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Open data
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Basic information
Entry | Database: PDB / ID: 8ofu | |||||||||
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Title | Human adenovirus type 53 fiber-knob protein | |||||||||
![]() | Fiber protein | |||||||||
![]() | VIRAL PROTEIN / Adenovirus / Fiber knob / Ad25 | |||||||||
Function / homology | ![]() viral capsid / cell adhesion / symbiont entry into host cell / virion attachment to host cell Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Rizkallah, P.J. / Parker, A.L. / Mundy, R.M. / Baker, A.T. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Broad sialic acid usage amongst species D human adenovirus. Authors: Mundy, R.M. / Baker, A.T. / Bates, E.A. / Cunliffe, T.G. / Teijeira-Crespo, A. / Moses, E. / 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 | ![]() | 466.5 KB | Display | ![]() |
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PDB format | ![]() | 385.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 515.3 KB | Display | ![]() |
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Full document | ![]() | 532.1 KB | Display | |
Data in XML | ![]() | 55.4 KB | Display | |
Data in CIF | ![]() | 77.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8ofpC ![]() 8ofqC ![]() 8ofrC ![]() 8ofsC ![]() 8oftC ![]() 8ofvC C: citing same article ( |
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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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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS ensembles :
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Components
#1: Protein | Mass: 21211.078 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-PEG / #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: 2.3 Å3/Da / Density % sol: 46.54 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.2 M potassium thiocyanate, 20 % w/v PEG 3350, pH unadjusted |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 14, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91188 Å / Relative weight: 1 |
Reflection | Resolution: 1.606→70.489 Å / Num. obs: 150644 / % possible obs: 99.7 % / Redundancy: 3.7 % / Biso Wilson estimate: 20.6 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.059 / Rrim(I) all: 0.116 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 1.606→1.633 Å / Redundancy: 3.5 % / Rmerge(I) obs: 1.569 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 7529 / CC1/2: 0.334 / Rpim(I) all: 0.972 / Rrim(I) all: 1.853 / % possible all: 99.4 |
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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: 25.206 Å2
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Refinement step | Cycle: 1 / Resolution: 1.61→68.42 Å
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Refine LS restraints |
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