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- PDB-8ako: Structure of EspB-EspK complex: the non-identical twin of the PE-... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8ako | |||||||||||||||
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Title | Structure of EspB-EspK complex: the non-identical twin of the PE-PPE-EspG secretion mechanism. | |||||||||||||||
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![]() | CHAPERONE / Secretion Mycrobial protein Virulence factor | |||||||||||||||
Function / homology | ![]() protein secretion by the type VII secretion system / biological process involved in interaction with host / extracellular region / identical protein binding / plasma membrane / cytosol Similarity search - Function | |||||||||||||||
Biological species | ![]() ![]() | |||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||
![]() | Gijsbers, A. / Eymery, M. / Menart, I. / Vinciauskaite, V. / Gao, Y. / Siliqi, D. / Peters, P. / Mccarthy, A. / Ravelli, R.B.G. | |||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: The crystal structure of the EspB-EspK virulence factor-chaperone complex suggests an additional type VII secretion mechanism in Mycobacterium tuberculosis. Authors: Gijsbers, A. / Eymery, M. / Gao, Y. / Menart, I. / Vinciauskaite, V. / Siliqi, D. / Peters, P.J. / McCarthy, A. / Ravelli, R.B.G. | |||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 161.1 KB | Display | ![]() |
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PDB format | ![]() | 121 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 439.6 KB | Display | ![]() |
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Full document | ![]() | 449.7 KB | Display | |
Data in XML | ![]() | 19.1 KB | Display | |
Data in CIF | ![]() | 26 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4xxxS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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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: 32711.186 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 26447.820 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 5.06 Å3/Da / Density % sol: 75.5 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.2-1.2 M sodium malonate 0.1 M HEPES (pH 7.8) 8-14% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 12, 2021 |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 2.29→85.82 Å / Num. obs: 28129 / % possible obs: 53.2 % / Redundancy: 6.2 % / Biso Wilson estimate: 63.86 Å2 / Rpim(I) all: 0.034 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 2.3→2.6 Å / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1406 / Rpim(I) all: 0.38 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4XXX Resolution: 2.293→85.816 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.91 / WRfactor Rfree: 0.28 / WRfactor Rwork: 0.247 / Average fsc free: 0.8555 / Average fsc work: 0.8707 / Cross valid method: THROUGHOUT / ESU R Free: 0.308 Details: Hydrogens have been used if present in the input file
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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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 84.479 Å2
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Refinement step | Cycle: LAST / Resolution: 2.293→85.816 Å
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Refine LS restraints |
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LS refinement shell |
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