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Yorodumi- PDB-8cnl: Lymphocytic choriomeningitis virus 3'-5' exonuclease domain of nu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8cnl | |||||||||
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Title | Lymphocytic choriomeningitis virus 3'-5' exonuclease domain of nucleoprotein | |||||||||
Components | Nucleoprotein | |||||||||
Keywords | VIRAL PROTEIN / exonuclease / arenavirus / LCMV | |||||||||
Function / homology | Function and homology information symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IKBKE activity / RNA-templated viral transcription / negative stranded viral RNA replication / helical viral capsid / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / viral nucleocapsid / host cell cytoplasm / hydrolase activity / ribonucleoprotein complex / virus-mediated perturbation of host defense response ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IKBKE activity / RNA-templated viral transcription / negative stranded viral RNA replication / helical viral capsid / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / viral nucleocapsid / host cell cytoplasm / hydrolase activity / ribonucleoprotein complex / virus-mediated perturbation of host defense response / RNA binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Arenavirus | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | |||||||||
Authors | Spiliopoulou, M. / Papageorgiou, N. / Ferron, F. | |||||||||
Funding support | Greece, European Union, 2items
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Citation | Journal: To Be Published Title: Lymphocytic choriomeningitis virus 3'-5' exonuclease domain of nucleoprotein Authors: Spiliopoulou, M. / Papageorgiou, N. / Ferron, F. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8cnl.cif.gz | 323 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8cnl.ent.gz | 263.7 KB | Display | PDB format |
PDBx/mmJSON format | 8cnl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8cnl_validation.pdf.gz | 481.6 KB | Display | wwPDB validaton report |
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Full document | 8cnl_full_validation.pdf.gz | 545.3 KB | Display | |
Data in XML | 8cnl_validation.xml.gz | 70.1 KB | Display | |
Data in CIF | 8cnl_validation.cif.gz | 82.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cn/8cnl ftp://data.pdbj.org/pub/pdb/validation_reports/cn/8cnl | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 24521.111 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arenavirus / Gene: N, Segment S / Production host: Escherichia phage T7 (virus) References: UniProt: P09992, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters #2: Chemical | ChemComp-ZN / Has ligand of interest | N | |
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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: 2.95 Å3/Da / Density % sol: 58.29 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.8 Details: 0.05M Sodium cacodylate pH 6.8, 0.01M Magnesium sulfate, 2M Ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97626 Å | |||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 3, 2022 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.97626 Å / Relative weight: 1 | |||||||||||||||
Reflection | Resolution: 2.8→94.254 Å / Num. obs: 310351 / % possible obs: 99.9 % / Redundancy: 6.5 % / CC1/2: 0.996 / Net I/σ(I): 10.2 | |||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→81.15 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.62 / 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: 2.8→81.15 Å
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Refine LS restraints |
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LS refinement shell |
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