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- PDB-5dim: Mutant toxin in 'native' space group -

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Basic information

Entry
Database: PDB / ID: 5dim
TitleMutant toxin in 'native' space group
ComponentsPerfringolysin O
KeywordsTOXIN / mutant
Function / homology
Function and homology information


hemolysis in another organism / cholesterol binding / toxin activity / host cell plasma membrane / extracellular region / membrane
Similarity search - Function
Carboxypeptidase Inhibitor; Chain A - #20 / Perfringolysin / HIV-1 Reverse Transcriptase; Chain A, domain 3 / Thiol-activated cytolysin superfamily/Thiol-activated cytolysin, alpha-beta domain / Perfringolysin, domain 4 / Carboxypeptidase Inhibitor; Chain A / Thiol-activated cytolysins signature. / Thiol-activated cytolysin C-terminal / Thiol-activated cytolysin, C-terminal domain superfamily / Thiol-activated cytolysin beta sandwich domain ...Carboxypeptidase Inhibitor; Chain A - #20 / Perfringolysin / HIV-1 Reverse Transcriptase; Chain A, domain 3 / Thiol-activated cytolysin superfamily/Thiol-activated cytolysin, alpha-beta domain / Perfringolysin, domain 4 / Carboxypeptidase Inhibitor; Chain A / Thiol-activated cytolysins signature. / Thiol-activated cytolysin C-terminal / Thiol-activated cytolysin, C-terminal domain superfamily / Thiol-activated cytolysin beta sandwich domain / Thiol-activated cytolysin / Thiol-activated cytolysin superfamily / Thiol-activated cytolysin, alpha-beta domain superfamily / Thiol-activated cytolysin / Glutaredoxin / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesClostridium perfringens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.32 Å
AuthorsParker, M.W. / Gorman, M.A. / Lawrence, S.L.
CitationJournal: To Be Published
Title: Structure of mutant toxin at 3.32 Angstrom resolution
Authors: Parker, M.W. / Gorman, M.A. / Lawrence, S.L. / Morton, C.J.
History
DepositionSep 1, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Perfringolysin O
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0132
Polymers52,7751
Non-polymers2381
Water362
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint1 kcal/mol
Surface area22330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.951, 207.332, 212.442
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 Perfringolysin O / Theta-toxin / Thiol-activated cytolysin


Mass: 52774.758 Da / Num. of mol.: 1 / Mutation: N197W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium perfringens (strain 13 / Type A) (bacteria)
Strain: 13 / Type A / Gene: pfo, pfoA, pfoR, CPE0163 / Production host: Escherichia coli (E. coli) / References: UniProt: P0C2E9
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 4.62 Å3/Da / Density % sol: 73.4 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 9% PEG 6000, 100 mM HEPES pH 7.0, 2% v/v dioxane

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 3.32→47.27 Å / Num. obs: 15939 / % possible obs: 100 % / Redundancy: 7.3 % / Biso Wilson estimate: 54.28 Å2 / Rmerge(I) obs: 0.2 / Net I/σ(I): 9.6
Reflection shellResolution: 3.32→3.59 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.726 / Mean I/σ(I) obs: 3.2 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PFO

1pfo


Resolution: 3.32→47.27 Å / Cor.coef. Fo:Fc: 0.81 / Cor.coef. Fo:Fc free: 0.76 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 1.409 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 1.392 / SU Rfree Blow DPI: 0.466 / SU Rfree Cruickshank DPI: 0.475
RfactorNum. reflection% reflectionSelection details
Rfree0.297 827 5.2 %RANDOM
Rwork0.236 ---
obs0.239 15908 100 %-
Displacement parametersBiso mean: 65.23 Å2
Baniso -1Baniso -2Baniso -3
1-20.6986 Å20 Å20 Å2
2---45.4269 Å20 Å2
3---24.7283 Å2
Refine analyzeLuzzati coordinate error obs: 0.51 Å
Refinement stepCycle: LAST / Resolution: 3.32→47.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3665 0 15 2 3682
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013766HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.285118HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1312SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes108HARMONIC2
X-RAY DIFFRACTIONt_gen_planes530HARMONIC5
X-RAY DIFFRACTIONt_it3766HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.9
X-RAY DIFFRACTIONt_other_torsion25.24
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion509SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4347SEMIHARMONIC4
LS refinement shellResolution: 3.32→3.55 Å / Rfactor Rfree error: 0 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.293 151 5.35 %
Rwork0.22 2670 -
all0.224 2821 -
obs--100 %

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