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Yorodumi- PDB-4b7m: H1N1 2009 Pandemic Influenza Virus: Resistance of the I223R Neura... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4b7m | |||||||||
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Title | H1N1 2009 Pandemic Influenza Virus: Resistance of the I223R Neuraminidase Mutant Explained by Kinetic and Structural Analysis | |||||||||
Components | NEURAMINIDASE | |||||||||
Keywords | HYDROLASE / ANTIVIRAL RESISTANCE / IMMUNOCOMPROMISED | |||||||||
Function / homology | Function and homology information exo-alpha-(2->3)-sialidase activity / exo-alpha-(2->6)-sialidase activity / exo-alpha-(2->8)-sialidase activity / exo-alpha-sialidase / viral budding from plasma membrane / carbohydrate metabolic process / host cell plasma membrane / virion membrane / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | INFLUENZA A VIRUS | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | |||||||||
Authors | van der Vries, E. / Vachieri, S.G. / Xiong, X. / Liu, J. / Collins, P.J. / Walker, P.A. / Haire, L.F. / Hay, A.J. / Schutten, M. / Osterhaus, A.D.M.E. ...van der Vries, E. / Vachieri, S.G. / Xiong, X. / Liu, J. / Collins, P.J. / Walker, P.A. / Haire, L.F. / Hay, A.J. / Schutten, M. / Osterhaus, A.D.M.E. / Martin, S.R. / Boucher, C.A.B. / Skehel, J.J. / Gamblin, S.J. | |||||||||
Citation | Journal: Plos Pathog. / Year: 2012 Title: H1N1 2009 Pandemic Influenza Virus: Resistance of the I223R Neuraminidase Mutant Explained by Kinetic and Structural Analysis Authors: Van Der Vries, E. / Collins, P.J. / Vachieri, S.G. / Xiong, X. / Liu, J. / Walker, P.A. / Haire, L.F. / Hay, A.J. / Schutten, M. / Osterhaus, A.D.M.E. / Martin, S.R. / Boucher, C.A.B. / ...Authors: Van Der Vries, E. / Collins, P.J. / Vachieri, S.G. / Xiong, X. / Liu, J. / Walker, P.A. / Haire, L.F. / Hay, A.J. / Schutten, M. / Osterhaus, A.D.M.E. / Martin, S.R. / Boucher, C.A.B. / Skehel, J.J. / Gamblin, S.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4b7m.cif.gz | 166.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4b7m.ent.gz | 130.6 KB | Display | PDB format |
PDBx/mmJSON format | 4b7m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b7/4b7m ftp://data.pdbj.org/pub/pdb/validation_reports/b7/4b7m | HTTPS FTP |
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-Related structure data
Related structure data | 4b7jC 4b7nC 4b7qC 4b7rC 3nssS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (2.0E-5, -0.00118, -1), Vector: |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 51698.707 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: APO STRUCTURE Source: (gene. exp.) INFLUENZA A VIRUS (A/NETHERLANDS/2631/2010(H1N1)) Description: PATIENT ISOLATE / Variant: H1N1 / Plasmid: PHW2000 / Production host: GALLUS GALLUS (chicken) / References: UniProt: F8UU09 |
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-Sugars , 2 types, 6 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Sugar | |
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-Non-polymers , 3 types, 247 molecules
#4: Chemical | ChemComp-PO4 / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.37 Å3/Da / Density % sol: 63.52 % / Description: NONE |
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Crystal grow | Details: 20% PEG 1000, 0.6 M AMMONIUM PHOSPHATE AND 0.1 M SODIUM ACETATE (PH 4.6) |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9173 |
Detector | Type: DECTRIS PILATUS / Detector: PIXEL / Date: Dec 3, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9173 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→30 Å / Num. obs: 37388 / % possible obs: 93.3 % / Observed criterion σ(I): 2 / Redundancy: 5.6 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 2.5→2.61 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 2.1 / % possible all: 92 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3NSS Resolution: 2.5→95.78 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.872 / SU B: 8.141 / SU ML: 0.184 / Cross valid method: THROUGHOUT / ESU R: 1.059 / ESU R Free: 0.324 / 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: 16.523 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→95.78 Å
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Refine LS restraints |
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