+Open data
-Basic information
Entry | Database: PDB / ID: 8owx | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of METTL6 bound to SAH | ||||||
Components | tRNA N(3)-methylcytidine methyltransferase METTL6 | ||||||
Keywords | RNA BINDING PROTEIN / tRNA modification / m3C / methyltransferase | ||||||
Function / homology | Function and homology information tRNA (cytidine-3-)-methyltransferase activity / tRNA methylation / tRNA modification / Transferases; Transferring one-carbon groups; Methyltransferases / enzyme binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.601 Å | ||||||
Authors | Throll, P. / Basu, S. / Dolce, L.G. / Kowalinski, E. | ||||||
Funding support | 1items
| ||||||
Citation | Journal: To Be Published Title: Structural basis of the cooperation between the m3C RNA-methyltransferase METTL6 with SerRS amino-acyl-synthetase for tRNA recognition Authors: Throll, P. / Dolce, L.G. / Lastres, P.R. / Arnold, K. / Tengo, L. / Kaiser, S. / Basu, S. / Schneider, R. / Kowalinski, E. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8owx.cif.gz | 114.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8owx.ent.gz | 86.3 KB | Display | PDB format |
PDBx/mmJSON format | 8owx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ow/8owx ftp://data.pdbj.org/pub/pdb/validation_reports/ow/8owx | HTTPS FTP |
---|
-Related structure data
Related structure data | 8owyC C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||
2 |
| ||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 32346.895 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: METTL6 / Production host: Escherichia coli (E. coli) References: UniProt: Q8TCB7, Transferases; Transferring one-carbon groups; Methyltransferases #2: Chemical | #3: Chemical | ChemComp-B3P / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.9 Å3/Da / Density % sol: 68.47 % |
---|---|
Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1 M BisTRIS propane pH 6.5, 0.2 M sodium sulfate, 20 % PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.9801 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 21, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9801 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→41.43 Å / Num. obs: 26988 / % possible obs: 98.36 % / Redundancy: 13.6 % / Biso Wilson estimate: 80.78 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.2006 / Net I/σ(I): 9.43 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 13.3 % / Rmerge(I) obs: 4.8 / Num. unique obs: 2653 / CC1/2: 0.143 / % possible all: 83.61 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 2.601→41.43 Å / SU ML: 0.53 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.11 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.601→41.43 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|