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- PDB-4qnp: Crystal structure of the 2009 pandemic H1N1 influenza virus neura... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4qnp | |||||||||
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Title | Crystal structure of the 2009 pandemic H1N1 influenza virus neuraminidase with a neutralizing antibody | |||||||||
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![]() | HYDROLASE/IMMUNE SYSTEM / influenza / neuraminidase / antibody / neutralizing antibody / HYDROLASE-IMMUNE SYSTEM complex | |||||||||
Function / homology | ![]() exo-alpha-(2->3)-sialidase activity / exo-alpha-(2->6)-sialidase activity / exo-alpha-(2->8)-sialidase activity / exo-alpha-sialidase / B cell differentiation / viral budding from plasma membrane / membrane => GO:0016020 / carbohydrate metabolic process / host cell plasma membrane / virion membrane ...exo-alpha-(2->3)-sialidase activity / exo-alpha-(2->6)-sialidase activity / exo-alpha-(2->8)-sialidase activity / exo-alpha-sialidase / B cell differentiation / viral budding from plasma membrane / membrane => GO:0016020 / carbohydrate metabolic process / host cell plasma membrane / virion membrane / extracellular region / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Wan, H.Q. / Yang, H. / Shore, D.A. / Garten, R.J. / Couzens, L. / Gao, J. / Jiang, L.L. / Carney, P.J. / Villanueva, J. / Stevens, J. / Eichelberger, M.C. | |||||||||
![]() | ![]() Title: Structural characterization of a protective epitope spanning A(H1N1)pdm09 influenza virus neuraminidase monomers. Authors: Wan, H. / Yang, H. / Shore, D.A. / Garten, R.J. / Couzens, L. / Gao, J. / Jiang, L. / Carney, P.J. / Villanueva, J. / Stevens, J. / Eichelberger, M.C. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 633.2 KB | Display | ![]() |
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PDB format | ![]() | 523 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 57.2 KB | Display | |
Data in CIF | ![]() | 80.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4b7mS 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Refine code: _
NCS ensembles :
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 42483.363 Da / Num. of mol.: 2 / Fragment: UNP residues 82-467 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: S5N0T0, UniProt: D5KL82*PLUS, exo-alpha-sialidase |
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-Antibody , 2 types, 4 molecules FLEH
#2: Antibody | Mass: 23269.615 Da / Num. of mol.: 2 / Fragment: Fab Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #3: Antibody | Mass: 24262.281 Da / Num. of mol.: 2 / Fragment: Fab Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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-Sugars , 2 types, 6 molecules ![](data/chem/img/NAG.gif)
#4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Sugar | ChemComp-NAG / |
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-Non-polymers , 2 types, 185 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#6: Chemical | ChemComp-CA / #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.93 Å3/Da / Density % sol: 57.98 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.09 M malonic acid, 0.013 M ammonium citrate tribasic, 0.006 M succinic acid, 0.015 M DL-malic acid, 0.02 M sodium acetate, 0.025 M sodium formate, 0.008 M ammonium tartrate dibasic, 0.1 M ...Details: 0.09 M malonic acid, 0.013 M ammonium citrate tribasic, 0.006 M succinic acid, 0.015 M DL-malic acid, 0.02 M sodium acetate, 0.025 M sodium formate, 0.008 M ammonium tartrate dibasic, 0.1 M HEPES/NaOH, 10% w/v PEG8000, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 15, 2012 |
Radiation | Monochromator: Rosenbaum-Rock double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→47.853 Å / Num. all: 52272 / Num. obs: 48574 / % possible obs: 99.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 2.8→2.87 Å / % possible all: 99.1 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4B7M Resolution: 2.8→47.85 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.912 / SU B: 26.084 / SU ML: 0.243 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.346 / 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: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.269 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→47.85 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
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LS refinement shell | Resolution: 2.8→2.872 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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