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- PDB-7p8u: Crystal Structure of leukotoxin LukE from Staphylococcus aureus i... -

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Basic information

Entry
Database: PDB / ID: 7p8u
TitleCrystal Structure of leukotoxin LukE from Staphylococcus aureus in complex with p-cresyl sulfate
ComponentsLeucotoxin LukEv
KeywordsTOXIN / leukotoxin / beta barrel pore forming toxin / cytolysis / hemolysis
Function / homology
Function and homology information


cytolysis in another organism / toxin activity / extracellular region
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
(4-methylphenyl) hydrogen sulfate / IMIDAZOLE / DI(HYDROXYETHYL)ETHER / Leucotoxin LukEv
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsLambey, P. / Hoh, F. / Peysson, F. / Granier, S. / Leyrat, C.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-17-CE15-0002-01 France
CitationJournal: Elife / Year: 2022
Title: Structural insights into recognition of chemokine receptors by Staphylococcus aureus leukotoxins.
Authors: Lambey, P. / Otun, O. / Cong, X. / Hoh, F. / Brunel, L. / Verdie, P. / Grison, C.M. / Peysson, F. / Jeannot, S. / Durroux, T. / Bechara, C. / Granier, S. / Leyrat, C.
History
DepositionJul 23, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 6, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Leucotoxin LukEv
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5237
Polymers34,6871
Non-polymers8366
Water4,684260
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area700 Å2
ΔGint-4 kcal/mol
Surface area13250 Å2
Unit cell
Length a, b, c (Å)62.583, 73.488, 79.338
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Leucotoxin LukEv / Variant of LukE


Mass: 34686.691 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: lukEv, SAOUHSC_01955 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2FXB0

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Non-polymers , 5 types, 266 molecules

#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-6EI / (4-methylphenyl) hydrogen sulfate / p-Cresol sulfate


Mass: 188.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H8O4S / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 260 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.63 Å3/Da / Density % sol: 53.23 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion
Details: 0.1 M Imidazole.HCl pH 8.0, 30% (w/v) MPD, 10% (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.96545 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jan 31, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96545 Å / Relative weight: 1
ReflectionResolution: 1.6→47.65 Å / Num. obs: 48967 / % possible obs: 99.3 % / Redundancy: 3.4 % / CC1/2: 0.996 / Net I/σ(I): 15.5
Reflection shellResolution: 1.6→1.63 Å / Num. unique obs: 2360 / CC1/2: 0.624

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7P8T

7p8t


Resolution: 1.6→47.65 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.929 / SU R Cruickshank DPI: 0.077 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.08 / SU Rfree Blow DPI: 0.079 / SU Rfree Cruickshank DPI: 0.077
RfactorNum. reflection% reflectionSelection details
Rfree0.2046 2545 -RANDOM
Rwork0.1812 ---
obs0.1825 48461 99 %-
Displacement parametersBiso mean: 34.24 Å2
Baniso -1Baniso -2Baniso -3
1--0.4669 Å20 Å20 Å2
2---5.3716 Å20 Å2
3---5.8385 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 1.6→47.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2272 0 53 260 2585
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0092475HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.13385HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d863SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes465HARMONIC5
X-RAY DIFFRACTIONt_it2439HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion314SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies11HARMONIC1
X-RAY DIFFRACTIONt_ideal_dist_contact2245SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion4.53
X-RAY DIFFRACTIONt_other_torsion16.51
LS refinement shellResolution: 1.6→1.61 Å
RfactorNum. reflection% reflection
Rfree0.2712 49 -
Rwork0.264 --
obs0.2644 970 98.79 %
Refinement TLS params.Origin x: 14.7474 Å / Origin y: -14.4656 Å / Origin z: -12.3236 Å
111213212223313233
T-0.0143 Å2-0.0074 Å20.0126 Å2--0.0561 Å2-0.0021 Å2---0.0446 Å2
L0.9485 °2-0.0173 °20.5718 °2-0.686 °2-0.0876 °2--2.404 °2
S0.0094 Å °-0.111 Å °0.1364 Å °-0.111 Å °0.0405 Å °0.0539 Å °0.1364 Å °0.0539 Å °-0.0499 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A27 - 312
2X-RAY DIFFRACTION1{ A|* }A401 - 801

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