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- PDB-4j0o: Structure of the Y246A Mutant of the PANTON-VALENTINE LEUCOCIDIN ... -

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Basic information

Entry
Database: PDB / ID: 4j0o
TitleStructure of the Y246A 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: 2.5 Å
AuthorsMaveyraud, L. / 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: 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 31, 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 / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LukS-PV
B: LukS-PV
C: LukS-PV
D: LukS-PV


Theoretical massNumber of molelcules
Total (without water)131,7334
Polymers131,7334
Non-polymers00
Water8,521473
1
A: LukS-PV


Theoretical massNumber of molelcules
Total (without water)32,9331
Polymers32,9331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: LukS-PV


Theoretical massNumber of molelcules
Total (without water)32,9331
Polymers32,9331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: LukS-PV


Theoretical massNumber of molelcules
Total (without water)32,9331
Polymers32,9331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: LukS-PV


Theoretical massNumber of molelcules
Total (without water)32,9331
Polymers32,9331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)94.110, 94.110, 306.440
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein
LukS-PV


Mass: 32933.293 Da / Num. of mol.: 4 / Fragment: UNP residues 30-312 / Mutation: Y246A
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 473 / 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: 2.58 Å3/Da / Density % sol: 52.24 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 40 % PEG 200, 0.1M NaMES, pH 7.50, VAPOR DIFFUSION, SITTING DROP, temperature 285K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 7, 2010
RadiationMonochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 2.5→47.05 Å / Num. all: 46924 / Num. obs: 46924 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 49.67 Å2 / Rmerge(I) obs: 0.149 / Rsym value: 0.149 / Net I/σ(I): 10
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.827 / Mean I/σ(I) obs: 1.9 / Num. unique all: 6622 / Rsym value: 0.827 / % possible all: 95.7

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Processing

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

1t5r


Resolution: 2.5→46.51 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.9075 / SU R Cruickshank DPI: 0.444 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: BUSTER/TNT
RfactorNum. reflection% reflectionSelection details
Rfree0.2282 2380 5.07 %RANDOM
Rwork0.1822 ---
all0.1846 46908 --
obs0.1846 46908 96.14 %-
Displacement parametersBiso mean: 42.75 Å2
Baniso -1Baniso -2Baniso -3
1--0.8531 Å20 Å20 Å2
2---0.8531 Å20 Å2
3---1.7063 Å2
Refine analyzeLuzzati coordinate error obs: 0.291 Å
Refinement stepCycle: LAST / Resolution: 2.5→46.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8761 0 0 473 9234
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.018979HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1712174HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3024SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes267HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1291HARMONIC5
X-RAY DIFFRACTIONt_it8979HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.69
X-RAY DIFFRACTIONt_other_torsion19.04
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1161SEMIHARMONIC5
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_contact10015SEMIHARMONIC4
LS refinement shellResolution: 2.5→2.56 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2768 169 5.05 %
Rwork0.2176 3175 -
all0.2206 3344 -
obs--96.14 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.68130.02750.38180.9450.35361.88160.0007-0.0043-0.1475-0.06820.0037-0.01590.0693-0.0381-0.0044-0.02130.019-0.0252-0.0278-0.0056-0.1502-42.811717.6273-10.4118
20.7313-0.00530.63110.9460.76894.5994-0.0153-0.1617-0.10390.14560.0602-0.01180.4506-0.1598-0.0448-0.0815-0.0182-0.0259-0.0221-0.0036-0.1945-74.8762-0.8279-35.3885
31.2183-0.65180.2031.526-0.36375.0945-0.1202-0.30740.11260.32880.20450.0498-0.62960.2993-0.0843-0.1256-0.03950.0239-0.0329-0.0076-0.2418-20.4173-0.9574-39.0121
40.93310.4237-0.79271.0664-0.83162.36910.01890.10650.1617-0.1420.0223-0.0078-0.03080.0256-0.0412-0.01170.0209-0.0024-0.04120.0353-0.1741-52.8562-19.8627-14.2942
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A3 - 284
2X-RAY DIFFRACTION2{ B|* }B3 - 284
3X-RAY DIFFRACTION3{ C|* }C3 - 284
4X-RAY DIFFRACTION4{ D|* }D3 - 284

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