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Open data
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Basic information
Entry | Database: PDB / ID: 6hcn | ||||||
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Title | Adenovirus Type 5 Fiber Knob protein at 1.49A resolution | ||||||
![]() | (Fiber protein) x 2 | ||||||
![]() | VIRAL PROTEIN / Fiber / Fiber-knob / tropism determinant / high resolution / structure determination. adenovirus / Mastadenovirus | ||||||
Function / homology | ![]() viral capsid, fiber / adhesion receptor-mediated virion attachment to host cell / 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: 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 | ![]() | 241.1 KB | Display | ![]() |
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PDB format | ![]() | 192.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6fjnC ![]() 6fjqC ![]() 1knbS C: citing same article ( S: Starting model for refinement |
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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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / Refine code: _
NCS ensembles :
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Components
#1: Protein | Mass: 20299.631 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | | Mass: 20542.916 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-MG / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.3 Å3/Da / Density % sol: 62.67 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: DL-Malic acid, MES monohydrate, Tris, pH 7.0 (condition D4 of PACT premier suite from Molecular Dimensions) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 26, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96859 Å / Relative weight: 1 |
Reflection | Resolution: 1.49→61.56 Å / Num. obs: 131951 / % possible obs: 99.8 % / Redundancy: 6.6 % / Biso Wilson estimate: 18.3 Å2 / CC1/2: 0.983 / Rmerge(I) obs: 0.134 / Rrim(I) all: 0.159 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 1.49→1.53 Å / Redundancy: 6.3 % / Rmerge(I) obs: 1.838 / Num. unique obs: 9638 / CC1/2: 0.565 / Rrim(I) all: 2.183 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1KNB Resolution: 1.49→61.56 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.953 / SU B: 5.205 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.077 / ESU R Free: 0.069 / 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: 30.628 Å2
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Refinement step | Cycle: 1 / Resolution: 1.49→61.56 Å
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Refine LS restraints |
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