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- PDB-8on5: Structure of the tail fibre from an extracellular contractile inj... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8on5 | ||||||
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Title | Structure of the tail fibre from an extracellular contractile injection system from Photorhabdus bacteria | ||||||
![]() | Adenoviral fiber protein | ||||||
![]() | CELL ADHESION / Tail fibre from an extracellular contractile injection system from bacteria / cell surface recognition / PVC / cell surface attachment / virulence. | ||||||
Function / homology | Attachment protein shaft domain superfamily / virion attachment to host cell / Adenoviral fiber protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Godfrey, A.E. / Diaz-Saez, L. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of the tail fibre from an extracellular contractile injection system from Photorhabdus bacteria Authors: Godfrey, A.E. / Diaz-Saez, 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 | ![]() | 255.5 KB | Display | ![]() |
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PDB format | ![]() | 206.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 502.2 KB | Display | ![]() |
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Full document | ![]() | 519.8 KB | Display | |
Data in XML | ![]() | 52.5 KB | Display | |
Data in CIF | ![]() | 72.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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: 23594.537 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: PAU_02236 / Production host: ![]() ![]() #2: Chemical | ChemComp-MPD / ( #3: Chemical | ChemComp-EDO / #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56.09 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 0.02 M CaCl2 dihydrate, 0.1M Na acetate pH 4.6, 30% MPD |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jan 28, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97951 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→60.03 Å / Num. obs: 70537 / % possible obs: 100 % / Redundancy: 6.2 % / Biso Wilson estimate: 37.715 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.046 / Rrim(I) all: 0.113 / Χ2: 0.96 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 2.3→2.35 Å / % possible obs: 99.5 % / Redundancy: 6 % / Rmerge(I) obs: 0.669 / Num. measured all: 26868 / Num. unique obs: 4480 / CC1/2: 0.941 / Rpim(I) all: 0.301 / Rrim(I) all: 0.735 / Χ2: 1.01 / Net I/σ(I) obs: 2.3 |
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Processing
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Refinement | Method to determine structure: ![]()
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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 mean: 42.635 Å2
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Refinement step | Cycle: 1 / Resolution: 2.3→60.03 Å
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Refine LS restraints |
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