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Yorodumi- PDB-5cyr: Crystal structure of Thosea asigna virus RNA-dependent RNA polyme... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5cyr | |||||||||
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Title | Crystal structure of Thosea asigna virus RNA-dependent RNA polymerase (RdRP) complexed with ATP and ssRNA | |||||||||
Components | RNA-dependent RNA polymerase | |||||||||
Keywords | TRANSCRIPTION / RdRP / complex / ATP / ssRNA | |||||||||
Function / homology | RNA-dependent RNA polymerase activity / DNA/RNA polymerase superfamily / ATP binding / metal ion binding / ADENOSINE-5'-TRIPHOSPHATE / PHOSPHATE ION / RNA-dependent RNA polymerase Function and homology information | |||||||||
Biological species | Thosea asigna virus | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.504 Å | |||||||||
Authors | Ferrero, D.S. / Buxaderas, M. / Rodriguez, J.F. / Verdaguer, N. | |||||||||
Funding support | Spain, 2items
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Citation | Journal: Plos Pathog. / Year: 2015 Title: The Structure of the RNA-Dependent RNA Polymerase of a Permutotetravirus Suggests a Link between Primer-Dependent and Primer-Independent Polymerases. Authors: Ferrero, D.S. / Buxaderas, M. / Rodriguez, J.F. / Verdaguer, N. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5cyr.cif.gz | 270.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5cyr.ent.gz | 215.5 KB | Display | PDB format |
PDBx/mmJSON format | 5cyr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5cyr_validation.pdf.gz | 740.4 KB | Display | wwPDB validaton report |
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Full document | 5cyr_full_validation.pdf.gz | 767.5 KB | Display | |
Data in XML | 5cyr_validation.xml.gz | 49.7 KB | Display | |
Data in CIF | 5cyr_validation.cif.gz | 66 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cy/5cyr ftp://data.pdbj.org/pub/pdb/validation_reports/cy/5cyr | HTTPS FTP |
-Related structure data
Related structure data | 4xhaC 4xhiSC 5cx6C 5cxe C: citing same article (ref.) S: Starting model for refinement |
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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: 79540.461 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thosea asigna virus / Gene: RdRp / Plasmid: pFastBac1-HM / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q6A562 #2: Chemical | ChemComp-ATP / | #3: Chemical | #4: Chemical | ChemComp-PO4 / #5: Chemical | ChemComp-MG / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.85 Å3/Da / Density % sol: 68.05 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: PEG 8000, Lithium sulfate |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: May 4, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.504→48.4 Å / Num. obs: 27974 / % possible obs: 89.61 % / Redundancy: 8.1 % / Rsym value: 0.15 / Net I/σ(I): 5.57 |
Reflection shell | Resolution: 3.504→3.629 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 2.3 / % possible all: 75.92 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4XHI Resolution: 3.504→47.599 Å / SU ML: 0.58 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.89 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.504→47.599 Å
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Refine LS restraints |
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LS refinement shell |
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