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- PDB-5bny: Crystal structure of hemagglutinin of A/Chicken/Guangdong/S1311/2... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5bny | |||||||||
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Title | Crystal structure of hemagglutinin of A/Chicken/Guangdong/S1311/2010 (H6N6) | |||||||||
![]() | (Hemagglutinin) x 2 | |||||||||
![]() | VIRAL PROTEIN / influenza / heamgglutinin | |||||||||
Function / homology | ![]() viral budding from plasma membrane / clathrin-dependent endocytosis of virus by 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. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural and Functional Studies of Influenza Virus A/H6 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 | ![]() | 314.3 KB | Display | ![]() |
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PDB format | ![]() | 255.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.8 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 56.3 KB | Display | |
Data in CIF | ![]() | 76.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5bqyC ![]() 5bqzC ![]() 5br0C ![]() 5br3C ![]() 5br6C ![]() 1ruzS S: Starting model for refinement C: citing same article ( |
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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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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Components
-Protein , 2 types, 6 molecules ACEBDF
#1: Protein | Mass: 36368.117 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: A/chicken/Guangdong/S1311/2010(H6N6) / Gene: HA / Production host: ![]() #2: Protein | Mass: 21945.318 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Sugars , 3 types, 13 molecules ![](data/chem/img/NAG.gif)
#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: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / triacetyl-beta-chitotriose | #5: Sugar | ChemComp-NAG / |
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-Non-polymers , 1 types, 324 molecules ![](data/chem/img/HOH.gif)
#6: Water | ChemComp-HOH / |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.86 % / Description: stick |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1 M Bis-Tris propane, 2.3 M (NH4)2SO4 |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Oct 24, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 2.66→49.69 Å / Num. obs: 53602 / % possible obs: 96.9 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.104 / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 2.66→2.8 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.487 / Mean I/σ(I) obs: 2.7 / Num. measured obs: 7114 / % possible all: 89.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1RUZ Resolution: 2.66→46.75 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.4 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 124.1 Å2 / Biso mean: 40.9847 Å2 / Biso min: 15.14 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.66→46.75 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19
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