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Yorodumi- PDB-3k3a: Crystal Structure of B/Perth Neuraminidase D197E mutant in comple... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3k3a | ||||||
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Title | Crystal Structure of B/Perth Neuraminidase D197E mutant in complex with Oseltamivir | ||||||
Components | Neuraminidase | ||||||
Keywords | HYDROLASE / INFLUENZA / NEURAMINIDASE / MUTATION / RESISTANCE / TAMIFLU / Oseltamivir / GS-4071 / 196618-13-0 / Cell membrane / Glycosidase / Membrane / Transmembrane / Virion | ||||||
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 / carbohydrate metabolic process / host cell plasma membrane / virion membrane / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Influenza B virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å | ||||||
Authors | Oakley, A.J. / McKimm-Breschkin, J.L. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2010 Title: Structural and Functional Basis of Resistance to Neuraminidase Inhibitors of Influenza B Viruses. Authors: Oakley, A.J. / Barrett, S. / Peat, T.S. / Newman, J. / Streltsov, V.A. / Waddington, L. / Saito, T. / Tashiro, M. / McKimm-Breschkin, J.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3k3a.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb3k3a.ent.gz | 956.1 KB | Display | PDB format |
PDBx/mmJSON format | 3k3a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k3/3k3a ftp://data.pdbj.org/pub/pdb/validation_reports/k3/3k3a | HTTPS FTP |
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-Related structure data
Related structure data | 3k36C 3k37C 3k38SC 3k39C 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: 1 / Auth seq-ID: 78 - 262 / Label seq-ID: 9 - 193
NCS ensembles :
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-Components
-Protein / Sugars , 2 types, 32 molecules ABCDEFGHIJKLMNOP
#1: Protein | Mass: 43838.863 Da / Num. of mol.: 16 / Fragment: UNP residues 70-466 / Mutation: D197E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza B virus / Strain: B/Perth/211/2001 / Plasmid: pFastBac / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf21 / References: UniProt: Q3S340, exo-alpha-sialidase #2: Sugar | ChemComp-NAG / |
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-Non-polymers , 4 types, 671 molecules
#3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-G39 / ( #5: Chemical | ChemComp-YT3 / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.73 % |
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Crystal grow | Temperature: 281.15 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 12-17% w/v PEG 3350, 0.2-0.3M Na2 SO4, 5mM YCl3, VAPOR DIFFUSION, HANGING DROP, temperature 281.15K, PH7 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å | ||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 29, 2008 / Details: BEAMLINE OPTICS | ||||||||||||||||||||||||||||||
Radiation | Monochromator: BEAMLINE OPTICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection twin |
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Reflection | Resolution: 2.25→50 Å / Num. all: 289650 / Num. obs: 289650 / % possible obs: 91.8 % / Observed criterion σ(F): -1 / Observed criterion σ(I): -1 / Redundancy: 2 % / Biso Wilson estimate: 29.746 Å2 / Rmerge(I) obs: 0.142 / Net I/σ(I): 7 | ||||||||||||||||||||||||||||||
Reflection shell | Resolution: 2.25→2.37 Å / Redundancy: 2 % / Rmerge(I) obs: 0.688 / Mean I/σ(I) obs: 1 / Num. unique all: 29350 / % possible all: 63.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3K38 Resolution: 2.59→49.69 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.902 / SU B: 9.53 / SU ML: 0.197 / Cross valid method: THROUGHOUT / ESU R Free: 0.066 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.491 Å2
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Refinement step | Cycle: LAST / Resolution: 2.59→49.69 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Ens-ID: 1 / Number: 3053 / Refine-ID: X-RAY DIFFRACTION
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