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- PDB-4iya: Structure of the Y250A mutant of the PANTON-VALENTINE LEUCOCIDIN ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4iya | ||||||
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Title | Structure of the Y250A mutant of the PANTON-VALENTINE LEUCOCIDIN S component from STAPHYLOCOCCUS AUREUS | ||||||
![]() | LukS-PV | ||||||
![]() | TOXIN / Staphylococcus aureus / S component leucocidin / bi-component leucotoxin / beta-barrel pore forming toxin | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Maveyraud, L. / Guerin, F. / Laventie, B.J. / Prevost, G. / Mourey, L. | ||||||
![]() | ![]() 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: ![]() 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: ![]() Title: Crystallization and preliminary crystallographic data of leucotoxin S component from Staphylococcus aureus Authors: Guillet, V. / Keller, D. / Prevost, G. / Mourey, L. #3: ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 133.6 KB | Display | ![]() |
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PDB format | ![]() | 103.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 449.2 KB | Display | ![]() |
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Full document | ![]() | 450.6 KB | Display | |
Data in XML | ![]() | 15.9 KB | Display | |
Data in CIF | ![]() | 23.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4iycC ![]() 4iytC ![]() 4izlC ![]() 4j0oC ![]() 1t5rS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | 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.) ![]() ![]() ![]() | ||||
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#2: Chemical | #3: Chemical | ChemComp-EDO / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.01 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 10, 2008 |
Radiation | Monochromator: channel cut ESRF monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.948 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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
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Refinement | Method to determine structure: ![]() Starting model: 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
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Displacement parameters | Biso mean: 22.36 Å2
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Refine analyze | Luzzati coordinate error obs: 0.16 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→22.69 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.59 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 51.6669 Å / Origin y: 29.373 Å / Origin z: 21.0996 Å
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Refinement TLS group | Selection details: { A|* } |