+Open data
-Basic information
Entry | Database: PDB / ID: 2wbv | |||||||||
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Title | Canine adenovirus 2 fibre head in complex with sialic acid | |||||||||
Components | FIBER PROTEINFibrous protein | |||||||||
Keywords | STRUCTURAL PROTEIN / KNOB / HEAD / FIBER / VIRUS / FIBRE / ADENOVIRUS / HEMAGGLUTINATION / RED BLOOD CELL / SIALYL-LACTOSE / CELL ATTACHMENT / ERYTHROCYTE / SIALIC ACID / FIBER PROTEIN | |||||||||
Function / homology | Function and homology information 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 | CANINE ADENOVIRUS 2 | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | |||||||||
Authors | Seiradake, E. / Henaff, D. / Wodrich, H. / Billet, O. / Perreau, M. / Hippert, C. / Mennechet, F. / Schoehn, G. / Lortat-Jacob, H. / Dreja, H. ...Seiradake, E. / Henaff, D. / Wodrich, H. / Billet, O. / Perreau, M. / Hippert, C. / Mennechet, F. / Schoehn, G. / Lortat-Jacob, H. / Dreja, H. / Ibanes, S. / Kalatzis, V. / Wang, J.P. / Finberg, R.W. / Cusack, S. / Kremer, E.J. | |||||||||
Citation | Journal: Plos Pathog. / Year: 2009 Title: The Cell Adhesion Molecule "Car" and Sialic Acid on Human Erythrocytes Influence Adenovirus in Vivo Biodistribution. Authors: Seiradake, E. / Henaff, D. / Wodrich, H. / Billet, O. / Perreau, M. / Hippert, C. / Mennechet, F. / Schoehn, G. / Lortat-Jacob, H. / Dreja, H. / Ibanes, S. / Kalatzis, V. / Wang, J.P. / ...Authors: Seiradake, E. / Henaff, D. / Wodrich, H. / Billet, O. / Perreau, M. / Hippert, C. / Mennechet, F. / Schoehn, G. / Lortat-Jacob, H. / Dreja, H. / Ibanes, S. / Kalatzis, V. / Wang, J.P. / Finberg, R.W. / Cusack, S. / Kremer, E.J. | |||||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wbv.cif.gz | 247 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wbv.ent.gz | 200.1 KB | Display | PDB format |
PDBx/mmJSON format | 2wbv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wb/2wbv ftp://data.pdbj.org/pub/pdb/validation_reports/wb/2wbv | HTTPS FTP |
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-Related structure data
Related structure data | 2w9lC 2wbwC 2j2jS C: citing same article (ref.) S: Starting model for refinement |
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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: 20626.408 Da / Num. of mol.: 6 / Fragment: FIBRE HEAD, RESIDUES 358-542 Source method: isolated from a genetically manipulated source Source: (gene. exp.) CANINE ADENOVIRUS 2 / Plasmid: PPROEX HTB / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 STAR / References: UniProt: Q65914 #2: Polysaccharide | N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose | Source method: isolated from a genetically manipulated source #3: Chemical | ChemComp-GOL / #4: Sugar | ChemComp-SIA / #5: 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: 2.54 Å3/Da / Density % sol: 51.18 % / Description: NONE |
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Crystal grow | Details: 5% PEG 4000, 5% ISOPROPANOL, 0.1 M HEPES PH 7.4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97626 |
Detector | Type: ADSC QUANTUM / Detector: CCD / Date: Sep 20, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97626 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→46.1 Å / Num. obs: 109731 / % possible obs: 99.4 % / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 10.22 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 4.06 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2J2J Resolution: 1.9→46.13 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.929 / SU B: 2.481 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THERE IS 6-FOLD NCS WHICH CAN BE DETECTED USING REGULAR CRYSTALLOGRAPHIC SOFTWARE.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 9.16 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→46.13 Å
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Refine LS restraints |
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