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- PDB-4iyt: Structure Of The Y184A Mutant Of The PANTON-VALENTINE LEUCOCIDIN ... -

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Basic information

Entry
Database: PDB / ID: 4iyt
TitleStructure Of The Y184A Mutant Of The PANTON-VALENTINE LEUCOCIDIN S Component From STAPHYLOCOCCUS AUREUS
ComponentsLukS-PV
KeywordsTOXIN / BI-COMPONENT LEUCOTOXIN / STAPHYLOCOCCUS AUREUS / S COMPONENT LEUCOCIDIN / beta-barrel pore forming toxin
Function / homology
Function and homology information


cytolysis in another organism / 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
Biological speciesStaphylococcus phage PVL (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsGuerin, F. / Laventie, B.J. / Prevost, G. / Mourey, L. / Maveyraud, L.
Citation
Journal: Plos One / Year: 2014
Title: Residues essential for panton-valentine leukocidin s component binding to its cell receptor suggest both plasticity and adaptability in its interaction surface
Authors: Laventie, B.J. / Guerin, F. / Mourey, L. / Tawk, M.Y. / Jover, E. / Maveyraud, L. / Prevost, G.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Crystallization and preliminary crystallographic data of a leucotoxin S component from Staphylococcus aureus
Authors: Guillet, V. / Keller, D. / Prevost, G. / Mourey, L.
#2: Journal: J.Biol.Chem. / Year: 2004
Title: Crystal Structure of Leucotoxin S Component NEW INSIGHT INTO THE STAPHYLOCOCCAL beta-BARREL PORE-FORMING TOXINS
Authors: Guillet, V. / Roblin, P. / Werner, S. / Coraiola, M. / Menestrina, G. / Monteil, H. / Prevost, G. / Mourey, L.
#3: Journal: Structure / Year: 1999
Title: The structure of a Staphylococcus aureus leucocidin component (LukF-PV) reveals the fold of the water-soluble species of a family of transmembrane pore-forming toxins
Authors: Pedelacq, J.D. / Maveyraud, L. / Prevost, G. / Baba-Moussa, L. / Gonzalez, A. / Courcelle, E. / Shepard, W. / Monteil, H. / Samama, J.P. / Mourey, L.
History
DepositionJan 29, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 29, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2014Group: Database references
Revision 1.2Apr 23, 2014Group: Database references
Revision 1.3Nov 8, 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 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: LukS-PV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2442
Polymers33,0481
Non-polymers1951
Water1,910106
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)104.870, 104.870, 106.890
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein LukS-PV


Mass: 33048.375 Da / Num. of mol.: 1 / Fragment: UNP residues 29-312 / Mutation: Y184A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus phage PVL (virus) / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: O80066
#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 4.45 Å3/Da / Density % sol: 72.34 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 40% PEG200, 0.1M NaMES, pH 6.50, VAPOR DIFFUSION, SITTING DROP, temperature 285K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.98012 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 12, 2008
RadiationMonochromator: silicon monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98012 Å / Relative weight: 1
ReflectionResolution: 2.2→47.6 Å / Num. obs: 30803 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 51.45 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 16.2
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.915 / Mean I/σ(I) obs: 2.7 / Num. unique all: 3759 / Rsym value: 0.915 / % possible all: 99.7

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
BUSTER2.10.0refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1T5R

1t5r


Resolution: 2.2→47.6 Å / Cor.coef. Fo:Fc: 0.9199 / Cor.coef. Fo:Fc free: 0.9225 / SU R Cruickshank DPI: 0.151 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.218 1548 5.02 %RANDOM
Rwork0.2096 ---
all0.21 30803 --
obs0.21 30803 99.78 %-
Displacement parametersBiso mean: 62.19 Å2
Baniso -1Baniso -2Baniso -3
1-7.8297 Å20 Å20 Å2
2--7.8297 Å20 Å2
3----15.6594 Å2
Refine analyzeLuzzati coordinate error obs: 0.371 Å
Refinement stepCycle: LAST / Resolution: 2.2→47.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2171 0 12 106 2289
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012274HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.123118HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d760SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes69HARMONIC2
X-RAY DIFFRACTIONt_gen_planes320HARMONIC5
X-RAY DIFFRACTIONt_it2274HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion4.14
X-RAY DIFFRACTIONt_other_torsion17.47
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion290SEMIHARMONIC5
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_contact2521SEMIHARMONIC4
LS refinement shellResolution: 2.2→2.28 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.2729 160 5.37 %
Rwork0.2317 2819 -
all0.2339 2979 -
obs--99.78 %
Refinement TLS params.Method: refined / Origin x: -13.0419 Å / Origin y: 0.8928 Å / Origin z: 12.4126 Å
111213212223313233
T-0.2544 Å20.0038 Å20.0973 Å2--0.2811 Å2-0.0269 Å2---0.3135 Å2
L4.2802 °2-1.6516 °20.5945 °2-2.75 °20.1566 °2--1.1903 °2
S0.1239 Å °-0.1304 Å °0.1782 Å °-0.004 Å °-0.1087 Å °0.0026 Å °0.0143 Å °0.0428 Å °-0.0152 Å °
Refinement TLS groupSelection details: { A|* }

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