+Open data
-Basic information
Entry | Database: PDB / ID: 5x6x | ||||||
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Title | Crystal structure of the capping enzyme P5 from Rice Dwarf Virus | ||||||
Components | mRNA capping enzyme P5 | ||||||
Keywords | TRANSFERASE / mRNA 5'-capping / guanylyltransferase / methyltransferase | ||||||
Function / homology | mRNA-capping enzyme P5, phytoreovirus / 7-methylguanosine mRNA capping / virion component / mRNA guanylyltransferase activity / mRNA guanylyltransferase / host cell cytoplasm / GTP binding / RNA binding / Putative mRNA-capping enzyme P5 Function and homology information | ||||||
Biological species | Rice dwarf virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / 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 | 5x6x.cif.gz | 629.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5x6x.ent.gz | 516.9 KB | Display | PDB format |
PDBx/mmJSON format | 5x6x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5x6x_validation.pdf.gz | 468.6 KB | Display | wwPDB validaton report |
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Full document | 5x6x_full_validation.pdf.gz | 498.9 KB | Display | |
Data in XML | 5x6x_validation.xml.gz | 114.3 KB | Display | |
Data in CIF | 5x6x_validation.cif.gz | 163 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x6/5x6x ftp://data.pdbj.org/pub/pdb/validation_reports/x6/5x6x | HTTPS FTP |
-Related 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-EDO / #3: 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: 2.4 Å3/Da / Density % sol: 48.71 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / 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: BL44XU / Wavelength: 0.9 Å |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Jun 4, 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: 194125 / % possible obs: 98.5 % / Redundancy: 4 % / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.042 / Net I/σ(I): 24.5 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 4 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 9600 / CC1/2: 0.853 / Rpim(I) all: 0.32 / % possible all: 97.7 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.1→44.504 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 26.85
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→44.504 Å
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Refine LS restraints |
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LS refinement shell |
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