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- PDB-7om7: Thosea asigna virus RdRP domain in complex with RNA and nucleotid... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7om7 | |||||||||
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Title | Thosea asigna virus RdRP domain in complex with RNA and nucleotide UMPNPP | |||||||||
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![]() | VIRAL PROTEIN / RdRP / polymerase | |||||||||
Function / homology | RNA-dependent RNA polymerase activity / DNA/RNA polymerase superfamily / ATP binding / metal ion binding / Chem-2KH / : / DI(HYDROXYETHYL)ETHER / RNA / RNA-dependent RNA polymerase![]() | |||||||||
Biological species | ![]() synthetic construct (others) | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Ferrero, D.S. / Falqui, M. / Verdaguer, N. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Snapshots of a Non-Canonical RdRP in Action. Authors: Ferrero, D.S. / Falqui, M. / Verdaguer, N. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 626.3 KB | Display | ![]() |
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PDB format | ![]() | 435.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 542.9 KB | Display | ![]() |
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Full document | ![]() | 569.6 KB | Display | |
Data in XML | ![]() | 92.5 KB | Display | |
Data in CIF | ![]() | 132 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7om2C ![]() 7om6C ![]() 7om9C ![]() 7omaC ![]() 4xhiS 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein / RNA chain , 2 types, 12 molecules ABCDEFGHIJKL
#1: Protein | Mass: 77110.609 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: RNA chain | Mass: 2495.545 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others) |
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-Non-polymers , 4 types, 528 molecules ![](data/chem/img/2KH.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | ChemComp-MN / | #5: Chemical | ChemComp-PEG / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.78 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1M sodium acetate pH4.6, 0.22M (NH4)SO4, 28% PEG2000MME |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 30, 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: 2.4→59.09 Å / Num. obs: 122219 / % possible obs: 99.44 % / Redundancy: 12 % / Biso Wilson estimate: 50.25 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.1305 / Rpim(I) all: 0.0389 / Rrim(I) all: 0.1363 / Net I/σ(I): 17.25 |
Reflection shell | Resolution: 2.4→2.49 Å / Rmerge(I) obs: 1.717 / Num. unique obs: 12216 / CC1/2: 0.725 / Rpim(I) all: 0.5098 / Rrim(I) all: 1.792 / % possible all: 99.58 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4XHI Resolution: 2.4→59.09 Å / SU ML: 0.3188 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.6247 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: 60.38 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→59.09 Å
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Refine LS restraints |
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LS refinement shell |
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