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- PDB-4izl: Structure Of The N248A Mutant of the PANTON-VALENTINE LEUCOCIDIN ... -

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Basic information

Entry
Database: PDB / ID: 4izl
TitleStructure Of The N248A 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: 2.8 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: TOXINS 2004 279 41028 41037 3 Structure 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 30, 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

Downloads & links

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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)132,3904
Polymers132,3904
Non-polymers00
Water1,72996
1
A: LukS-PV


Theoretical massNumber of molelcules
Total (without water)33,0971
Polymers33,0971
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: LukS-PV


Theoretical massNumber of molelcules
Total (without water)33,0971
Polymers33,0971
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: LukS-PV


Theoretical massNumber of molelcules
Total (without water)33,0971
Polymers33,0971
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: LukS-PV


Theoretical massNumber of molelcules
Total (without water)33,0971
Polymers33,0971
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)93.970, 93.970, 309.330
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: 33097.445 Da / Num. of mol.: 4 / Fragment: UNP residues 29-312 / Mutation: N248A
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 / Water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 52.31 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 40 % PEG200, 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: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 6, 2008
RadiationMonochromator: Si (111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.8→46.99 Å / Num. obs: 34936 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.3 % / Biso Wilson estimate: 70.58 Å2 / Rmerge(I) obs: 0.122 / Rsym value: 0.122 / Net I/σ(I): 16
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.649 / Mean I/σ(I) obs: 1.9 / Num. unique all: 3263 / Rsym value: 0.649 / % possible all: 94.6

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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: 2.8→46.99 Å / Cor.coef. Fo:Fc: 0.9073 / Cor.coef. Fo:Fc free: 0.8856 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2445 1772 5.07 %RANDOM
Rwork0.2227 ---
all0.2238 34936 --
obs0.2238 34936 99.14 %-
Displacement parametersBiso mean: 56.1 Å2
Baniso -1Baniso -2Baniso -3
1--4.9141 Å20 Å20 Å2
2---4.9141 Å20 Å2
3---9.8281 Å2
Refine analyzeLuzzati coordinate error obs: 0.413 Å
Refinement stepCycle: LAST / Resolution: 2.8→46.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8719 0 0 96 8815
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0088939HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0912150HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2956SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes262HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1302HARMONIC5
X-RAY DIFFRACTIONt_it8939HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.79
X-RAY DIFFRACTIONt_other_torsion19.5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1170SEMIHARMONIC5
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_contact9386SEMIHARMONIC4
LS refinement shellResolution: 2.8→2.88 Å / Total num. of bins used: 18
RfactorNum. reflection% reflection
Rfree0.2703 121 4.54 %
Rwork0.2382 2547 -
all0.2397 2668 -
obs--99.14 %
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)
10.6561-0.01380.44261.17390.57782.54550.06290.0045-0.0641-0.1541-0.0201-0.06930.16410.0509-0.0427-0.02160.0245-0.0042-0.14580.0139-0.0937-42.526217.507-10.4102
20.91070.20020.71241.15180.68514.69010.0203-0.1475-0.15940.2590.0705-0.03760.3902-0.103-0.0908-0.14650.0027-0.047-0.10050.0148-0.118-74.9548-0.6779-35.5731
31.1436-0.2534-0.00970.8379-0.28853.5787-0.0656-0.21280.07350.10710.1184-0.0827-0.5040.1238-0.0528-0.09340.01740.003-0.07110.0146-0.1575-20.5188-0.4323-39.965
40.90780.3143-0.75010.7669-0.48592.23660.03480.05430.2099-0.05930.00690.0874-0.07550.0343-0.0417-0.06820.0310.0104-0.09210.0204-0.0634-52.6563-19.6512-14.6901
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A2 - 284
2X-RAY DIFFRACTION2{ B|* }B2 - 284
3X-RAY DIFFRACTION3{ C|* }C3 - 284
4X-RAY DIFFRACTION4{ D|* }D2 - 284

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