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Yorodumi- PDB-6eks: Vibrio cholerae neuraminidase complexed with oseltamivir carboxylate -
+Open data
-Basic information
Entry | Database: PDB / ID: 6eks | ||||||
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Title | Vibrio cholerae neuraminidase complexed with oseltamivir carboxylate | ||||||
Components | SialidaseNeuraminidase | ||||||
Keywords | HYDROLASE / sialidase / bacterial protein / infection | ||||||
Function / homology | Function and homology information ganglioside catabolic process / sialic acid binding / oligosaccharide catabolic process / exo-alpha-sialidase activity / exo-alpha-(2->3)-sialidase activity / exo-alpha-(2->6)-sialidase activity / exo-alpha-(2->8)-sialidase activity / exo-alpha-sialidase / intracellular membrane-bounded organelle / extracellular region ...ganglioside catabolic process / sialic acid binding / oligosaccharide catabolic process / exo-alpha-sialidase activity / exo-alpha-(2->3)-sialidase activity / exo-alpha-(2->6)-sialidase activity / exo-alpha-(2->8)-sialidase activity / exo-alpha-sialidase / intracellular membrane-bounded organelle / extracellular region / membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Vibrio cholerae serotype O1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å | ||||||
Authors | Schuetz, A. / Heinemann, U. | ||||||
Citation | Journal: Molecules / Year: 2017 Title: Different Inhibitory Potencies of Oseltamivir Carboxylate, Zanamivir, and Several Tannins on Bacterial and Viral Neuraminidases as Assessed in a Cell-Free Fluorescence-Based Enzyme Inhibition Assay. Authors: Quosdorf, S. / Schuetz, A. / Kolodziej, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6eks.cif.gz | 320.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6eks.ent.gz | 254.7 KB | Display | PDB format |
PDBx/mmJSON format | 6eks.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ek/6eks ftp://data.pdbj.org/pub/pdb/validation_reports/ek/6eks | HTTPS FTP |
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-Related structure data
Related structure data | 6ekuC 1kitS S: Starting model for refinement C: citing same article (ref.) |
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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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-Components
#1: Protein | Mass: 83039.477 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae serotype O1 (bacteria) / Strain: ATCC 39315 / El Tor Inaba N16961 / Gene: nanH, VC_1784 / Production host: Escherichia coli (E. coli) / References: UniProt: P0C6E9, exo-alpha-sialidase | ||||||
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#2: Chemical | ChemComp-CA / #3: Chemical | #4: Chemical | ChemComp-G39 / ( | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 55.27 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% (w/v) PEG 3350, 0.2 M lithium acetate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 30, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918409 Å / Relative weight: 1 |
Reflection | Resolution: 1.87→44.33 Å / Num. obs: 75805 / % possible obs: 99.2 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.1012 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 1.87→1.94 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.4956 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 7401 / % possible all: 97.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1KIT Resolution: 1.87→44.33 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.44
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.87→44.33 Å
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Refine LS restraints |
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LS refinement shell |
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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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