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- PDB-2wy6: Clostridium perfringens alpha-toxin strain NCTC8237 mutant T74I -

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Basic information

Entry
Database: PDB / ID: 2wy6
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 / toxin activity / hydrolase activity / zinc ion binding / extracellular region
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: 3.2 Å
AuthorsVachieri, S.G. / Naylor, C.E. / Basak, A.K.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2011
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 12, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 24, 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_asym_id / _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_asym_id / _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_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_asym_id / _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_asym_id / _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
B: PHOSPHOLIPASE C
C: PHOSPHOLIPASE C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,02727
Polymers127,8003
Non-polymers2,22724
Water00
1
A: PHOSPHOLIPASE C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1357
Polymers42,6001
Non-polymers5356
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PHOSPHOLIPASE C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,53211
Polymers42,6001
Non-polymers93210
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: PHOSPHOLIPASE C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3609
Polymers42,6001
Non-polymers7608
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)107.238, 107.238, 225.087
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 1:74 OR RESSEQ 81:246 OR RESSEQ 253:370 )
211CHAIN B AND (RESSEQ 1:74 OR RESSEQ 81:246 OR RESSEQ 253:370 )
311CHAIN C AND (RESSEQ 1:73 OR RESSEQ 82:246 OR RESSEQ 253:370 )

NCS oper:
IDCodeMatrixVector
1given(0.99942, 0.02486, 0.02323), (-0.00554, -0.55481, 0.83196), (0.03357, -0.8316, -0.55435)-37.43333, -23.07965, 29.22728
2given(0.00806, -0.49631, -0.86811), (0.99828, 0.05448, -0.02187), (0.05815, -0.86644, 0.49589)13.81216, 35.6664, -33.15755
3given(-0.02484, -0.44676, 0.89431), (0.99856, -0.05363, 0.00095), (0.04754, 0.89305, 0.44745)-23.56683, 71.78883, -23.84705

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Components

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


Mass: 42599.906 Da / Num. of mol.: 3 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CLOSTRIDIUM PERFRINGENS (bacteria) / Strain: NCTC8237 / Plasmid: PT7BLUE / 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.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Cd
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
Compound detailsENGINEERED RESIDUE IN CHAIN A, THR 102 TO ILE ENGINEERED RESIDUE IN CHAIN B, THR 102 TO ILE ...ENGINEERED RESIDUE IN CHAIN A, THR 102 TO ILE ENGINEERED RESIDUE IN CHAIN B, THR 102 TO ILE ENGINEERED RESIDUE IN CHAIN C, 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: 2.6 Å3/Da / Density % sol: 52.6 % / Description: NONE
Crystal growpH: 7.6
Details: 1 M NA ACETATE, 0,1 M NA-HEPES, PH 7.6, 0.05 M CDSO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 11, 2003 / Details: MIRRORS
RadiationMonochromator: SILICON (311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 3.2→29.74 Å / Num. obs: 22436 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 7.8 % / Biso Wilson estimate: 88.88 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 22.4
Reflection shellResolution: 3.2→3.4 Å / Redundancy: 8 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 3.5 / % possible all: 100

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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: 3.2→24.914 Å / SU ML: 0.41 / σ(F): 1.39 / Phase error: 27.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2813 1088 4.9 %
Rwork0.219 --
obs0.2221 22375 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.698 Å2 / ksol: 0.306 e/Å3
Displacement parametersBiso mean: 92.37 Å2
Baniso -1Baniso -2Baniso -3
1--1.1193 Å20 Å20 Å2
2---1.1193 Å20 Å2
3---2.2387 Å2
Refinement stepCycle: LAST / Resolution: 3.2→24.914 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8395 0 34 0 8429
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.018630
X-RAY DIFFRACTIONf_angle_d1.13811775
X-RAY DIFFRACTIONf_dihedral_angle_d19.9842829
X-RAY DIFFRACTIONf_chiral_restr0.0741237
X-RAY DIFFRACTIONf_plane_restr0.0041546
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2707X-RAY DIFFRACTIONPOSITIONAL
12B2707X-RAY DIFFRACTIONPOSITIONAL0.063
13C2723X-RAY DIFFRACTIONPOSITIONAL0.054
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2001-3.34540.32581330.26452595X-RAY DIFFRACTION100
3.3454-3.52130.3591220.25562624X-RAY DIFFRACTION100
3.5213-3.74120.32711470.2322592X-RAY DIFFRACTION100
3.7412-4.0290.30441380.21892621X-RAY DIFFRACTION100
4.029-4.43240.27151300.18582652X-RAY DIFFRACTION100
4.4324-5.06910.23421480.18052647X-RAY DIFFRACTION100
5.0691-6.36880.24281120.20152724X-RAY DIFFRACTION100
6.3688-24.91490.2781580.23032832X-RAY DIFFRACTION100

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