+Open data
-Basic information
Entry | Database: PDB / ID: 7f1e | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of METTL6 bound with SAM | ||||||
Components | tRNA N(3)-methylcytidine methyltransferase METTL6 | ||||||
Keywords | TRANSFERASE / RNA methyltransferase / RNA | ||||||
Function / homology | Function and homology information tRNA (cytidine-3-)-methyltransferase activity / tRNA modification / tRNA methylation / Transferases; Transferring one-carbon groups; Methyltransferases / enzyme binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.589 Å | ||||||
Authors | Li, S. / Liao, S. / Xu, C. | ||||||
Funding support | China, 1items
| ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2021 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7f1e.cif.gz | 203.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7f1e.ent.gz | 161.7 KB | Display | PDB format |
PDBx/mmJSON format | 7f1e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7f1e_validation.pdf.gz | 986.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7f1e_full_validation.pdf.gz | 994.1 KB | Display | |
Data in XML | 7f1e_validation.xml.gz | 20.1 KB | Display | |
Data in CIF | 7f1e_validation.cif.gz | 26.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f1/7f1e ftp://data.pdbj.org/pub/pdb/validation_reports/f1/7f1e | HTTPS FTP |
-Related structure data
Related structure data | 4necS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 33491.250 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 BL21(DE3) (bacteria) References: UniProt: Q8TCB7, Transferases; Transferring one-carbon groups; Methyltransferases #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.37 Å3/Da / Density % sol: 63.52 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9792 Å |
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: 0.9792 Å / Relative weight: 1 |
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 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 25.5556 Å / Origin y: -27.9604 Å / Origin z: 25.2045 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|