+Open data
-Basic information
Entry | Database: PDB / ID: 3f5t | |||||||||
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Title | X-ray Structure of H5N1 NS1 | |||||||||
Components | Nonstructural protein 1 | |||||||||
Keywords | VIRAL PROTEIN / NS1 / H5N1 / Influenza / Host-virus interaction / Interferon antiviral system evasion / Nucleus / RNA-binding / Suppressor of RNA silencing | |||||||||
Function / homology | Function and homology information symbiont-mediated suppression of host mRNA processing / symbiont-mediated suppression of host PKR/eIFalpha signaling / protein serine/threonine kinase inhibitor activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / host cell cytoplasm / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / RNA binding / identical protein binding Similarity search - Function | |||||||||
Biological species | Influenza virus | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | |||||||||
Authors | Bornholdt, Z.A. / Prasad, B.V.V. | |||||||||
Citation | Journal: Nature / Year: 2008 Title: X-ray structure of NS1 from a highly pathogenic H5N1 influenza virus Authors: Bornholdt, Z.A. / Prasad, B.V.V. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3f5t.cif.gz | 48.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3f5t.ent.gz | 35 KB | Display | PDB format |
PDBx/mmJSON format | 3f5t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f5/3f5t ftp://data.pdbj.org/pub/pdb/validation_reports/f5/3f5t | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 24252.779 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Full length A/Vietnam/1203/2004(H5N1) sequence / Source: (natural) Influenza virus / Strain: A/Vietnam/1203/2004 / References: UniProt: A5A5U1 |
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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: 2.33 Å3/Da / Density % sol: 47.29 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID |
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Detector | Type: ADSC QUANTUM 210 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.7→35 Å / Num. all: 6721 / Num. obs: 6721 / Observed criterion σ(I): 0 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→35 Å / Cor.coef. Fo:Fc: 0.886 / Cor.coef. Fo:Fc free: 0.895 / Occupancy max: 1 / Occupancy min: 1 / SU B: 36.894 / SU ML: 0.338 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 2.284 / ESU R Free: 0.408 / 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 max: 68 Å2 / Biso mean: 50.422 Å2 / Biso min: 37.42 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.77 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -6.8464 Å / Origin y: 41.2618 Å / Origin z: -0.4336 Å
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Refinement TLS group |
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