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- PDB-2ygt: Clostridium perfringens delta-toxin -

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Basic information

Entry
Database: PDB / ID: 2ygt
TitleClostridium perfringens delta-toxin
ComponentsDELTA TOXIN
KeywordsTOXIN / BETA-PORE-FORMING TOXIN / HAEMOLYSIN / ENTEROTOXIN
Function / homology
Function and homology information


cytolysis in another organism / : / extracellular region / metal ion binding
Similarity search - Function
Leukocidin/porin MspA / Leukocidin-like / Bi-component toxin, staphylococci / Leukocidin/Hemolysin toxin / Leukocidin/Hemolysin toxin family / Leukocidin/porin MspA superfamily / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
IMIDAZOLE / Alpha hemolysin
Similarity search - Component
Biological speciesCLOSTRIDIUM PERFRINGENS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsHuyet, J. / Naylor, C.E. / Gibert, M. / Popoff, M.R. / Basak, A.K.
Citation
Journal: Plos One / Year: 2013
Title: Structural Insights Into Clostridium Perfringens Delta Toxin Pore Formation.
Authors: Huyet, J. / Naylor, C.E. / Savva, C.G. / Gibert, M. / Popoff, M.R. / Basak, A.K.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2011
Title: Crystallization and Preliminary X-Ray Diffraction Studies of Delta-Toxin from Clostridium Perfringens.
Authors: Huyet, J. / Gilbert, M. / Popoff, M.R. / Basak, A.
History
DepositionApr 20, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 16, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2013Group: Database references
Revision 1.2Apr 27, 2016Group: Database references
Revision 1.3Mar 6, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _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_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_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: DELTA TOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1718
Polymers33,6291
Non-polymers5427
Water4,035224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)112.932, 49.664, 58.477
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-1293-

IMD

21A-2217-

HOH

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Components

#1: Protein DELTA TOXIN


Mass: 33629.211 Da / Num. of mol.: 1 / Fragment: RESIDUES 29-318
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CLOSTRIDIUM PERFRINGENS (bacteria) / Strain: CP24-03 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CODONPLUS RIL / References: UniProt: B8QGZ7
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 224 / 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: 2.3 Å3/Da / Density % sol: 47 % / Description: NONE
Crystal growTemperature: 293 K / pH: 6
Details: 6.6 MG/ML PROTEIN AGAINST 25-30% PEG 550 25 MM ZNSO4, 100 MM MES-NAOH PH 6.0, AT 293K.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.0332
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 5, 2008 / Details: MIRROR
RadiationMonochromator: SI(111) CUT CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.4→113.2 Å / Num. obs: 13432 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 10.4 % / Biso Wilson estimate: 38.1 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 15.8
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 10.6 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 3.5 / % possible all: 99.8

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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 1PVL

1pvl


Resolution: 2.4→58.477 Å / SU ML: 0.78 / σ(F): 1.5 / Phase error: 19.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2283 664 4.9 %
Rwork0.1788 --
obs0.1812 13409 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.672 Å2 / ksol: 0.37 e/Å3
Displacement parametersBiso mean: 29.6 Å2
Baniso -1Baniso -2Baniso -3
1-3.9141 Å20 Å20 Å2
2---2.3899 Å20 Å2
3----1.5242 Å2
Refinement stepCycle: LAST / Resolution: 2.4→58.477 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2173 0 26 224 2423
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082239
X-RAY DIFFRACTIONf_angle_d0.7723035
X-RAY DIFFRACTIONf_dihedral_angle_d15.93781
X-RAY DIFFRACTIONf_chiral_restr0.052345
X-RAY DIFFRACTIONf_plane_restr0.002387
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.58530.26791290.19062470X-RAY DIFFRACTION100
2.5853-2.84550.27121330.18452516X-RAY DIFFRACTION100
2.8455-3.25720.25331350.17222518X-RAY DIFFRACTION100
3.2572-4.10360.18341500.14962533X-RAY DIFFRACTION100
4.1036-58.49380.19691170.17462708X-RAY DIFFRACTION100
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)
1-0.133-0.0543-0.05320.03350.00410.08860.0446-0.2002-0.0847-0.0640.49680.33170.0437-0.5425-0.00050.3542-0.01790.05760.31270.1210.14525.78117.49754.2287
20.0070.01730.00110.0247-0.00060.0496-0.1159-0.4933-0.25360.3338-0.1254-0.10460.0071-0.0812-0.00240.432-0.01040.06320.7048-0.0760.29615.033721.152861.5772
30.473-0.3163-0.19280.40760.20441.16650.02360.0287-0.00160.0169-0.02240.0273-0.02340.0392-0.00010.11260.0079-0.03510.0945-0.0270.097214.570713.570131.4892
4-0.06040.01580.0409-0.1346-0.12130.10670.10420.0412-0.11130.7806-0.20820.19930.16170.0105-0.00680.65850.0503-0.00580.1219-0.05560.590720.11065.156346.1435
50.6933-0.1535-0.48110.73530.82981.1482-0.0350.1015-0.0404-0.0916-0.11750.1839-0.0122-0.0184-0.00470.09450.01-0.03820.095-0.01720.093417.95992.738822.185
60.6804-0.0032-0.05370.37880.1170.51280.13610.050.1317-0.4903-0.0142-0.1249-0.49920.00540.1610.22010.0374-0.03390.07770.0470.068312.476113.691120.8594
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESID 9:21
2X-RAY DIFFRACTION2CHAIN A AND RESID 22:26
3X-RAY DIFFRACTION3CHAIN A AND RESID 27:134
4X-RAY DIFFRACTION4CHAIN A AND RESID 135:142
5X-RAY DIFFRACTION5CHAIN A AND RESID 143:257
6X-RAY DIFFRACTION6CHAIN A AND RESID 258:290

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