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Yorodumi- PDB-6eb8: Crystal Structure of the Nipah Virus Phosphoprotein Multimerizati... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6eb8 | |||||||||||||||||||||
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Title | Crystal Structure of the Nipah Virus Phosphoprotein Multimerization Domain G519N | |||||||||||||||||||||
Components | Phosphoprotein | |||||||||||||||||||||
Keywords | VIRAL PROTEIN / Phosphoprotein / RNA-dependent RNA polymerase / coiled coil / oligomerization | |||||||||||||||||||||
Function / homology | Function and homology information negative stranded viral RNA transcription / negative stranded viral RNA replication / virion component / host cell cytoplasm / molecular adaptor activity / virus-mediated perturbation of host defense response Similarity search - Function | |||||||||||||||||||||
Biological species | Nipah virus | |||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | |||||||||||||||||||||
Authors | Bruhn, J.F. / Saphire, E.O. | |||||||||||||||||||||
Funding support | United States, 6items
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Citation | Journal: Structure / Year: 2019 Title: A Conserved Basic Patch and Central Kink in the Nipah Virus Phosphoprotein Multimerization Domain Are Essential for Polymerase Function. Authors: Bruhn, J.F. / Hotard, A.L. / Spiropoulou, C.F. / Lo, M.K. / 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 | 6eb8.cif.gz | 171.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6eb8.ent.gz | 137.1 KB | Display | PDB format |
PDBx/mmJSON format | 6eb8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eb/6eb8 ftp://data.pdbj.org/pub/pdb/validation_reports/eb/6eb8 | HTTPS FTP |
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-Related structure data
Related structure data | 6eb9C 4n5bS 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: 12679.389 Da / Num. of mol.: 8 / Mutation: G519N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nipah virus / Gene: P/V/C / Plasmid: pET46 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9IK91 #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: 2.85 Å3/Da / Density % sol: 56.79 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Protein at 12 mg/ml in 300mM NaCl and 10 mM Tris pH 8 mixed 1:1 with 10% (v/v) Glycerol, 5% (w/v) PEG 3000, 30% (v/v) PEG 400 and 0.1 M HEPES pH 7.5 Temp details: Room Temperature |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 18, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→38.204 Å / Num. obs: 35317 / % possible obs: 98.6 % / Redundancy: 3.7 % / Biso Wilson estimate: 36.26 Å2 / CC1/2: 0.97 / Rmerge(I) obs: 0.31 / Rpim(I) all: 0.21 / Net I/σ(I): 4.1 |
Reflection shell | Resolution: 2.5→2.6 Å / Redundancy: 3.8 % / Rmerge(I) obs: 2.01 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 3976 / CC1/2: 0.1 / Rpim(I) all: 1.49 / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4N5B Resolution: 2.5→38.204 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 40.35 / 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: 2.5→38.204 Å
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Refine LS restraints |
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LS refinement shell |
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