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- PDB-6te4: Structural insights into Pseudomonas aeruginosa Type six secretio... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6te4 | ||||||
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Title | Structural insights into Pseudomonas aeruginosa Type six secretion system exported effector 8: Tse8 in complex with a peptide | ||||||
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![]() | TOXIN / Amidase Signature (AS) superfamily complex | ||||||
Function / homology | Amidase signature domain / Amidase signature (AS) superfamily / Amidase / metal ion binding / Amidase domain-containing protein![]() | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sainz-Polo, M.A. / Capuni, R. / Lucas, M. / Altuna, J. / Fucini, P. / Montanchez, I. / Albesa-Jove, D. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural insights into Pseudomonas aeruginosaType six secretion system exported effector 8. Authors: Gonzalez-Magana, A. / Sainz-Polo, M.A. / Pretre, G. / Capuni, R. / Lucas, M. / Altuna, J. / Montanchez, I. / Fucini, P. / Albesa-Jove, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 229.5 KB | Display | ![]() |
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PDB format | ![]() | 180.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 445.4 KB | Display | ![]() |
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Full document | ![]() | 450 KB | Display | |
Data in XML | ![]() | 42.7 KB | Display | |
Data in CIF | ![]() | 61.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6yhvC ![]() 1m22S 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: 63517.316 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein/peptide | | Mass: 612.738 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: peptide that might be cleaved from the C-terminal part of the protein as identified by MS analysis. Source: (natural) ![]() ![]() #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.71 % / Description: prisms |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 1.6 M magnesium sulfate heptahydrate, 0.1 M MES buffer pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 17, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.29→56.632 Å / Num. obs: 53333 / % possible obs: 94.85 % / Redundancy: 3.4 % / Biso Wilson estimate: 22.48 Å2 / CC1/2: 0.979 / CC star: 0.995 / Rmerge(I) obs: 0.1873 / Rpim(I) all: 0.1199 / Rrim(I) all: 0.2233 / Net I/σ(I): 6.96 |
Reflection shell | Resolution: 2.29→2.32 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.7321 / Mean I/σ(I) obs: 2.25 / Num. unique obs: 2646 / CC1/2: 0.852 / CC star: 0.959 / R split: 0.4686 / Rrim(I) all: 0.8725 / % possible all: 90.26 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1m22 Resolution: 2.29→56.632 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 29.02
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 101.97 Å2 / Biso mean: 24.63 Å2 / Biso min: 12.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.29→56.632 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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