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- PDB-2wxt: Clostridium perfringens alpha-toxin strain NCTC8237 -

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Basic information

Entry
Database: PDB / ID: 2wxt
TitleClostridium perfringens alpha-toxin strain NCTC8237
ComponentsPHOSPHOLIPASE C
KeywordsHYDROLASE / CYTOLYSIS / HEMOLYSIS / MEMBRANE BINDING / GANGRENE DETERMINANT / C2 DOMAIN / VIRULENCE
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: 2 Å
AuthorsJustin, N. / 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.
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.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

Downloads & links

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Assembly

Deposited unit
A: PHOSPHOLIPASE C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,62312
Polymers42,5781
Non-polymers1,04511
Water4,378243
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.180, 174.370, 79.530
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 42577.816 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CLOSTRIDIUM PERFRINGENS (bacteria) / Strain: NCTC8237 / Plasmid: PKSA3 / Production host: ESCHERICHIA COLI (E. coli) / Variant (production host): JM109 / References: UniProt: Q0TV31, 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.: 8 / Source method: obtained synthetically / Formula: Cd
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 51 % / 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: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 25, 1997 / Details: MIRRORS
RadiationMonochromator: SILICON (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2→38.35 Å / Num. obs: 25562 / % possible obs: 89.3 % / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 18.15 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 11.3
Reflection shellResolution: 2→2.13 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 4 / % possible all: 91.6

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CA1

1ca1


Resolution: 2→29.062 Å / SU ML: 0.24 / σ(F): 1.39 / Phase error: 20.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2321 1378 5.4 %
Rwork0.1747 --
obs0.1778 25554 88.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.25 Å2 / ksol: 0.428 e/Å3
Displacement parametersBiso mean: 31.58 Å2
Baniso -1Baniso -2Baniso -3
1-7.5508 Å2-0 Å2-0 Å2
2---4.7914 Å2-0 Å2
3----2.7594 Å2
Refinement stepCycle: LAST / Resolution: 2→29.062 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2900 0 11 243 3154
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142973
X-RAY DIFFRACTIONf_angle_d1.3464021
X-RAY DIFFRACTIONf_dihedral_angle_d17.4271052
X-RAY DIFFRACTIONf_chiral_restr0.089411
X-RAY DIFFRACTIONf_plane_restr0.006521
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.07150.26351390.21592445X-RAY DIFFRACTION92
2.0715-2.15440.26721370.18772460X-RAY DIFFRACTION91
2.1544-2.25240.22741600.1692403X-RAY DIFFRACTION91
2.2524-2.37110.21321320.16562433X-RAY DIFFRACTION90
2.3711-2.51960.25231430.16392411X-RAY DIFFRACTION90
2.5196-2.7140.24371390.16732434X-RAY DIFFRACTION90
2.714-2.98690.22861220.172427X-RAY DIFFRACTION89
2.9869-3.41850.2371510.16382392X-RAY DIFFRACTION88
3.4185-4.30470.20591130.15512414X-RAY DIFFRACTION87
4.3047-29.06470.22651420.19272357X-RAY DIFFRACTION82
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)
10.8452-0.0425-0.22472.2034-0.33751.67260.0480.0232-0.0244-0.088-0.07620.0604-0.1345-0.04910.02880.07440.0485-0.01790.0784-0.01640.093715.933169.049838.1608
21.51180.55270.48681.5271-0.04040.85110.0702-0.19670.14320.0170.01360.0442-0.0035-0.1271-0.06070.0492-0.00240.03530.25080.03290.2303-5.65251.349336.9425
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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