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Yorodumi- PDB-7ex7: Crystal structure of Ebinur Lake virus cap snatching endonuclease... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ex7 | |||||||||
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Title | Crystal structure of Ebinur Lake virus cap snatching endonuclease in complex with inhibitor 16 | |||||||||
Components | Replicase | |||||||||
Keywords | HYDROLASE / endonuclease | |||||||||
Function / homology | Function and homology information host cell endoplasmic reticulum / host cell endoplasmic reticulum-Golgi intermediate compartment / host cell Golgi apparatus / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / DNA-templated transcription / metal ion binding Similarity search - Function | |||||||||
Biological species | Abbey lake orthobunyavirus | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | |||||||||
Authors | Kuang, W. / Hu, Z. / Gong, P. | |||||||||
Funding support | China, 2items
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Citation | Journal: J.Virol. / Year: 2022 Title: Structural and Biochemical Basis for Development of Diketo Acid Inhibitors Targeting the Cap-Snatching Endonuclease of the Ebinur Lake Virus (Order: Bunyavirales ). Authors: Kuang, W. / Zhang, H. / Cai, Y. / Zhang, G. / Deng, F. / Li, H. / Zhou, Y. / Wang, M. / Gong, P. / Guo, Y. / Hu, Z. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ex7.cif.gz | 162.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ex7.ent.gz | 125.1 KB | Display | PDB format |
PDBx/mmJSON format | 7ex7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ex/7ex7 ftp://data.pdbj.org/pub/pdb/validation_reports/ex/7ex7 | HTTPS FTP |
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-Related structure data
Related structure data | 7ex2C 7ex3C 7ex4C 7ex6C 7ex8C 7ex9C 2xi5S 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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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 25181.875 Da / Num. of mol.: 4 / Fragment: N-terminal endonuclease domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Abbey lake orthobunyavirus / Strain: Cu20-XJ / Gene: RdRp / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0A059WLS9, RNA-directed RNA polymerase #2: Chemical | ChemComp-MN / #3: Chemical | ChemComp-1I6 / #4: Chemical | ChemComp-CL / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.07 Å3/Da / Density % sol: 40.46 % / Mosaicity: 0.443 ° |
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Crystal grow | Temperature: 289 K / Method: evaporation / pH: 4.9 / Details: PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 31, 2019 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.3→50 Å / Num. obs: 33393 / % possible obs: 89.2 % / Redundancy: 3.7 % / Biso Wilson estimate: 25.84 Å2 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.075 / Rrim(I) all: 0.152 / Χ2: 1.055 / Net I/σ(I): 5.8 / Num. measured all: 122217 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2XI5 Resolution: 2.3→44.94 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.01 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 74.73 Å2 / Biso mean: 32.8099 Å2 / Biso min: 12.89 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.3→44.94 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12
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