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Yorodumi- PDB-3k39: Crystal Structure of B/Perth Neuraminidase D197E mutant in comple... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3k39 | ||||||
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Title | Crystal Structure of B/Perth Neuraminidase D197E mutant in complex with Peramivir | ||||||
Components | Neuraminidase | ||||||
Keywords | HYDROLASE / INFLUENZA / NEURAMINIDASE / MUTATION / RESISTANCE / BIOCRYST / Peramivir / RWJ-270201 / BCX-1812 / 229614-55-5 / 229615-12-7 / 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: 2.54 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 | 3k39.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb3k39.ent.gz | 978 KB | Display | PDB format |
PDBx/mmJSON format | 3k39.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k3/3k39 ftp://data.pdbj.org/pub/pdb/validation_reports/k3/3k39 | HTTPS FTP |
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-Related structure data
Related structure data | 3k36C 3k37C 3k38SC 3k3aC 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: LEU / End label comp-ID: LEU / Refine code: 4 / Auth seq-ID: 78 - 466 / Label seq-ID: 9 - 397
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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, 964 molecules
#3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-BCZ / #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: 2.49 Å3/Da / Density % sol: 50.69 % |
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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: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95665 Å | ||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 17, 2008 / Details: BEAMLINE OPTICS | ||||||||||||||||||||
Radiation | Monochromator: BEAMLINE OPTICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||
Radiation wavelength | Wavelength: 0.95665 Å / Relative weight: 1 | ||||||||||||||||||||
Reflection twin |
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Reflection | Resolution: 2.3→62.58 Å / Num. all: 286795 / Num. obs: 286795 / % possible obs: 95.2 % / Observed criterion σ(F): -1 / Observed criterion σ(I): -1 / Redundancy: 3.4 % / Biso Wilson estimate: 20.47 Å2 / Rmerge(I) obs: 0.209 / Net I/σ(I): 4.7 | ||||||||||||||||||||
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.557 / Mean I/σ(I) obs: 2 / Num. unique all: 39780 / % possible all: 90.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3K38 Resolution: 2.54→55.9 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.883 / SU B: 8.877 / SU ML: 0.189 / Cross valid method: THROUGHOUT / ESU R Free: 0.062 / 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: 22.374 Å2
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Refinement step | Cycle: LAST / Resolution: 2.54→55.9 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Ens-ID: 1 / Number: 3112 / Refine-ID: X-RAY DIFFRACTION
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