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- PDB-6qw0: Structure and function of toscana virus cap snatching endonucleases -
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Open data
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Basic information
Entry | Database: PDB / ID: 6qw0 | ||||||
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Title | Structure and function of toscana virus cap snatching endonucleases | ||||||
![]() | RNA-dependent RNA polymerase | ||||||
![]() | HYDROLASE / Cap snatching endonuclease / Toscana virus / L protein | ||||||
Function / homology | ![]() RNA-templated viral transcription / nucleoside binding / negative stranded viral RNA replication / host cell endoplasmic reticulum / virion component / host cell endoplasmic reticulum-Golgi intermediate compartment / host cell Golgi apparatus / Hydrolases; Acting on ester bonds / hydrolase activity / RNA-directed RNA polymerase ...RNA-templated viral transcription / nucleoside binding / negative stranded viral RNA replication / host cell endoplasmic reticulum / virion component / host cell endoplasmic reticulum-Golgi intermediate compartment / host cell Golgi apparatus / Hydrolases; Acting on ester bonds / hydrolase activity / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / nucleotide binding / DNA-templated transcription / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Reguera, J. / Jones, R. / Bragagniolo, G. / Lessoued, S. / Mate, M. | ||||||
![]() | ![]() Title: Structure and function of the Toscana virus cap-snatching endonuclease. Authors: Jones, R. / Lessoued, S. / Meier, K. / Devignot, S. / Barata-Garcia, S. / Mate, M. / Bragagnolo, G. / Weber, F. / Rosenthal, M. / Reguera, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 101 KB | Display | ![]() |
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PDB format | ![]() | 76.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 453.9 KB | Display | ![]() |
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Full document | ![]() | 456.3 KB | Display | |
Data in XML | ![]() | 19.5 KB | Display | |
Data in CIF | ![]() | 28.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6qvvC ![]() 6qw5SC C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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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: 23892.383 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() References: UniProt: S4ZA26, UniProt: P37800*PLUS #2: Chemical | ChemComp-MN3 / #3: Chemical | ChemComp-SO4 / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.35 Å3/Da / Density % sol: 63.28 % |
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Crystal grow | Temperature: 293 K / Method: counter-diffusion / Details: 0.1 M Hepes pH 7.5 0.75 M LiSO4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 3, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→47.553 Å / Num. obs: 99878 / % possible obs: 97.9 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.042 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 5.4 % / Rmerge(I) obs: 2.497 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 4745 / CC1/2: 0.318 / % possible all: 94.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6QW5 Resolution: 1.5→47.553 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.35
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→47.553 Å
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Refine LS restraints |
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LS refinement shell |
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