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Yorodumi- PDB-5x6y: Crystal structure of Rice Dwarf Virus P5 in complex with S-adenos... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5x6y | ||||||
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Title | Crystal structure of Rice Dwarf Virus P5 in complex with S-adenosylmethionine | ||||||
Components | mRNA capping enzyme P5 | ||||||
Keywords | TRANSFERASE / mRNA 5'-capping enzyme / guanylyltransferase / methyltransferase | ||||||
Function / homology | Function and homology information 7-methylguanosine mRNA capping / virion component / mRNA guanylyltransferase activity / mRNA guanylyltransferase / host cell cytoplasm / GTP binding / RNA binding Similarity search - Function | ||||||
Biological species | Rice dwarf virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Nakamichi, Y. / Higashiura, A. / Nakagawa, A. | ||||||
Funding support | Japan, 1items
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Citation | Journal: To Be Published Title: Crystal structure of the capping enzyme P5 from Rice Dwarf Virus Authors: Nakamichi, Y. / Higashiura, A. / Narita, H. / Hagiwara, K. / Uehara-Ichiki, T. / Omura, T. / Nakagawa, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5x6y.cif.gz | 597.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5x6y.ent.gz | 485.8 KB | Display | PDB format |
PDBx/mmJSON format | 5x6y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5x6y_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 5x6y_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 5x6y_validation.xml.gz | 106 KB | Display | |
Data in CIF | 5x6y_validation.cif.gz | 146.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x6/5x6y ftp://data.pdbj.org/pub/pdb/validation_reports/x6/5x6y | HTTPS FTP |
-Related structure data
Related structure data | 5x6xSC 5x6zC 5x71C 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 90802.461 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rice dwarf virus (isolate O) / Strain: isolate O / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P14583*PLUS, mRNA guanylyltransferase #2: Chemical | ChemComp-SAM / #3: Chemical | ChemComp-EDO / #4: Chemical | #5: Water | ChemComp-HOH / | Sequence details | THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT ...THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEB | |
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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: 2.52 Å3/Da / Density % sol: 51.26 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 16% PEG 3350, 0.03M sodium citrate, 0.07M bis-tris propane, 0.2M sodium chloride, 0.01M tris(2-carboxyethyl)phosphine, 5mM S-adenosylmethionine, 1mM GpppG, 5mM magnesium chloride |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Jul 23, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 198192 / % possible obs: 96 % / Redundancy: 2.1 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 24 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 2 % / Rmerge(I) obs: 0.389 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 9820 / % possible all: 95 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5X6X Resolution: 2.1→38.226 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 25.18
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→38.226 Å
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Refine LS restraints |
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LS refinement shell |
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