Activity of Clostridium Perfringens Alpha-Toxin.
Authors: Nagahama, M. / Sakurai, J.
History
DepositionNov 10, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 17, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 10, 2019Group: Data collection / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_proc / pdbx_database_status
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_variant / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PHOSPHOLIPASE C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,65314
Polymers42,6001
Non-polymers1,05313
Water7,242402
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.861, 173.643, 78.564
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-2196-

HOH

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Components

#1: Protein PHOSPHOLIPASE C / PLC / PHOSPHATIDYLCHOLINE CHOLINEPHOSPHOHYDROLASE / ALPHA-TOXIN / HEMOLYSIN / LECITHINASE


Mass: 42599.906 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CLOSTRIDIUM PERFRINGENS (bacteria) / Strain: NCTC8237 / Description: T74I INACTIVATING MUTANT / Variant: T74I / Plasmid: PT7BLUE / Production host: ESCHERICHIA COLI (E. coli) / Variant (production host): JM109 / References: UniProt: Q0TV31, phospholipase C
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 402 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, THR 102 TO ILE

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.9 % / Description: NONE
Crystal growpH: 7.6
Details: 1 M NA ACETATE, 0.1 M NA-HEPES, PH7.6, 0.05 M CDSO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.993
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 13, 2004 / Details: MIRRORS
RadiationMonochromator: SILICON (311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.993 Å / Relative weight: 1
ReflectionResolution: 1.8→24.64 Å / Num. obs: 38029 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Biso Wilson estimate: 17.57 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 13.8
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 3.9 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CA1 WITHOUT RESIDUES 75-84

1ca1


Resolution: 1.8→24.641 Å / SU ML: 0.22 / σ(F): 1.41 / Phase error: 19.96 / Stereochemistry target values: ML / Details: RESIDUES 75-83 ARE DISORDERED
RfactorNum. reflection% reflection
Rfree0.2163 1899 5 %
Rwork0.1753 --
obs0.1773 38005 99.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.471 Å2 / ksol: 0.352 e/Å3
Displacement parametersBiso mean: 27.1 Å2
Baniso -1Baniso -2Baniso -3
1-1.6472 Å2-0 Å2-0 Å2
2---0.9569 Å2-0 Å2
3----0.6903 Å2
Refinement stepCycle: LAST / Resolution: 1.8→24.641 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2902 0 13 402 3317
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072981
X-RAY DIFFRACTIONf_angle_d0.9834038
X-RAY DIFFRACTIONf_dihedral_angle_d17.391045
X-RAY DIFFRACTIONf_chiral_restr0.068412
X-RAY DIFFRACTIONf_plane_restr0.005526
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.86430.29131870.26083598X-RAY DIFFRACTION100
1.8643-1.93890.25421860.22763570X-RAY DIFFRACTION100
1.9389-2.02710.24741890.18953586X-RAY DIFFRACTION100
2.0271-2.1340.23552130.17383591X-RAY DIFFRACTION100
2.134-2.26760.20151850.16223585X-RAY DIFFRACTION99
2.2676-2.44250.24141730.16393608X-RAY DIFFRACTION99
2.4425-2.6880.21381940.16583617X-RAY DIFFRACTION99
2.688-3.07640.20421780.15873628X-RAY DIFFRACTION99
3.0764-3.87350.18811980.15873617X-RAY DIFFRACTION98
3.8735-24.64360.20121960.17423706X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.44640.26420.01411.5263-0.22840.9181-0.0335-0.0103-0.0178-0.06370.023-0.1062-0.0524-0.0027-0.00220.04180.03160.01960.0581-0.00770.059514.742368.674937.8237
20.6525-0.04660.32330.7621-0.21450.75240.0365-0.2013-0.01820.10490.06950.01710.0271-0.2378-0.06890.0603-0.00890.02470.24140.02580.1637-5.965651.058236.422
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESID 1:244
2X-RAY DIFFRACTION2CHAIN A AND RESID 245:370

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