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- PDB-4iya: Structure of the Y250A mutant of the PANTON-VALENTINE LEUCOCIDIN ... -

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Basic information

Entry
Database: PDB / ID: 4iya
TitleStructure of the Y250A mutant of the PANTON-VALENTINE LEUCOCIDIN S component from STAPHYLOCOCCUS AUREUS
ComponentsLukS-PV
KeywordsTOXIN / Staphylococcus aureus / S component leucocidin / bi-component leucotoxin / 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
CITRATE ANION / LukS-PV
Similarity search - Component
Biological speciesStaphylococcus phage PVL (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsMaveyraud, L. / Guerin, F. / Laventie, B.J. / Prevost, G. / Mourey, 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: 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.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Crystallization and preliminary crystallographic data of leucotoxin S component from Staphylococcus aureus
Authors: Guillet, V. / Keller, D. / 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, M. / Shepard, W. / Monteil, H. / Samama, J.P. / Mourey, L.
History
DepositionJan 28, 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 / pdbx_struct_special_symmetry / 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

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Assembly

Deposited unit
A: LukS-PV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4894
Polymers33,0481
Non-polymers4403
Water5,350297
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)85.340, 89.320, 38.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-302-

FLC

21A-595-

HOH

31A-598-

HOH

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Components

#1: Protein LukS-PV


Mass: 33048.375 Da / Num. of mol.: 1 / Fragment: UNP residues 29-312 / Mutation: Y250A
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-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 297 / 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: 2.2 Å3/Da / Density % sol: 44.01 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 5% PEG 6000, 0.1M NaCitrate , pH 4.00, VAPOR DIFFUSION, SITTING DROP, temperature 285K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.948 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 10, 2008
RadiationMonochromator: channel cut ESRF monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.948 Å / Relative weight: 1
ReflectionResolution: 1.5→30.84 Å / Num. all: 43049 / Num. obs: 43049 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 18.72 Å2 / Rmerge(I) obs: 0.067 / Rsym value: 0.067 / Net I/σ(I): 18.8
Reflection shellResolution: 1.5→1.6 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.753 / Mean I/σ(I) obs: 3.2 / Num. unique all: 3855 / Rsym value: 0.753 / % possible all: 99.9

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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: 1.55→22.69 Å / Cor.coef. Fo:Fc: 0.9598 / Cor.coef. Fo:Fc free: 0.9537 / SU R Cruickshank DPI: 0.073 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: BUSTER TNT
RfactorNum. reflection% reflectionSelection details
Rfree0.1893 2161 5.02 %RANDOM
Rwork0.1653 ---
obs0.1665 43037 99.75 %-
Displacement parametersBiso mean: 22.36 Å2
Baniso -1Baniso -2Baniso -3
1--1.1181 Å20 Å20 Å2
2--4.0269 Å20 Å2
3----2.9089 Å2
Refine analyzeLuzzati coordinate error obs: 0.16 Å
Refinement stepCycle: LAST / Resolution: 1.55→22.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2242 0 30 297 2569
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0092425HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.063318HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d826SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes72HARMONIC2
X-RAY DIFFRACTIONt_gen_planes359HARMONIC5
X-RAY DIFFRACTIONt_it2425HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion4.37
X-RAY DIFFRACTIONt_other_torsion15.45
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion306SEMIHARMONIC5
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_contact2954SEMIHARMONIC4
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2268 166 5.24 %
Rwork0.2001 2999 -
all0.2014 3165 -
obs--99.75 %
Refinement TLS params.Method: refined / Origin x: 51.6669 Å / Origin y: 29.373 Å / Origin z: 21.0996 Å
111213212223313233
T-0.0393 Å2-0.0022 Å2-0.002 Å2--0.0234 Å20.0008 Å2---0.0308 Å2
L0.2239 °2-0.0514 °2-0.005 °2-1.0553 °20.5603 °2--0.5022 °2
S0.0257 Å °-0.0299 Å °0.0025 Å °0.009 Å °-0.0036 Å °-0.0347 Å °0.0175 Å °0.0052 Å °-0.0221 Å °
Refinement TLS groupSelection details: { A|* }

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