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Yorodumi- PDB-7ex1: Crystal structure of Ebinur Lake virus cap snatching endonuclease... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ex1 | |||||||||
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Title | Crystal structure of Ebinur Lake virus cap snatching endonuclease (Y109A mutant) | |||||||||
Components | ReplicaseRNA-dependent RNA polymerase | |||||||||
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: Insights into Two-Metal-Ion Catalytic Mechanism of Cap-Snatching Endonuclease of Ebinur Lake Virus in Bunyavirales. Authors: Kuang, W. / Zhang, H. / Cai, Y. / Zhang, G. / Deng, F. / Li, H. / Hu, Z. / Guo, Y. / Wang, M. / Zhou, Y. / Gong, P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ex1.cif.gz | 83.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ex1.ent.gz | 59.3 KB | Display | PDB format |
PDBx/mmJSON format | 7ex1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ex/7ex1 ftp://data.pdbj.org/pub/pdb/validation_reports/ex/7ex1 | HTTPS FTP |
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-Related structure data
Related structure data | 7ewuC 7ewvC 7ewwC 7ewxC 7ewyC 7ewzC 7ex0C 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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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 25089.779 Da / Num. of mol.: 2 / Fragment: N-terminal endonuclease domain / Mutation: Y109A 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 | #3: 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: 2.13 Å3/Da / Density % sol: 42.26 % / Mosaicity: 0.57 ° |
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Crystal grow | Temperature: 289 K / Method: evaporation / pH: 5 / 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: 0.9792 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 8, 2019 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.3→50 Å / Num. obs: 18574 / % possible obs: 97 % / Redundancy: 3.9 % / Biso Wilson estimate: 42.8 Å2 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.052 / Rrim(I) all: 0.106 / Χ2: 0.963 / Net I/σ(I): 8.6 / Num. measured all: 72606 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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→46.5 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.93 / 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: 93.05 Å2 / Biso mean: 48.3128 Å2 / Biso min: 27.41 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.3→46.5 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6
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