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Yorodumi- PDB-5x70: Crystal structure of Rice Dwarf Virus P5 in complex with a ssRNA ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5x70 | ||||||
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Title | Crystal structure of Rice Dwarf Virus P5 in complex with a ssRNA oligomer | ||||||
Components |
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Keywords | TRANSFERASE/RNA / mRNA 5'-capping enzyme / guanylyltransferase / methyltransferase / TRANSFERASE-RNA complex | ||||||
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: 3.3 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 capping enzyme 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 | 5x70.cif.gz | 595.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5x70.ent.gz | 488.3 KB | Display | PDB format |
PDBx/mmJSON format | 5x70.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x7/5x70 ftp://data.pdbj.org/pub/pdb/validation_reports/x7/5x70 | HTTPS FTP |
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-Related structure data
Related structure data | 5x6xS 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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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: RNA chain | Mass: 1938.253 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Rice dwarf virus 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: 2.39 Å3/Da / Density % sol: 48.61 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 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: BL44B2 / Wavelength: 0.9 Å |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Jul 23, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→50 Å / Num. obs: 50777 / % possible obs: 98.7 % / Redundancy: 2.1 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 3.3→3.36 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.435 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2528 / % possible all: 97.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5X6X Resolution: 3.3→38.527 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 31.04
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.3→38.527 Å
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Refine LS restraints |
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LS refinement shell |
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