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- PDB-8iib: Crystal structure of Israeli acute paralysis virus RNA-dependent ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8iib | |||||||||
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Title | Crystal structure of Israeli acute paralysis virus RNA-dependent RNA polymerase delta85 mutant (residues 86-546) | |||||||||
![]() | Polymerase polyprotein | |||||||||
![]() | TRANSFERASE / RNA-dependent RNA polymerase | |||||||||
Function / homology | : ![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Fang, X. / Lu, G. / Hou, C. / Gong, P. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Unusual substructure conformations observed in crystal structures of a dicistrovirus RNA-dependent RNA polymerase suggest contribution of the N-terminal extension in proper folding. Authors: Fang, X. / Lu, G. / Deng, Y. / Yang, S. / Hou, C. / 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 | ![]() | 157.6 KB | Display | ![]() |
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PDB format | ![]() | 117.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 5 MB | Display | ![]() |
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Full document | ![]() | 5 MB | Display | |
Data in XML | ![]() | 27.7 KB | Display | |
Data in CIF | ![]() | 38.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8iicC C: citing same article ( |
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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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 54888.414 Da / Num. of mol.: 2 / Mutation: N510D Source method: isolated from a genetically manipulated source Details: GB:MG599488.1 / Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-CD / #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-CL / #5: 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: 3.12 Å3/Da / Density % sol: 60.53 % |
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Crystal grow | Temperature: 289 K / Method: evaporation / pH: 8.5 / Details: PEG 4000 |
-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 6, 2018 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.69→23.8 Å / Num. obs: 38083 / % possible obs: 100 % / Redundancy: 10.1 % / Rmerge(I) obs: 0.041 / Rpim(I) all: 0.014 / Rrim(I) all: 0.043 / Χ2: 0.922 / Net I/σ(I): 16.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]()
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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: 94.46 Å2 / Biso mean: 40.2077 Å2 / Biso min: 10.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.69→23.41 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13
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