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- PDB-4iyc: Structure of the T244A mutant of the PANTON-VALENTINE LEUCOCIDIN ... -

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Basic information

Entry
Database: PDB / ID: 4iyc
TitleStructure of the T244A mutant of the PANTON-VALENTINE LEUCOCIDIN 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
Biological speciesStaphylococcus phage PVL (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsMaveyraud, L. / Guerin, F. / Lavnetie, 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 / 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)132,4424
Polymers132,4424
Non-polymers00
Water5,747319
1
A: LukS-PV


Theoretical massNumber of molelcules
Total (without water)33,1101
Polymers33,1101
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: LukS-PV


Theoretical massNumber of molelcules
Total (without water)33,1101
Polymers33,1101
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: LukS-PV


Theoretical massNumber of molelcules
Total (without water)33,1101
Polymers33,1101
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: LukS-PV


Theoretical massNumber of molelcules
Total (without water)33,1101
Polymers33,1101
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)94.480, 94.480, 310.370
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: 33110.445 Da / Num. of mol.: 4 / Fragment: UNP residues 29-312 / Mutation: T244A
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.: 319 / 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: 2.61 Å3/Da / Density % sol: 52.96 %
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: 2.75→46.7 Å / Num. all: 36657 / Num. obs: 36657 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Biso Wilson estimate: 77.85 Å2 / Rmerge(I) obs: 0.11 / Rsym value: 0.11 / Net I/σ(I): 15.1
Reflection shellResolution: 2.75→2.8 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.834 / Mean I/σ(I) obs: 2 / Num. unique all: 1606 / Rsym value: 0.834 / % possible all: 83.4

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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: 2.75→46.7 Å / Cor.coef. Fo:Fc: 0.9288 / Cor.coef. Fo:Fc free: 0.8946 / SU R Cruickshank DPI: 4.034 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: buster tnt
RfactorNum. reflection% reflectionSelection details
Rfree0.2458 1859 5.07 %RANDOM
Rwork0.1951 ---
all0.1977 36657 --
obs0.1977 36656 97.34 %-
Displacement parametersBiso mean: 65.3 Å2
Baniso -1Baniso -2Baniso -3
1--2.4287 Å20 Å20 Å2
2---2.4287 Å20 Å2
3---4.8575 Å2
Refine analyzeLuzzati coordinate error obs: 0.354 Å
Refinement stepCycle: LAST / Resolution: 2.75→46.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8800 0 0 319 9119
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.019025HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.2112254HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3016SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes269HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1307HARMONIC5
X-RAY DIFFRACTIONt_it9025HARMONIC20
X-RAY DIFFRACTIONt_omega_torsion3.34
X-RAY DIFFRACTIONt_other_torsion20.31
X-RAY DIFFRACTIONt_chiral_improper_torsion1172SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact9551SEMIHARMONIC4
LS refinement shellResolution: 2.75→2.83 Å / Total num. of bins used: 18
RfactorNum. reflection% reflection
Rfree0.3072 122 4.88 %
Rwork0.2144 2378 -
all0.219 2500 -
obs-2500 97.34 %
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)
10.90460.35110.54781.51260.82393.82970.01230.0322-0.057-0.2864-0.0267-0.01190.24240.03250.0144-0.01810.0624-0.0194-0.22480.0434-0.2858-42.804917.4368-11.0479
21.43450.42031.13371.29090.96974.9752-0.0339-0.2349-0.28140.35770.1136-0.02760.4902-0.274-0.0797-0.11910.0538-0.0252-0.17960.0553-0.2522-74.9553-0.7138-35.4437
31.0798-0.3552-0.09880.7931-0.46494.7199-0.1023-0.23640.03970.20710.1408-0.0503-0.62370.2028-0.0385-0.0574-0.0271-0.0085-0.0307-0.0019-0.3511-20.559-0.4121-39.9252
40.8750.3012-0.78621.1056-0.51473.64220.0520.09350.1922-0.1093-0.02780.074-0.11120.0486-0.0242-0.09680.0372-0.0233-0.16610.0341-0.2655-52.6348-19.5922-14.874
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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