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Yorodumi- PDB-4n5b: Crystal structure of the Nipah virus phosphoprotein tetramerizati... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4n5b | ||||||
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Title | Crystal structure of the Nipah virus phosphoprotein tetramerization domain | ||||||
Components | Phosphoprotein | ||||||
Keywords | VIRAL PROTEIN / Viral Polymerase Co-Factor / Nucleoprotein Chaperone / Interferon Inhibitor | ||||||
Function / homology | Function and homology information Phosphoprotein P region PNT disordered / Phosphoprotein P region PNT disordered / Paramyxovirus structural protein P/V, N-terminal domain / Paramyxovirus structural protein V/P N-terminus / Phosphoprotein P soyouz module / N-terminal region of Paramyxovirinae phosphoprotein (P) / P/V phosphoprotein, paramyxoviral / Paramyxovirus P/V phosphoprotein C-terminal Similarity search - Domain/homology | ||||||
Biological species | Nipah virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 2.2 Å | ||||||
Authors | Bruhn, J.F. / Barnett, K. / Bibby, J. / Thomas, J. / Keegan, R. / Rigden, D. / Bornholdt, Z.A. / Saphire, E.O. | ||||||
Citation | Journal: J.Virol. / Year: 2014 Title: Crystal structure of the nipah virus phosphoprotein tetramerization domain. Authors: Bruhn, J.F. / Barnett, K.C. / Bibby, J. / Thomas, J.M. / Keegan, R.M. / Rigden, D.J. / Bornholdt, Z.A. / Saphire, E.O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4n5b.cif.gz | 192.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4n5b.ent.gz | 153.9 KB | Display | PDB format |
PDBx/mmJSON format | 4n5b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n5/4n5b ftp://data.pdbj.org/pub/pdb/validation_reports/n5/4n5b | HTTPS FTP |
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-Related structure data
Related structure data | 4eijS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Details | Chains A, B, C and D / Chains E, F, G and H |
-Components
#1: Protein | Mass: 12622.337 Da / Num. of mol.: 8 / Fragment: Tetramerization Domain residues 470-578 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nipah virus / Strain: Ind-Nipah-07-FG / Gene: P/V/W/C / Plasmid: pET46 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 / References: UniProt: D2DEB8 #2: Chemical | ChemComp-IMD / #3: 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: 2.67 Å3/Da / Density % sol: 53.93 % |
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Crystal grow | Temperature: 295.5 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.1M imidazole pH 7.0, 25% PEG MME 550, 15% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 100K, temperature 295.5K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 9, 2013 |
Radiation | Monochromator: Double-crystal, Si(111) liquid N2 cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→46.37 Å / Num. obs: 51813 / % possible obs: 97.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.063 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 3.85 % / Rmerge(I) obs: 0.298 / Mean I/σ(I) obs: 3 / % possible all: 97.2 |
-Processing
Software |
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Refinement | Method to determine structure: AB INITIO PHASING Starting model: PDB ENTRY 4EIJ Resolution: 2.2→46.369 Å / SU ML: 0.23 / σ(F): 1.97 / Phase error: 27.07 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→46.369 Å
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Refine LS restraints |
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LS refinement shell |
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