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- PDB-7ex0: Crystal structure of Ebinur Lake virus cap snatching endonuclease... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7ex0 | |||||||||
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Title | Crystal structure of Ebinur Lake virus cap snatching endonuclease (K108A mutant) | |||||||||
![]() | Replicase | |||||||||
![]() | HYDROLASE / endonuclease | |||||||||
Function / homology | ![]() 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 | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Kuang, W. / Hu, Z. / Gong, P. | |||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 92.1 KB | Display | ![]() |
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PDB format | ![]() | 66.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 443.6 KB | Display | ![]() |
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Full document | ![]() | 444.5 KB | Display | |
Data in XML | ![]() | 16.1 KB | Display | |
Data in CIF | ![]() | 22.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7ewuC ![]() 7ewvC ![]() 7ewwC ![]() 7ewxC ![]() 7ewyC ![]() 7ewzC ![]() 7ex1C ![]() 2xi5S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 25123.773 Da / Num. of mol.: 2 / Fragment: N-terminal endonuclease domain / Mutation: K108A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: A0A059WLS9, RNA-directed RNA polymerase #2: Chemical | ChemComp-MN / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.5 % / Mosaicity: 0.883 ° |
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Crystal grow | Temperature: 289 K / Method: evaporation / pH: 5.1 / Details: PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 2.07→50 Å / Num. obs: 29345 / % possible obs: 99.8 % / Redundancy: 3.6 % / Biso Wilson estimate: 35.91 Å2 / Rmerge(I) obs: 0.04 / Rpim(I) all: 0.024 / Rrim(I) all: 0.047 / Χ2: 0.935 / Net I/σ(I): 15.3 / Num. measured all: 104989 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2XI5 Resolution: 2.07→30.21 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.42 / 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: 124.69 Å2 / Biso mean: 41.8006 Å2 / Biso min: 20.48 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.07→30.21 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10
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