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- PDB-5dhl: Crystal structure of Toxin, mutant N197W -

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Basic information

Entry
Database: PDB / ID: 5dhl
TitleCrystal structure of Toxin, mutant N197W
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: 2.67 Å
AuthorsParker, M.W. / Gorman, M.A. / Lawrence, S.L.
CitationJournal: To Be Published
Title: Structure of mutant toxin
Authors: Parker, M.W. / Gorman, M.A. / Lawrence, S.L. / Morton, C.J.
History
DepositionAug 31, 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
B: Perfringolysin O
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,0264
Polymers105,5502
Non-polymers4772
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4320 Å2
ΔGint7 kcal/mol
Surface area42060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.629, 212.398, 46.958
Angle α, β, γ (deg.)90.00, 97.17, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Perfringolysin O / Theta-toxin / Thiol-activated cytolysin


Mass: 52774.758 Da / Num. of mol.: 2 / 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 / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 3.58 Å3/Da / Density % sol: 65.61 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7 / 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: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.67→46.59 Å / Num. obs: 44020 / % possible obs: 98.7 % / Redundancy: 3.8 % / Biso Wilson estimate: 68.8 Å2 / Rmerge(I) obs: 0.118 / Net I/σ(I): 7.9
Reflection shellResolution: 2.67→2.77 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.904 / Mean I/σ(I) obs: 1.5 / % possible all: 94.7

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
MOLREPphasing
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PF0

1pf0
PDB Unreleased entry


Resolution: 2.67→45.25 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.893 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.344 / SU Rfree Blow DPI: 0.254
RfactorNum. reflection% reflectionSelection details
Rfree0.239 2192 4.99 %RANDOM
Rwork0.191 ---
obs0.193 43968 98.9 %-
Displacement parametersBiso mean: 58.91 Å2
Baniso -1Baniso -2Baniso -3
1--6.0043 Å20 Å2-4.5433 Å2
2---9.6222 Å20 Å2
3---15.6265 Å2
Refine analyzeLuzzati coordinate error obs: 0.36 Å
Refinement stepCycle: LAST / Resolution: 2.67→45.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7364 0 30 103 7497
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0114643HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1626373HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3284SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes218HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2104HARMONIC5
X-RAY DIFFRACTIONt_it14643HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.26
X-RAY DIFFRACTIONt_other_torsion18.93
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1022SEMIHARMONIC5
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_contact15884SEMIHARMONIC4
LS refinement shellResolution: 2.67→2.74 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 158 4.95 %
Rwork0.252 3031 -
all0.254 3189 -
obs--96.53 %

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