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- PDB-4i0n: Pore forming protein -

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Basic information

Entry
Database: PDB / ID: 4i0n
TitlePore forming protein
ComponentsNecrotic enteritis toxin B
KeywordsTOXIN / alpha-hemolysin fold / pore forming protein
Function / homology
Function and homology information


hemolysis 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
Biological speciesClostridium perfringens (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsYan, X. / Porter, C.J. / Hardy, S.P. / Steer, D. / Smith, A.I. / Quinset, N. / Hughes, V. / Cheung, J.K. / Keyburn, A.L. / Kaldhusdal, M. ...Yan, X. / Porter, C.J. / Hardy, S.P. / Steer, D. / Smith, A.I. / Quinset, N. / Hughes, V. / Cheung, J.K. / Keyburn, A.L. / Kaldhusdal, M. / Moore, R.J. / Bannam, T.L. / Whisstock, J.C. / Rood, J.I.
CitationJournal: MBio / Year: 2013
Title: Structural and functional analysis of the pore-forming toxin NetB from Clostridium perfringens
Authors: Yan, X.X. / Porter, C.J. / Hardy, S.P. / Steer, D. / Smith, A.I. / Quinsey, N.S. / Hughes, V. / Cheung, J.K. / Keyburn, A.L. / Kaldhusdal, M. / Moore, R.J. / Bannam, T.L. / Whisstock, J.C. / Rood, J.I.
History
DepositionNov 16, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 20, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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.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.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.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_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: Necrotic enteritis toxin B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0467
Polymers32,8631
Non-polymers1846
Water4,648258
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)167.444, 29.698, 56.265
Angle α, β, γ (deg.)90.00, 99.09, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Necrotic enteritis toxin B / NetB


Mass: 32862.520 Da / Num. of mol.: 1 / Fragment: UNP residues 34-322
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium perfringens (bacteria) / Gene: netB / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3)pLysS / References: UniProt: A8ULG6
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 258 / 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: 2.1 Å3/Da / Density % sol: 41.48 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M Bis-Tris propane, 0.8M LiSO4, 5%(v/v) glycerol , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 3, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.8→26.4 Å / Num. obs: 25514 / % possible obs: 98.3 %

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→26.4 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.941 / SU B: 3.989 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2047 1294 5.1 %RANDOM
Rwork0.16824 ---
obs0.17016 24220 98.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.821 Å2
Baniso -1Baniso -2Baniso -3
1--0.54 Å20 Å2-0.3 Å2
2--1.17 Å20 Å2
3----0.73 Å2
Refinement stepCycle: LAST / Resolution: 1.8→26.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2100 0 9 258 2367
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222180
X-RAY DIFFRACTIONr_angle_refined_deg1.3231.9322961
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0255273
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.31125.429105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.51515373
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.134156
X-RAY DIFFRACTIONr_chiral_restr0.0980.2321
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211667
X-RAY DIFFRACTIONr_mcbond_it0.6461.51328
X-RAY DIFFRACTIONr_mcangle_it1.25722153
X-RAY DIFFRACTIONr_scbond_it2.2383852
X-RAY DIFFRACTIONr_scangle_it3.6034.5802
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 69 -
Rwork0.28 1483 -
obs--79.92 %
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)
112.00311.0072-2.97150.728-0.27971.61-0.01980.85650.2801-0.01170.138-0.04630.0206-0.1922-0.11830.010.00890.00240.10530.03930.061372.11120.91925.089
20.9655-0.05520.34050.1989-0.07760.8634-0.0516-0.00440.0155-0.05830.0187-0.0170.006-0.0560.03280.0532-0.0150.0050.0182-0.00320.040942.047927.853414.9173
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A45 - 64
2X-RAY DIFFRACTION2A65 - 292

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