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- PDB-4tw1: Crystal structure of the octameric pore complex of the Staphyloco... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4tw1 | ||||||
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Title | Crystal structure of the octameric pore complex of the Staphylococcus aureus Bi-component Toxin LukGH | ||||||
![]() | (Possible leukocidin subunit) x 2 | ||||||
![]() | TOXIN / octamer leukocidin pore-forming toxin | ||||||
Function / homology | Leukocidin/porin MspA / Leukocidin-like / Distorted Sandwich / Mainly Beta / : / : ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Logan, D.T. / Hakansson, M. / Saline, M. / Kimbung, R. / Badarau, A. / Rouha, H. / Nagy, E. | ||||||
![]() | ![]() Title: Structure-Function Analysis of Heterodimer Formation, Oligomerization, and Receptor Binding of the Staphylococcus aureus Bi-component Toxin LukGH. Authors: Badarau, A. / Rouha, H. / Malafa, S. / Logan, D.T. / Hakansson, M. / Stulik, L. / Dolezilkova, I. / Teubenbacher, A. / Gross, K. / Maierhofer, B. / Weber, S. / Jagerhofer, M. / Hoffman, D. / Nagy, E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 910.6 KB | Display | ![]() |
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PDB format | ![]() | 753.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 585.7 KB | Display | ![]() |
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Full document | ![]() | 720.5 KB | Display | |
Data in XML | ![]() | 164.4 KB | Display | |
Data in CIF | ![]() | 223.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3b07S S: Starting model for refinement |
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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: 35825.539 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | Mass: 37682.680 Da / Num. of mol.: 8 / Fragment: Residues 28-351 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.39 Å3/Da / Density % sol: 71.96 % / Description: Thin plates |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Drops consisted of 100 nl protein in 20 mM HEPES buffer pH 7.5 and 100 nl reservoir 30 mM MgCl2, 30 mM CaCl2, 0.1 M Na HEPES/MOPS buffer pH 7.5, 12.5 % v/v MPD, 12.5 % w/v PEG 1000, 12.5 % ...Details: Drops consisted of 100 nl protein in 20 mM HEPES buffer pH 7.5 and 100 nl reservoir 30 mM MgCl2, 30 mM CaCl2, 0.1 M Na HEPES/MOPS buffer pH 7.5, 12.5 % v/v MPD, 12.5 % w/v PEG 1000, 12.5 % w/v PEG 3350. Crystals appeared after 7 days. |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 12, 2013 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.8→48.188 Å / Num. all: 222018 / Num. obs: 222018 / % possible obs: 97.9 % / Redundancy: 3.1 % / Biso Wilson estimate: 56.4 Å2 / Rpim(I) all: 0.109 / Rrim(I) all: 0.194 / Rsym value: 0.16 / Net I/av σ(I): 4.824 / Net I/σ(I): 10.1 / Num. measured all: 685808 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3B07 prepared using CHAINSAW Resolution: 2.8→48 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.856 / WRfactor Rfree: 0.2318 / WRfactor Rwork: 0.1798 / FOM work R set: 0.6812 / SU B: 20.998 / SU ML: 0.362 / SU R Cruickshank DPI: 0.512 / SU Rfree: 0.3468 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.512 / ESU R Free: 0.347 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
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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: 132.12 Å2 / Biso mean: 36.001 Å2 / Biso min: 2 Å2
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Refinement step | Cycle: final / Resolution: 2.8→48 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.869 Å
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