+Open data
-Basic information
Entry | Database: PDB / ID: 5x71 | ||||||
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Title | Crystal structure of Rice Dwarf Virus P5 in space group P212121 | ||||||
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: 2.568 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 | 5x71.cif.gz | 319.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5x71.ent.gz | 257.5 KB | Display | PDB format |
PDBx/mmJSON format | 5x71.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x7/5x71 ftp://data.pdbj.org/pub/pdb/validation_reports/x7/5x71 | HTTPS FTP |
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-Related structure data
Related structure data | 5x6xSC 5x6yC 5x6zC 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: 90802.461 Da / Num. of mol.: 2 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 | 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: 2.49 Å3/Da / Density % sol: 50.66 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 1mM GpppG, 5mM Magnesium chloride, 16% PEG 3350, 0.1M MES, pH 6.0 |
-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: Dec 18, 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: 2.55→50 Å / Num. obs: 57936 / % possible obs: 100 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 18.9 |
Reflection shell | Resolution: 2.55→2.59 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.507 / Mean I/σ(I) obs: 3.8 / Num. unique obs: 2839 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5X6X Resolution: 2.568→44.304 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.6
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.568→44.304 Å
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Refine LS restraints |
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LS refinement shell |
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