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Yorodumi- PDB-5n8d: Structure of the distal domain of mouse adenovirus 2 fibre, P21 native -
+Open data
-Basic information
Entry | Database: PDB / ID: 5n8d | |||||||||||||||
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Title | Structure of the distal domain of mouse adenovirus 2 fibre, P21 native | |||||||||||||||
Components | Fiber | |||||||||||||||
Keywords | VIRAL PROTEIN / Triple beta-spiral / 3-bladed propeller / ABCJ-GHID topology / N-acetyl-glucosamine binding | |||||||||||||||
Function / homology | Function and homology information adhesion receptor-mediated virion attachment to host cell / virion component / cell adhesion / symbiont entry into host cell / host cell nucleus Similarity search - Function | |||||||||||||||
Biological species | Murine adenovirus 2 | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | |||||||||||||||
Authors | Singh, A.K. / van Raaij, M.J. | |||||||||||||||
Funding support | Spain, 4items
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Citation | Journal: J. Gen. Virol. / Year: 2018 Title: Structure and N-acetylglucosamine binding of the distal domain of mouse adenovirus 2 fibre. Authors: Singh, A.K. / Nguyen, T.H. / Vidovszky, M.Z. / Harrach, B. / Benko, M. / Kirwan, A. / Joshi, L. / Kilcoyne, M. / Berbis, M.A. / Canada, F.J. / Jimenez-Barbero, J. / Menendez, M. / Wilson, S. ...Authors: Singh, A.K. / Nguyen, T.H. / Vidovszky, M.Z. / Harrach, B. / Benko, M. / Kirwan, A. / Joshi, L. / Kilcoyne, M. / Berbis, M.A. / Canada, F.J. / Jimenez-Barbero, J. / Menendez, M. / Wilson, S.S. / Bromme, B.A. / Smith, J.G. / van Raaij, M.J. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5n8d.cif.gz | 282.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5n8d.ent.gz | 225.3 KB | Display | PDB format |
PDBx/mmJSON format | 5n8d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5n8d_validation.pdf.gz | 496.9 KB | Display | wwPDB validaton report |
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Full document | 5n8d_full_validation.pdf.gz | 509.1 KB | Display | |
Data in XML | 5n8d_validation.xml.gz | 62.4 KB | Display | |
Data in CIF | 5n8d_validation.cif.gz | 93.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n8/5n8d ftp://data.pdbj.org/pub/pdb/validation_reports/n8/5n8d | HTTPS FTP |
-Related structure data
Related structure data | 5n83SC 5nbhC 5nc1C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 25810.922 Da / Num. of mol.: 6 / Fragment: UNP residues 587-787 Source method: isolated from a genetically manipulated source Details: GSSHHHHHHSSGLVPRGSHMASMTGGQQMGRGSEF was an expression and purification tag, invisible in the electron density. The N-terminal residues GALTAQGA of the protein also did not show density. Source: (gene. exp.) Murine adenovirus 2 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: E7CH51 #2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-CL / #4: 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: 2.61 Å3/Da / Density % sol: 52.88 % / Description: Plate |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 10 mM Tris-HCl, 4.0 M ammonium formate, 0.1 M HEPES-NaOH |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 1.0023 Å |
Detector | Type: Dectris / Detector: PIXEL / Date: Jan 31, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0023 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→29.66 Å / Num. obs: 144435 / % possible obs: 98.2 % / Redundancy: 2.8 % / Biso Wilson estimate: 16.5 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.078 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.334 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 7096 / CC1/2: 0.857 / % possible all: 97.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5N83 Resolution: 1.8→29.66 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.643 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.103 / ESU R Free: 0.102 / 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: 24.019 Å2
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Refinement step | Cycle: 1 / Resolution: 1.8→29.66 Å
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Refine LS restraints |
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