+Open data
-Basic information
Entry | Database: PDB / ID: 6sx8 | ||||||
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Title | Mopeia Virus Exonuclease domain complexed with Manganese | ||||||
Components | Nucleoprotein | ||||||
Keywords | METAL BINDING PROTEIN / 3-5 Exonuclease / complex | ||||||
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 | Mopeia virus AN20410 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å | ||||||
Authors | Nguyen, T.H.V. / Ferron, F. | ||||||
Funding support | France, 1items
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Citation | Journal: Iucrj / Year: 2022 Title: Inhibition of Arenaviridae nucleoprotein exonuclease by bisphosphonate Authors: Nguyen, T.H.V. / Yekwa, E. / Selisko, B. / Canard, B. / Alvarez, K. / Ferron, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6sx8.cif.gz | 98.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6sx8.ent.gz | 73.8 KB | Display | PDB format |
PDBx/mmJSON format | 6sx8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6sx8_validation.pdf.gz | 429.6 KB | Display | wwPDB validaton report |
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Full document | 6sx8_full_validation.pdf.gz | 433.1 KB | Display | |
Data in XML | 6sx8_validation.xml.gz | 18.4 KB | Display | |
Data in CIF | 6sx8_validation.cif.gz | 26.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sx/6sx8 ftp://data.pdbj.org/pub/pdb/validation_reports/sx/6sx8 | HTTPS FTP |
-Related structure data
Related structure data | 6sy8C 6t2aC 6t6lC 5ls4S 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: 23563.014 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mopeia virus AN20410 / Gene: NP / Production host: Escherichia coli (E. coli) References: UniProt: Q5S581, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | 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: 2.52 Å3/Da / Density % sol: 51.13 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MES, PEG 8000 manganese / PH range: 6.2-6.8 |
-Data collection
Diffraction | Mean temperature: 173 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 25, 2018 / Details: monochromator | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.79→68.52 Å / Num. obs: 44791 / % possible obs: 99.4 % / Redundancy: 3.7 % / Biso Wilson estimate: 29.19 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.041 / Rpim(I) all: 0.025 / Rrim(I) all: 0.048 / Net I/σ(I): 14 / Num. measured all: 163593 / Scaling rejects: 7 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5LS4 Resolution: 1.8→38.82 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 35.42
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 87.39 Å2 / Biso mean: 43.9773 Å2 / Biso min: 26.27 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.8→38.82 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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