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- PDB-7p8s: Crystal Structure of leukotoxin LukE from Staphylococcus aureus a... -

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Basic information

Entry
Database: PDB / ID: 7p8s
TitleCrystal Structure of leukotoxin LukE from Staphylococcus aureus at 1.9 Angstrom resolution
ComponentsLeucotoxin LukEv
KeywordsTOXIN / leukotoxin / beta barrel pore forming toxin / cytolysis / hemolysis
Function / homologyBi-component toxin, staphylococci / Leukocidin/Hemolysin toxin / Leukocidin/Hemolysin toxin family / Leukocidin/porin MspA superfamily / cytolysis in another organism / toxin activity / extracellular region / (CARBAMOYLMETHYL-CARBOXYMETHYL-AMINO)-ACETIC ACID / Leucotoxin LukEv
Function and homology information
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLambey, P. / Hoh, 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)35,5437
Polymers34,6871
Non-polymers8576
Water5,873326
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1200 Å2
ΔGint-44 kcal/mol
Surface area14920 Å2
Unit cell
Length a, b, c (Å)135.79, 135.79, 63.533
Angle α, β, γ (deg.)90, 90, 90
Int Tables number79
Space group name H-MI4
Components on special symmetry positions
IDModelComponents
11A-605-

HOH

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Components

#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
#2: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#3: Chemical ChemComp-MHA / (CARBAMOYLMETHYL-CARBOXYMETHYL-AMINO)-ACETIC ACID / N-(2-ACETAMIDO)IMINODIACETIC ACID / ADA (buffer)


Mass: 190.154 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H10N2O5 / Comment: pH buffer*YM
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 326 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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

Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Ammonium sulfate, 0.05 M Magnesium sulfate heptahydrate, 0.1 M Sodium citrate pH 5.5 and 22.5 % v/v PEG Smear Medium

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→48.01 Å / Num. obs: 45734 / % possible obs: 100 % / Redundancy: 13.7 % / CC1/2: 0.984 / Net I/σ(I): 19.2
Reflection shellResolution: 1.9→1.94 Å / Num. unique obs: 2930 / CC1/2: 0.748

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ROH

3roh


Resolution: 1.9→48.01 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.954 / SU R Cruickshank DPI: 0.1 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.105 / SU Rfree Blow DPI: 0.099 / SU Rfree Cruickshank DPI: 0.095
RfactorNum. reflection% reflectionSelection details
Rfree0.2033 2232 -RANDOM
Rwork0.185 ---
obs0.1859 45726 100 %-
Displacement parametersBiso mean: 39.47 Å2
Baniso -1Baniso -2Baniso -3
1-4.1523 Å20 Å20 Å2
2--4.1523 Å20 Å2
3----8.3046 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: LAST / Resolution: 1.9→48.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2319 0 52 326 2697
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0092526HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.113421HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d888SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes433HARMONIC5
X-RAY DIFFRACTIONt_it2526HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion319SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies10HARMONIC1
X-RAY DIFFRACTIONt_ideal_dist_contact2450SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion4.13
X-RAY DIFFRACTIONt_other_torsion17.88
LS refinement shellResolution: 1.9→1.91 Å
RfactorNum. reflection% reflection
Rfree0.2839 48 -
Rwork0.26 --
obs0.2612 915 99.89 %
Refinement TLS params.Origin x: -23.7148 Å / Origin y: 25.8749 Å / Origin z: -19.6096 Å
111213212223313233
T-0.0164 Å20.0608 Å2-0.025 Å2--0.0238 Å2-0.0014 Å2---0.0373 Å2
L2.7687 °2-1.9236 °21.1739 °2-1.3852 °2-0.7976 °2--0.7176 °2
S0.0391 Å °-0.0882 Å °-0.1168 Å °-0.0882 Å °0.0058 Å °-0.0796 Å °-0.1168 Å °-0.0796 Å °-0.0449 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A12 - 311
2X-RAY DIFFRACTION1{ A|* }A401

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