+Open data
-Basic information
Entry | Database: PDB / ID: 4opa | ||||||
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Title | X-ray structure of H6N6-NS1 delta(80-84) mutant | ||||||
Components | Nonstructural protein 1 | ||||||
Keywords | VIRAL PROTEIN / alpha-helix beta-crescent fold / interferon antagonist / phosphorylation / sumoylation / nucleus | ||||||
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 / virus-mediated perturbation of host defense response / host cell nucleus / RNA binding Similarity search - Function | ||||||
Biological species | Influenza A virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Carrillo, B. | ||||||
Citation | Journal: J.Virol. / Year: 2014 Title: The Influenza A Virus Protein NS1 Displays Structural Polymorphism. Authors: Carrillo, B. / Choi, J.M. / Bornholdt, Z.A. / Sankaran, B. / Rice, A.P. / Prasad, B.V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4opa.cif.gz | 87.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4opa.ent.gz | 66.4 KB | Display | PDB format |
PDBx/mmJSON format | 4opa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4opa_validation.pdf.gz | 445.5 KB | Display | wwPDB validaton report |
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Full document | 4opa_full_validation.pdf.gz | 455.9 KB | Display | |
Data in XML | 4opa_validation.xml.gz | 16.9 KB | Display | |
Data in CIF | 4opa_validation.cif.gz | 22.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/op/4opa ftp://data.pdbj.org/pub/pdb/validation_reports/op/4opa | HTTPS FTP |
-Related structure data
Related structure data | 4ophC 2gx9S 3f5tS 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: 25486.070 Da / Num. of mol.: 2 / Mutation: R38A, K41A, and missing residues 80-84 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus / Strain: A/blue-winged teal/MN/993/1980 / Gene: NS1 / Plasmid: pET46 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q20NS3 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.35 % |
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Crystal grow | Temperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 200 mM potassium thiocyanate, 20% PEG3350, 100 mM HEPES, pH 7.0, a 10 mM stock of GSH/GSSG (Hampton Additive Screen) was used as additive, VAPOR DIFFUSION, HANGING DROP, temperature 295.15K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 11, 2012 / Details: mirrors |
Radiation | Monochromator: Asymmetric curved crystal Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→60.42 Å / Num. all: 14850 / Num. obs: 14455 / % possible obs: 97.29 % / Redundancy: 4 % / Biso Wilson estimate: 72.231 Å2 / Rmerge(I) obs: 0.096 |
Reflection shell | Highest resolution: 2.7 Å / Redundancy: 4 % / Rmerge(I) obs: 0.706 / Mean I/σ(I) obs: 1.8 / % possible all: 96.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 2GX9 AND 3F5T Resolution: 2.7→60.42 Å / SU ML: 0.69 / σ(F): 0 / Phase error: 25.75 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.796 Å2 / ksol: 0.338 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.7→60.42 Å
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Refine LS restraints |
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LS refinement shell |
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