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- PDB-6nsg: Crystal structure of the A/Brisbane/10/2007 (H3N2) influenza viru... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6nsg | |||||||||
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Title | Crystal structure of the A/Brisbane/10/2007 (H3N2) influenza virus hemagglutinin G186V/L194P mutant in complex with 6'-SLNLN | |||||||||
![]() | (Hemagglutinin ...![]() | |||||||||
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Function / homology | ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Wu, N.C. / Wilson, I.A. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. Authors: Wu, N.C. / Lv, H. / Thompson, A.J. / Wu, D.C. / Ng, W.W.S. / Kadam, R.U. / Lin, C.W. / Nycholat, C.M. / McBride, R. / Liang, W. / Paulson, J.C. / Mok, C.K.P. / Wilson, I.A. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 222.3 KB | Display | ![]() |
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PDB format | ![]() | 176.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6ns9C ![]() 6nsaC ![]() 6nsbC ![]() 6nscC ![]() 6nsfC ![]() 6aoqS 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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1 | ![]()
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Unit cell |
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Components
-Hemagglutinin ... , 2 types, 2 molecules AB
#1: Protein | Mass: 35763.336 Da / Num. of mol.: 1 / Fragment: residues 27-345 / Mutation: L194P Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 20109.355 Da / Num. of mol.: 1 / Fragment: residues 330-505 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
-Sugars , 5 types, 8 molecules ![](data/chem/img/NAG.gif)
![](data/chem/img/SIA.gif)
![](data/chem/img/SIA.gif)
#3: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose![]() Source method: isolated from a genetically manipulated source | ||||
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#4: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose![]() Source method: isolated from a genetically manipulated source | ||||
#5: Polysaccharide | ![]() Source method: isolated from a genetically manipulated source #6: Sugar | ![]() #7: Sugar | ChemComp-SIA / | ![]() |
-Non-polymers , 1 types, 172 molecules ![](data/chem/img/HOH.gif)
#8: Water | ChemComp-HOH / ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.32 Å3/Da / Density % sol: 62.96 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M CAPS pH 10.5 and 29% PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 20, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.4→50 Å / Num. obs: 29754 / % possible obs: 100 % / Redundancy: 19.4 % / Biso Wilson estimate: 41 Å2 / CC1/2: 1 / Rpim(I) all: 0.02 / Rsym value: 0.1 / Net I/σ(I): 25.5 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 19.4 % / Mean I/σ(I) obs: 2.7 / Num. unique obs: 2921 / CC1/2: 0.92 / Rpim(I) all: 0.21 / Rsym value: 0.92 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 6AOQ Resolution: 2.4→50 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.922 / SU B: 13.994 / SU ML: 0.164 / Cross valid method: THROUGHOUT / ESU R: 0.285 / ESU R Free: 0.22 / 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: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 71.072 Å2
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Refinement step | Cycle: 1 / Resolution: 2.4→50 Å
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Refine LS restraints |
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