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Open data
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Basic information
Entry | Database: PDB / ID: 8bxk | ||||||
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Title | Ntaya virus methyltransferase | ||||||
![]() | Ntaya virus methyltransferase | ||||||
![]() | TRANSFERASE / methyltransferase / NS5 / flavivirus | ||||||
Function / homology | SINEFUNGIN![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Boura, E. / Krafcikova, P. | ||||||
Funding support | European Union, 1items
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![]() | ![]() Title: Ntaya virus methyltransferase Authors: Boura, E. / Krafcikova, 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 | ![]() | 150.6 KB | Display | ![]() |
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PDB format | ![]() | 95.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 911.6 KB | Display | ![]() |
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Full document | ![]() | 903.5 KB | Display | |
Data in XML | ![]() | 25.7 KB | Display | |
Data in CIF | ![]() | 35.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5mrkS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 30153.566 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.92 Å3/Da / Density % sol: 57.89 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: 4.0 M Sodium formate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Nov 8, 2020 |
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54187 Å / Relative weight: 1 |
Reflection | Resolution: 2.31→39.96 Å / Num. obs: 27743 / % possible obs: 87.16 % / Redundancy: 6.3 % / Biso Wilson estimate: 24.36 Å2 / CC1/2: 0.998 / CC star: 1 / Net I/σ(I): 16.4 |
Reflection shell | Resolution: 2.31→2.39 Å / Mean I/σ(I) obs: 3.7 / Num. unique obs: 1077 / CC1/2: 0.966 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5MRK Resolution: 2.31→39.96 Å / SU ML: 0.242 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.8576 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 28.56 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.31→39.96 Å
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Refine LS restraints |
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LS refinement shell |
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