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Open data
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Basic information
Entry | Database: PDB / ID: 7f1e | ||||||
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Title | Structure of METTL6 bound with SAM | ||||||
![]() | tRNA N(3)-methylcytidine methyltransferase METTL6 | ||||||
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Function / homology | ![]() tRNA (cytidine-3-)-methyltransferase activity / tRNA methylation / tRNA modification / ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Li, S. / Liao, S. / Xu, C. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis for METTL6-mediated m3C RNA methylation. Authors: Li, S. / Zhou, H. / Liao, S. / Wang, X. / Zhu, Z. / Zhang, J. / Xu, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 203.7 KB | Display | ![]() |
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PDB format | ![]() | 161.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4necS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 33491.250 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: Q8TCB7, ![]() #2: Chemical | ![]() #3: Water | ChemComp-HOH / | ![]() Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.37 Å3/Da / Density % sol: 63.52 % |
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Crystal grow![]() | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1M Sodium acetate pH5.2, 2.0M sodium formate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 24, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.589→26.857 Å / Num. obs: 41739 / % possible obs: 99.9 % / Redundancy: 12.5 % / CC1/2: 0.992 / Rmerge(I) obs: 0.094 / Net I/σ(I): 20.8 |
Reflection shell | Resolution: 2.589→2.63 Å / Rmerge(I) obs: 1.056 / Num. unique obs: 870 / CC1/2: 0.699 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 4nec Resolution: 2.589→26.857 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.6 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 149.64 Å2 / Biso mean: 51.4533 Å2 / Biso min: 14.04 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.589→26.857 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: 25.5556 Å / Origin y: -27.9604 Å / Origin z: 25.2045 Å
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Refinement TLS group |
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