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Yorodumi- PDB-2wgt: Structure of human adenovirus serotype 37 fibre head in complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wgt | |||||||||
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Title | Structure of human adenovirus serotype 37 fibre head in complex with a sialic acid derivative, O-Methyl 5-N-propaonyl-3,5-dideoxy-D- glycero-a-D-galacto-2-nonulopyranosylonic acid | |||||||||
Components | FIBER PROTEIN | |||||||||
Keywords | VIRAL PROTEIN / SIALIC ACID / CONJUNCTIVITIS / DAF / AD37 / CD46 / RECEPTOR / NEURAMINIC ACID | |||||||||
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 / metal ion binding Similarity search - Function | |||||||||
Biological species | HUMAN ADENOVIRUS 37 | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | |||||||||
Authors | Johansson, S. / Nilsson, E. / Qian, W. / Guilligay, D. / Crepin, T. / Cusack, S. / Arnberg, N. / Elofsson, M. | |||||||||
Citation | Journal: J.Med.Chem. / Year: 2009 Title: Design, Synthesis, and Evaluation of N-Acyl Modified Sialic Acids as Inhibitors of Adenoviruses Causing Epidemic Keratoconjunctivitis. Authors: Johansson, S. / Nilsson, E. / Qian, W. / Guilligay, D. / Crepin, T. / Cusack, S. / Arnberg, N. / Elofsson, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wgt.cif.gz | 136.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wgt.ent.gz | 107.1 KB | Display | PDB format |
PDBx/mmJSON format | 2wgt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2wgt_validation.pdf.gz | 872 KB | Display | wwPDB validaton report |
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Full document | 2wgt_full_validation.pdf.gz | 920.2 KB | Display | |
Data in XML | 2wgt_validation.xml.gz | 30.8 KB | Display | |
Data in CIF | 2wgt_validation.cif.gz | 45.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wg/2wgt ftp://data.pdbj.org/pub/pdb/validation_reports/wg/2wgt | HTTPS FTP |
-Related structure data
Related structure data | 2wguC 1uxaS 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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Unit cell |
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-Components
#1: Protein | Mass: 21716.535 Da / Num. of mol.: 3 / Fragment: FIBRE HEAD, RESIDUES 177-365 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HUMAN ADENOVIRUS 37 / Plasmid: PPROEX HTB / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21STAR(DE3) / References: UniProt: Q64823 #2: Sugar | #3: Chemical | #4: Water | ChemComp-HOH / | Nonpolymer details | ZINC ION (ZN): FROM CRYSTALLIZ | |
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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: 2.43 Å3/Da / Density % sol: 49 % / Description: NONE |
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Crystal grow | Details: 25-27 % POLYETHYLENE GLYCOL 8000, 50 MM ZINC ACETATE, AND 100 MM HEPES PH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Feb 16, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. obs: 58545 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 3.74 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 18.4 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 3.73 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.88 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1UXA Resolution: 1.8→30 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.774 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.129 / ESU R Free: 0.126 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.36 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→30 Å
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Refine LS restraints |
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