+Open data
-Basic information
Entry | Database: PDB / ID: 7om9 | |||||||||
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Title | Thosea asigna virus RdRP domain | |||||||||
Components | RNA-dependent RNA polymerase | |||||||||
Keywords | VIRAL PROTEIN / RdRP / polymerase | |||||||||
Function / homology | RNA-dependent RNA polymerase activity / DNA/RNA polymerase superfamily / ATP binding / metal ion binding / RNA-dependent RNA polymerase Function and homology information | |||||||||
Biological species | Thosea asigna virus | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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 | 7om9.cif.gz | 305.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7om9.ent.gz | 200.6 KB | Display | PDB format |
PDBx/mmJSON format | 7om9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7om9_validation.pdf.gz | 317.9 KB | Display | wwPDB validaton report |
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Full document | 7om9_full_validation.pdf.gz | 329.7 KB | Display | |
Data in XML | 7om9_validation.xml.gz | 42.3 KB | Display | |
Data in CIF | 7om9_validation.cif.gz | 57.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/om/7om9 ftp://data.pdbj.org/pub/pdb/validation_reports/om/7om9 | HTTPS FTP |
-Related structure data
Related structure data | 7om2C 7om6C 7om7C 7omaC 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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Unit cell |
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-Components
#1: Protein | Mass: 77110.609 Da / Num. of mol.: 2 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 |
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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: 2.43 Å3/Da / Density % sol: 49.29 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1M sodium acetate pH4.6, 0.25M (NH4)SO4, 26% PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97934 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 18, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 3→48.52 Å / Num. obs: 29359 / % possible obs: 98.22 % / Redundancy: 4.8 % / Biso Wilson estimate: 78.86 Å2 / CC1/2: 0.941 / Rpim(I) all: 0.1552 / Rrim(I) all: 0.3546 / Net I/σ(I): 10.52 |
Reflection shell | Resolution: 3→3.107 Å / Rmerge(I) obs: 1.217 / Mean I/σ(I) obs: 1.45 / Num. unique obs: 2956 / CC1/2: 0.514 / Rpim(I) all: 0.573 / % possible all: 99.29 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4XHI Resolution: 3→48.52 Å / SU ML: 0.4582 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.2728 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: 90.24 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→48.52 Å
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Refine LS restraints |
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LS refinement shell |
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