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Yorodumi- PDB-5i62: Crystal structure of the insertion loop deletion mutant of the RN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5i62 | ||||||
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Title | Crystal structure of the insertion loop deletion mutant of the RNA-dependent RNA polymerase of a human picorbirnavirus | ||||||
Components | Potential RNA-dependent RNA polymerase | ||||||
Keywords | viral protein / replication / dsRNA / transcription / insertion loop | ||||||
Function / homology | Function and homology information virion component / RNA-directed RNA polymerase / RNA-dependent RNA polymerase activity / nucleotide binding / DNA-templated transcription / RNA binding Similarity search - Function | ||||||
Biological species | Human picobirnavirus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.001 Å | ||||||
Authors | Collier, A.M. / Guo, Y.R. / Tao, Y.J. | ||||||
Funding support | United States, 1items
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Citation | Journal: Plos Pathog. / Year: 2016 Title: Initiation of RNA Polymerization and Polymerase Encapsidation by a Small dsRNA Virus. Authors: Collier, A.M. / Lyytinen, O.L. / Guo, Y.R. / Toh, Y. / Poranen, M.M. / Tao, Y.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5i62.cif.gz | 123 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5i62.ent.gz | 93.7 KB | Display | PDB format |
PDBx/mmJSON format | 5i62.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5i62_validation.pdf.gz | 425.2 KB | Display | wwPDB validaton report |
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Full document | 5i62_full_validation.pdf.gz | 429.5 KB | Display | |
Data in XML | 5i62_validation.xml.gz | 23.2 KB | Display | |
Data in CIF | 5i62_validation.cif.gz | 34.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i6/5i62 ftp://data.pdbj.org/pub/pdb/validation_reports/i6/5i62 | HTTPS FTP |
-Related 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: 60977.539 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human picobirnavirus (strain Human/Thailand/Hy005102/-) Strain: Human/Thailand/Hy005102/- / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: Q50LE4, RNA-directed RNA polymerase |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.4 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 200 mM sodium acetate, 100 mM sodium cacodylate pH 6.5, and 35% PEG 8000 |
-Data collection
Diffraction | Mean temperature: 77 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.12719 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 15, 2012 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.12719 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2→50 Å / Num. obs: 38794 / % possible obs: 99.9 % / Redundancy: 13 % / Rmerge(I) obs: 0.09 / Χ2: 5.946 / Net I/av σ(I): 71.584 / Net I/σ(I): 19.6 / Num. measured all: 505906 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Crystal structure of the RNA-dependent RNA polymerase of a human picorbirnavirus Resolution: 2.001→35.721 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.04 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 78.42 Å2 / Biso mean: 26.7779 Å2 / Biso min: 11.99 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.001→35.721 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
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