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Yorodumi- PDB-6iry: Crystal structure of the zebrafish cap-specific adenosine methylt... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6iry | ||||||
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Title | Crystal structure of the zebrafish cap-specific adenosine methyltransferase bound to SAH | ||||||
Components | PDX1 C-terminal-inhibiting factor 1 | ||||||
Keywords | TRANSFERASE / RNA METHYLATION / METHYLTRANSFERASE / M6A / N6-METHYLADENOSINE | ||||||
Function / homology | Function and homology information mRNA (2'-O-methyladenosine-N6-)-methyltransferase / mRNA (2'-O-methyladenosine-N6-)-methyltransferase activity / : / S-adenosyl-L-methionine binding / RNA polymerase II C-terminal domain binding / positive regulation of translation / nucleus Similarity search - Function | ||||||
Biological species | Danio rerio (zebrafish) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Hirano, S. / Nishimasu, H. / Ishitani, R. / Nureki, O. | ||||||
Citation | Journal: Science / Year: 2019 Title: Cap-specific terminal N 6 -methylation of RNA by an RNA polymerase II-associated methyltransferase. Authors: Akichika, S. / Hirano, S. / Shichino, Y. / Suzuki, T. / Nishimasu, H. / Ishitani, R. / Sugita, A. / Hirose, Y. / Iwasaki, S. / Nureki, O. / Suzuki, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6iry.cif.gz | 213.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6iry.ent.gz | 167.2 KB | Display | PDB format |
PDBx/mmJSON format | 6iry.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6iry_validation.pdf.gz | 741.3 KB | Display | wwPDB validaton report |
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Full document | 6iry_full_validation.pdf.gz | 742.5 KB | Display | |
Data in XML | 6iry_validation.xml.gz | 20.4 KB | Display | |
Data in CIF | 6iry_validation.cif.gz | 29.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ir/6iry ftp://data.pdbj.org/pub/pdb/validation_reports/ir/6iry | HTTPS FTP |
-Related structure data
Related structure data | 6irvC 6irwC 6irxSC 6irzC 6is0C 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: 57570.781 Da / Num. of mol.: 1 / Mutation: A308V, H344N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Danio rerio (zebrafish) / Gene: pcif1 / Plasmid: pE-SUMO / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 / References: UniProt: A0A0R4IKJ1 | ||
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#2: Chemical | ChemComp-SAH / | ||
#3: Chemical | #4: 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: 2.37 Å3/Da / Density % sol: 48.04 % / Mosaicity: 0.08 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 13% PEG 3350, 0.1M potassium thiocyanate, 0.1M bis-Tris propane |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 5, 2017 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.8→46.623 Å / Num. obs: 51421 / % possible obs: 100 % / Redundancy: 6.7 % / Biso Wilson estimate: 32.27 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.04 / Rpim(I) all: 0.017 / Rrim(I) all: 0.044 / Net I/σ(I): 21.2 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6IRX Resolution: 1.8→46.623 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.24
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 114.29 Å2 / Biso mean: 46.4289 Å2 / Biso min: 22.47 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.8→46.623 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18 / % reflection obs: 100 %
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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