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- PDB-4m40: Crystal structure of hemagglutinin of influenza virus B/Yamanashi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4m40 | |||||||||
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Title | Crystal structure of hemagglutinin of influenza virus B/Yamanashi/166/1998 | |||||||||
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![]() | VIRAL PROTEIN / receptor binding / fusion / sialic acid | |||||||||
Function / homology | ![]() viral budding from plasma membrane / endocytosis involved in viral entry into host cell / host cell surface receptor binding / apical plasma membrane / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Ni, F. / Kondrashkina, E. / Wang, Q. | |||||||||
![]() | ![]() Title: Structural basis for the divergent evolution of influenza B virus hemagglutinin. Authors: Ni, F. / Kondrashkina, E. / Wang, Q. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 300.2 KB | Display | ![]() |
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PDB format | ![]() | 250.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.1 MB | Display | ![]() |
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Full document | ![]() | 3.1 MB | Display | |
Data in XML | ![]() | 55.3 KB | Display | |
Data in CIF | ![]() | 73.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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: 37543.043 Da / Num. of mol.: 3 / Fragment: Hemagglutinin HA1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() #2: Protein | Mass: 19542.980 Da / Num. of mol.: 3 / Fragment: Hemagglutinin HA2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() #3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #4: Sugar | ChemComp-NAG / |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.2 Å3/Da / Density % sol: 61.59 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 23% PEG2000MME, 0.1 M Tris, 0.2 M TMNO, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 70 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Jun 6, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 3.54→43.6 Å / Num. all: 26547 / Num. obs: 26547 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 3.8 % / Biso Wilson estimate: 109.1 Å2 / Rmerge(I) obs: 0.098 |
Reflection shell | Resolution: 3.54→3.73 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.497 / Mean I/σ(I) obs: 2.3 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: 3.54→42.66 Å
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Refine LS restraints |
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LS refinement shell |
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