+Open data
-Basic information
Entry | Database: PDB / ID: 7oma | |||||||||
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Title | Thosea asigna virus RdRP domain elongation complex | |||||||||
Components |
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Keywords | VIRAL PROTEIN / RdRP / polymerase | |||||||||
Function / homology | RNA-dependent RNA polymerase activity / DNA/RNA polymerase superfamily / ATP binding / PYROPHOSPHATE 2- / RNA / RNA-dependent RNA polymerase Function and homology information | |||||||||
Biological species | Thosea asigna virus synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | |||||||||
Authors | Ferrero, D.S. / Falqui, M. / Verdaguer, N. | |||||||||
Funding support | Spain, 2items
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Citation | Journal: Viruses / Year: 2021 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7oma.cif.gz | 608.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7oma.ent.gz | 426.2 KB | Display | PDB format |
PDBx/mmJSON format | 7oma.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/om/7oma ftp://data.pdbj.org/pub/pdb/validation_reports/om/7oma | HTTPS FTP |
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-Related structure data
Related structure data | 7om2C 7om6C 7om7C 7om9C 4xhiS 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: 77110.609 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thosea asigna virus / Gene: RdRp / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q6A562 #2: RNA chain | Mass: 2801.710 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others) #3: RNA chain | Mass: 2495.545 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others) #4: Chemical | #5: Chemical | ChemComp-MG / 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: 2.47 Å3/Da / Density % sol: 50.24 % |
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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: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 29, 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: 3.1→67.78 Å / Num. obs: 57906 / % possible obs: 99.89 % / Redundancy: 6.9 % / Biso Wilson estimate: 57.14 Å2 / CC1/2: 0.951 / Rmerge(I) obs: 0.3841 / Net I/σ(I): 6.79 |
Reflection shell | Resolution: 3.1→3.211 Å / Rmerge(I) obs: 2.066 / Mean I/σ(I) obs: 1.22 / Num. unique obs: 5770 / CC1/2: 0.391 / Rpim(I) all: 0.8418 / % possible all: 99.84 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4XHI Resolution: 3.1→67.78 Å / SU ML: 0.425 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.6409 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: 50.06 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.1→67.78 Å
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Refine LS restraints |
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LS refinement shell |
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