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Yorodumi- PDB-7fgd: A naturally-occurring neuraminidase-inhibitors-resistant NA from ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7fgd | ||||||
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Title | A naturally-occurring neuraminidase-inhibitors-resistant NA from asiatic toad influenza B-like virus | ||||||
Components | toad NA (OSE) | ||||||
Keywords | VIRAL PROTEIN / neuraminidase | ||||||
Function / homology | Chem-G39 Function and homology information | ||||||
Biological species | unidentified influenza virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Chai, Y. / Wu, Y. / Gao, F. | ||||||
Funding support | China, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2022 Title: Structural and inhibitor sensitivity analysis of influenza B-like viral neuraminidases derived from Asiatic toad and spiny eel. Authors: Li, L. / Chai, Y. / Peng, W. / Li, D. / Sun, L. / Gao, G.F. / Qi, J. / Xiao, H. / Liu, W.J. / von Itzstein, M. / Gao, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7fgd.cif.gz | 394.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7fgd.ent.gz | 264.9 KB | Display | PDB format |
PDBx/mmJSON format | 7fgd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7fgd_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 7fgd_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 7fgd_validation.xml.gz | 36.2 KB | Display | |
Data in CIF | 7fgd_validation.cif.gz | 54.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fg/7fgd ftp://data.pdbj.org/pub/pdb/validation_reports/fg/7fgd | HTTPS FTP |
-Related structure data
Related structure data | 7fgbC 7fgcC 7fgeC 7xvrC 7xvuC 7xvvC 7xvwC 1b9sS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: LEU / End label comp-ID: LEU / Auth seq-ID: 80 - 466 / Label seq-ID: 103 - 489
NCS oper: (Code: givenMatrix: (-0.000244111562515, -0.0075643481082, 0.999971360113), (-0.000186416839343, 0.999971372877, 0.00756430269694), (-0.999999952829, -0.000184564966635, -0.00024551469617) ...NCS oper: (Code: given Matrix: (-0.000244111562515, -0.0075643481082, 0.999971360113), Vector: |
-Components
#1: Protein | Mass: 53583.793 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) unidentified influenza virus / Production host: Baculovirus expression vector pFastBac1-HM #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.4 Å3/Da / Density % sol: 48.76 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.2 M lithium sulfate monohydrate, 0.1 M sodium citrate tribasic dihydrate pH 5.0, 26% v/v polyethylene 200 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 Å |
Detector | Type: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Sep 1, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 60226 / % possible obs: 99.9 % / Redundancy: 13.2 % / Biso Wilson estimate: 35.8 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.031 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 2.1→2.18 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 5980 / CC1/2: 0.772 / Rpim(I) all: 0.389 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1B9S Resolution: 2.1→18.35 Å / SU ML: 0.241 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.2531 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.07 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→18.35 Å
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Refine LS restraints |
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Refine LS restraints NCS | Type: Torsion NCS / Rms dev position: 0.408508224935 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 78.5181247455 Å / Origin y: 20.1939961068 Å / Origin z: 22.7059816648 Å
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Refinement TLS group | Selection details: all |