+Open data
-Basic information
Entry | Database: PDB / ID: 8oft | |||||||||
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Title | Human adenovirus type 32 fiber-knob protein | |||||||||
Components | Fiber | |||||||||
Keywords | VIRAL PROTEIN / Adenovirus / Fiber knob / Ad25 | |||||||||
Function / homology | Function and homology information adhesion receptor-mediated virion attachment to host cell / viral capsid / cell adhesion / symbiont entry into host cell Similarity search - Function | |||||||||
Biological species | Human adenovirus 32 | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Rizkallah, P.J. / Parker, A.L. / Mundy, R.M. / Baker, A.T. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: Npj Viruses / Year: 2023 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8oft.cif.gz | 250.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8oft.ent.gz | 202.6 KB | Display | PDB format |
PDBx/mmJSON format | 8oft.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8oft_validation.pdf.gz | 439.9 KB | Display | wwPDB validaton report |
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Full document | 8oft_full_validation.pdf.gz | 447.4 KB | Display | |
Data in XML | 8oft_validation.xml.gz | 26 KB | Display | |
Data in CIF | 8oft_validation.cif.gz | 36.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/of/8oft ftp://data.pdbj.org/pub/pdb/validation_reports/of/8oft | HTTPS FTP |
-Related structure data
Related structure data | 8ofpC 8ofqC 8ofrC 8ofsC 8ofuC 8ofvC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
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-Components
#1: Protein | Mass: 22044.746 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human adenovirus 32 / Strain: 32 / Gene: L5 / Production host: Escherichia coli (E. coli) / References: UniProt: M0QUV7 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.68 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.1 M SPG Buffer, 25% PEG 1500 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91188 Å |
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: 2→93.81 Å / Num. obs: 39152 / % possible obs: 99.4 % / Redundancy: 3.6 % / Biso Wilson estimate: 28 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.062 / Rrim(I) all: 0.119 / Net I/σ(I): 5.9 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.551 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2762 / CC1/2: 0.831 / Rpim(I) all: 0.353 / Rrim(I) all: 0.658 / % possible all: 94.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→93.81 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.931 / SU B: 12.74 / SU ML: 0.173 / Cross valid method: THROUGHOUT / ESU R: 0.245 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.047 Å2
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Refinement step | Cycle: 1 / Resolution: 2→93.81 Å
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Refine LS restraints |
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