[English] 日本語
Yorodumi- PDB-6sy8: Mopeia Virus Exonuclease domain fully depleted of Manganese un AL... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6sy8 | ||||||
---|---|---|---|---|---|---|---|
Title | Mopeia Virus Exonuclease domain fully depleted of Manganese un ALD compound | ||||||
Components | Nucleoprotein | ||||||
Keywords | METAL BINDING PROTEIN / 3-5 Exonuclease | ||||||
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 / RNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | Mopeia virus AN20410 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 Å | ||||||
Authors | Nguyen, T.H.V. / Ferron, F. | ||||||
Funding support | France, 1items
| ||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6sy8.cif.gz | 94.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6sy8.ent.gz | 71.7 KB | Display | PDB format |
PDBx/mmJSON format | 6sy8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sy/6sy8 ftp://data.pdbj.org/pub/pdb/validation_reports/sy/6sy8 | HTTPS FTP |
---|
-Related structure data
Related structure data | 6sx8SC 6t2aC 6t6lC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-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, N / Production host: Escherichia coli (E. coli) References: UniProt: Q5S581, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 51.86 % |
---|---|
Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M MES 25 % (M/W) PEG 8000) 3mM Mn |
-Data collection
Diffraction | Mean temperature: 93.15 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 25, 2018 Details: Kirkpatrick-Baez pair of bi-morph mirrors plus channel cut cryogenically cooled monochromator crystal | ||||||||||||||||||||||||||||||
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.08→137.17 Å / Num. obs: 28863 / % possible obs: 99.6 % / Redundancy: 5.3 % / Biso Wilson estimate: 37.23 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.058 / Rrim(I) all: 0.135 / Net I/σ(I): 10.6 / Num. measured all: 151996 / Scaling rejects: 2387 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6SX8 Resolution: 2.08→68.58 Å / Cor.coef. Fo:Fc: 0.859 / Cor.coef. Fo:Fc free: 0.856 / SU R Cruickshank DPI: 0.237 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.235 / SU Rfree Blow DPI: 0.196 / SU Rfree Cruickshank DPI: 0.199
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 128.17 Å2 / Biso mean: 53.84 Å2 / Biso min: 20.87 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.44 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.08→68.58 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.08→2.1 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
|