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- PDB-4iyt: Structure Of The Y184A Mutant Of The PANTON-VALENTINE LEUCOCIDIN ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4iyt | ||||||
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Title | Structure Of The Y184A Mutant Of The PANTON-VALENTINE LEUCOCIDIN S Component From STAPHYLOCOCCUS AUREUS | ||||||
![]() | LukS-PV | ||||||
![]() | TOXIN / BI-COMPONENT LEUCOTOXIN / STAPHYLOCOCCUS AUREUS / S COMPONENT LEUCOCIDIN / beta-barrel pore forming toxin | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Guerin, F. / Laventie, B.J. / Prevost, G. / Mourey, L. / Maveyraud, 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: Crystallization and preliminary crystallographic data of a leucotoxin S component from Staphylococcus aureus Authors: Guillet, V. / Keller, D. / Prevost, G. / Mourey, L. #2: ![]() 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: ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 129 KB | Display | ![]() |
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PDB format | ![]() | 99.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4iyaC ![]() 4iycC ![]() 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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Unit cell |
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Components
#1: Protein | Mass: 33048.375 Da / Num. of mol.: 1 / Fragment: UNP residues 29-312 / Mutation: Y184A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-MES / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.45 Å3/Da / Density % sol: 72.34 % |
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Crystal grow | Temperature: 285 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 40% PEG200, 0.1M NaMES, pH 6.50, 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: Apr 12, 2008 |
Radiation | Monochromator: silicon monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98012 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→47.6 Å / Num. obs: 30803 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 51.45 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 16.2 |
Reflection shell | Resolution: 2.2→2.3 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.915 / Mean I/σ(I) obs: 2.7 / Num. unique all: 3759 / Rsym value: 0.915 / % possible all: 99.7 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 1T5R Resolution: 2.2→47.6 Å / Cor.coef. Fo:Fc: 0.9199 / Cor.coef. Fo:Fc free: 0.9225 / SU R Cruickshank DPI: 0.151 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 62.19 Å2
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Refine analyze | Luzzati coordinate error obs: 0.371 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→47.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.28 Å / Total num. of bins used: 15
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Refinement TLS params. | Method: refined / Origin x: -13.0419 Å / Origin y: 0.8928 Å / Origin z: 12.4126 Å
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Refinement TLS group | Selection details: { A|* } |