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- PDB-3i48: Crystal structure of beta toxin from Staphylococcus aureus F277A,... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3i48 | ||||||
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Title | Crystal structure of beta toxin from Staphylococcus aureus F277A, P278A mutant with bound magnesium ions | ||||||
![]() | Beta-hemolysin | ||||||
![]() | TOXIN / beta toxin / hemolysin / sphingomyelinase | ||||||
Function / homology | ![]() sphingomyelin metabolic process / sphingomyelin phosphodiesterase activity / killing of cells of another organism / extracellular region / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Huseby, M. / Shi, K. / Kruse, A.C. / Ohlendorf, D.H. | ||||||
![]() | ![]() Title: Structure and biological functions of beta toxin from Staphylococcus aureus: Role of the hydrophobic beta hairpin in virulence Authors: Huseby, M. / Shi, K. / Kruse, A.C. / Digre, J. / Mengistu, F. / Bohach, G.A. / Schlievert, P.S. / Ohlendorf, D.H. / Earhart, C.A. #1: Journal: J.Bacteriol. / Year: 2007 Title: Structure and biological activities of beta toxin from Staphylococcus aureus. Authors: Huseby, M. / Shi, K. / Brown, C.K. / Digre, J. / Mengistu, F. / Seo, K.S. / Bohach, G.A. / Schlievert, P.M. / Ohlendorf, D.H. / Earhart, C.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 140.3 KB | Display | ![]() |
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PDB format | ![]() | 107.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 457.5 KB | Display | ![]() |
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Full document | ![]() | 467.6 KB | Display | |
Data in XML | ![]() | 28.3 KB | Display | |
Data in CIF | ![]() | 41.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3i41SC ![]() 3i46C ![]() 3i5vC 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 36092.156 Da / Num. of mol.: 2 / Fragment: UNP residues 35-330 / Mutation: F310A, P311A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: RN2440 / Gene: hlb / Plasmid: pET28b / Production host: ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.89 Å3/Da / Density % sol: 34.94 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: PEG 4000, 0.1 M MES, 5mM MgCl2, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 11, 2007 / Details: mirrors |
Radiation | Monochromator: bent Ge(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9002 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. all: 51464 / Num. obs: 51464 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Rmerge(I) obs: 0.055 / Χ2: 1.387 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.472 / Mean I/σ(I) obs: 2.6 / Num. unique all: 2493 / Χ2: 0.982 / % possible all: 99.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 3I41 Resolution: 1.8→28.16 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.947 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / ESU R: 0.144 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 113.87 Å2 / Biso mean: 28.979 Å2 / Biso min: 13.34 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→28.16 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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