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- PDB-5b2d: Crystal structure of Mumps virus hemagglutinin-neuraminidase boun... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5b2d | |||||||||
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Title | Crystal structure of Mumps virus hemagglutinin-neuraminidase bound to 3-sialyllactose | |||||||||
![]() | HN protein | |||||||||
![]() | VIRAL PROTEIN / glycoprotein / beta-propeller / receptor binding / sugar | |||||||||
Function / homology | ![]() exo-alpha-sialidase activity / host cell surface receptor binding / symbiont entry into host cell / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Kubota, M. / Takeuchi, K. / Watanabe, S. / Ohno, S. / Matsuoka, R. / Kohda, D. / Hiramatsu, H. / Suzuki, Y. / Nakayama, T. / Terada, T. ...Kubota, M. / Takeuchi, K. / Watanabe, S. / Ohno, S. / Matsuoka, R. / Kohda, D. / Hiramatsu, H. / Suzuki, Y. / Nakayama, T. / Terada, T. / Shimizu, K. / Shimizu, N. / Yanagi, Y. / Hashiguchi, T. | |||||||||
![]() | ![]() Title: Trisaccharide containing alpha 2,3-linked sialic acid is a receptor for mumps virus Authors: Kubota, M. / Takeuchi, K. / Watanabe, S. / Ohno, S. / Matsuoka, R. / Kohda, D. / Nakakita, S.I. / Hiramatsu, H. / Suzuki, Y. / Nakayama, T. / Terada, T. / Shimizu, K. / Shimizu, N. / ...Authors: Kubota, M. / Takeuchi, K. / Watanabe, S. / Ohno, S. / Matsuoka, R. / Kohda, D. / Nakakita, S.I. / Hiramatsu, H. / Suzuki, Y. / Nakayama, T. / Terada, T. / Shimizu, K. / Shimizu, N. / Shiroishi, M. / Yanagi, Y. / Hashiguchi, T. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 198.9 KB | Display | ![]() |
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PDB format | ![]() | 156.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 36.3 KB | Display | |
Data in CIF | ![]() | 50.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5b2cC ![]() 1e8vS 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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Components
#1: Protein | Mass: 54267.961 Da / Num. of mol.: 2 / Fragment: UNP residues 106-582 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Polysaccharide | #3: Sugar | ChemComp-NAG / #4: Chemical | ChemComp-SO4 / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.42 Å3/Da / Density % sol: 72.15 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: sodium acetate, ammonium sulfate, glycerol, 3-sialyllactose |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 13, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.177→177.274 Å / Num. obs: 98249 / % possible obs: 100 % / Redundancy: 10 % / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 2.177→2.184 Å / Redundancy: 8.3 % / Rmerge(I) obs: 1.083 / Mean I/σ(I) obs: 2 / % possible all: 99.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1E8V Resolution: 2.177→118.537 Å / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.98 / Stereochemistry target values: TWIN_LSQ_F
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.177→118.537 Å
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Refine LS restraints |
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LS refinement shell |
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