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Yorodumi- PDB-3p38: Crystal structure of the NS1 effector domain W182A mutant from in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3p38 | ||||||
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Title | Crystal structure of the NS1 effector domain W182A mutant from influenza A/Vietnam/1203/2004 (H5N1) virus | ||||||
Components | Nonstructural protein 1 | ||||||
Keywords | VIRAL PROTEIN | ||||||
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: 2.76 Å | ||||||
Authors | Chen, S. / Xiao, Y.B. / Bricogne, G. / Sharff, A.J. / Hilgenfeld, R. | ||||||
Citation | Journal: To be Published Title: X-ray structures of the NS1 effector domain from highly pathogenic influenza A/Vietnam/1203/2004 (H5N1) virus Authors: Chen, S. / Xiao, Y.B. / Bricogne, G. / Sharff, A.J. / Hilgenfeld, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3p38.cif.gz | 161.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3p38.ent.gz | 129.8 KB | Display | PDB format |
PDBx/mmJSON format | 3p38.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3p38_validation.pdf.gz | 443.1 KB | Display | wwPDB validaton report |
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Full document | 3p38_full_validation.pdf.gz | 448.9 KB | Display | |
Data in XML | 3p38_validation.xml.gz | 16.6 KB | Display | |
Data in CIF | 3p38_validation.cif.gz | 22.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p3/3p38 ftp://data.pdbj.org/pub/pdb/validation_reports/p3/3p38 | HTTPS FTP |
-Related structure data
Related structure data | 3p31SC 3p39C 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 16346.924 Da / Num. of mol.: 3 / Fragment: C-terminal effector domain, UNP residues 73-215 / Mutation: W182A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus / Strain: A/environment/Viet Nam/1203/2004(H5N1) / Gene: NS1 / Production host: Escherichia coli (E. coli) / References: UniProt: D1LP63 #2: 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: 2.96 Å3/Da / Density % sol: 58.38 % |
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Crystal grow | Temperature: 285 K / pH: 8.4 Details: 0.1M Bicine, 1.8 M MgCl2, pH 8.4, VAPOR DIFFUSION, SITTING DROP, temperature 285K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Feb 19, 2010 |
Radiation | Monochromator: SI 111 CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 2.76→25.4 Å / Num. obs: 15754 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 68.92 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 19.7 |
Reflection shell | Resolution: 2.76→2.95 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.365 / Mean I/σ(I) obs: 2.6 / % possible all: 42.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3P31 Resolution: 2.76→25.27 Å / Cor.coef. Fo:Fc: 0.895 / Cor.coef. Fo:Fc free: 0.8543 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 67.58 Å2
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Refine analyze | Luzzati coordinate error obs: 0.531 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.76→25.27 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.76→2.95 Å / Total num. of bins used: 8
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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