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- PDB-4iyc: Structure of the T244A mutant of the PANTON-VALENTINE LEUCOCIDIN ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4iyc | ||||||
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Title | Structure of the T244A mutant of the PANTON-VALENTINE LEUCOCIDIN 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. / Lavnetie, 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 | ![]() | 453.4 KB | Display | ![]() |
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PDB format | ![]() | 376.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 457 KB | Display | ![]() |
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Full document | ![]() | 468 KB | Display | |
Data in XML | ![]() | 42.3 KB | Display | |
Data in CIF | ![]() | 59.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4iyaC ![]() 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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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | 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.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.96 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 6, 2008 |
Radiation | Monochromator: Si (111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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
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Refinement | Method to determine structure: ![]() Starting model: 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
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Displacement parameters | Biso mean: 65.3 Å2
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Refine analyze | Luzzati coordinate error obs: 0.354 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.75→46.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.75→2.83 Å / Total num. of bins used: 18
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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