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Open data
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Basic information
Entry | Database: PDB / ID: 6fjo | ||||||
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Title | Adenovirus species 26 knob protein, very high resolution | ||||||
![]() | Fiber | ||||||
![]() | VIRAL PROTEIN / Fiber / Fiber-knob / tropism determinant / high resolution / structure determination. adenovirus / Mastadenovirus | ||||||
Function / homology | ![]() adhesion receptor-mediated virion attachment to host cell / viral capsid / cell adhesion / symbiont entry into host cell / host cell nucleus Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Rizkallah, P.J. / Parker, A.L. / Baker, A.T. | ||||||
![]() | ![]() Title: Human adenovirus type 26 uses sialic acid-bearing glycans as a primary cell entry receptor. Authors: Baker, A.T. / Mundy, R.M. / Davies, J.A. / Rizkallah, P.J. / Parker, A.L. #1: ![]() Title: Diversity within the adenovirus fiber knob hypervariable loops influences primary receptor interactions. Authors: Baker, A.T. / Greenshields-Watson, A. / Coughlan, L. / Davies, J.A. / Uusi-Kerttula, H. / Cole, D.K. / Rizkallah, P.J. / Parker, A.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 | ![]() | 96.8 KB | Display | ![]() |
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PDB format | ![]() | 73.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 460.6 KB | Display | ![]() |
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Full document | ![]() | 462.6 KB | Display | |
Data in XML | ![]() | 11.6 KB | Display | |
Data in CIF | ![]() | 16.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6qu6C ![]() 6qu8C ![]() 1knbS 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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Unit cell |
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Components
#1: Protein | Mass: 20648.195 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-GLU / |
#3: Chemical | ChemComp-SO4 / |
#4: Chemical | ChemComp-GOL / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.71 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: PACT premier A01: 0.1 M SPG buffer, 25% PEG 1500 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 12, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.17→85.78 Å / Num. obs: 71878 / % possible obs: 100 % / Redundancy: 21.8 % / Biso Wilson estimate: 12.2 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.065 / Rrim(I) all: 0.066 / Net I/σ(I): 24.8 |
Reflection shell | Resolution: 1.17→1.23 Å / Redundancy: 21.2 % / Rmerge(I) obs: 1.37 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 10438 / CC1/2: 0.825 / Rrim(I) all: 1.404 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1KNB Resolution: 1.17→60.65 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.185 / SU ML: 0.026 / Cross valid method: THROUGHOUT / ESU R: 0.034 / ESU R Free: 0.036 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.89 Å2
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Refinement step | Cycle: 1 / Resolution: 1.17→60.65 Å
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Refine LS restraints |
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