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- PDB-1t5r: STRUCTURE OF THE PANTON-VALENTINE LEUCOCIDIN S COMPONENT FROM STA... -

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Basic information

Entry
Database: PDB / ID: 1t5r
TitleSTRUCTURE OF THE PANTON-VALENTINE LEUCOCIDIN S COMPONENT FROM STAPHYLOCOCCUS AUREUS
ComponentsLukS-PV
KeywordsUNKNOWN FUNCTION / BI-COMPONENT LEUCOTOXIN / PORE-FORMING TOXIN / STAPHYLOCOCCUS AUREUS / S COMPONENT LEUCOCIDIN
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 Å
AuthorsGuillet, V. / Roblin, P. / Keller, D. / Prevost, G. / Mourey, L.
Citation
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. / Mourey, L.
#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: 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. / GONZALES, A. / COURCELLE, E. / SHEPARD, W. / MONTEIL, H. / SAMAMA, J.P. / MOUREY, L.
History
DepositionMay 5, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
E: LukS-PV
F: LukS-PV
G: LukS-PV
H: LukS-PV


Theoretical massNumber of molelcules
Total (without water)258,8458
Polymers258,8458
Non-polymers00
Water14,790821
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.85, 94.85, 306.11
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein
LukS-PV / LUKS-PV / Leucotoxin


Mass: 32355.621 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Staphylococcus phage PVL (virus) / Cellular location: CHROMOSOME / Strain: v8 / References: UniProt: O80066, UniProt: Q783R1*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 821 / 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: 2.7 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 8
Details: CRYSTALLIZATION CONDITIONS: VAPOR EQUILIBRIUM USING THE HANGING METHOD AT 285K. THE PROTEINS WERE CONCENTRATED AT 20-25 MG/ML IN MES-NAOH PH 6.0 (50MM), NACL (50MM). DROPS WERE PREPARED BY ...Details: CRYSTALLIZATION CONDITIONS: VAPOR EQUILIBRIUM USING THE HANGING METHOD AT 285K. THE PROTEINS WERE CONCENTRATED AT 20-25 MG/ML IN MES-NAOH PH 6.0 (50MM), NACL (50MM). DROPS WERE PREPARED BY MIXING EQUAL VOLUMES OF PROTEIN AND RESERVOIR SOLUTIONS AND USING RESERVOIR VOLUMES OF 500 microL CONTAINING 30% JEFFAMINE M-600, 0.1 M TRIS-HCL AT PH VALUES RANGING FROM 8.0 TO 8.9. MICRO- AND MACRO-SEEDING TECHNIQUES, INCLUDING CROSS-SEEDINGS, WERE USED TO GROW CRYSTALS. CRYSTAL SIZE (200X200X200 MM3) IN 6-10microL HANGING DROPS. , VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 8, 2002 / Details: bent multilayer
RadiationMonochromator: double crystal monochromator (thin diamond and focusing Germanium crystals)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2→35.5 Å / Num. all: 169450 / Num. obs: 169450 / % possible obs: 93.6 % / Redundancy: 5.9 % / Biso Wilson estimate: 34.3 Å2 / Rsym value: 0.055 / Net I/σ(I): 9.1
Reflection shellResolution: 2→2.11 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 1.6 / Num. unique all: 16649 / Rsym value: 0.47 / % possible all: 67.5

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Processing

Software
NameVersionClassification
MOLREPphasing
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PVL

1pvl


Resolution: 2→35.5 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.247 13575 -random
Rwork0.209 ---
all0.226 169349 --
obs-136851 75.6 %-
Displacement parametersBiso mean: 36.3 Å2
Baniso -1Baniso -2Baniso -3
1-1.89 Å21.89 Å2-3.79 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.34 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2→35.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17092 0 0 821 17913
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0061.5
X-RAY DIFFRACTIONc_angle_deg1.32
X-RAY DIFFRACTIONc_dihedral_angle_deg27.72
X-RAY DIFFRACTIONc_improper_angle_deg0.652.5
X-RAY DIFFRACTIONc_mcangle_it2.04
X-RAY DIFFRACTIONc_mcbond_it1.36
X-RAY DIFFRACTIONc_scangle_it2.9
X-RAY DIFFRACTIONc_scbond_it2.07
LS refinement shellResolution: 2→2.13 Å
RfactorNum. reflection% reflection
Rfree0.291 794 -
Rwork0.24 --
obs-7540 27.7 %

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