+Open data
-Basic information
Entry | Database: PDB / ID: 3ckk | ||||||
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Title | Crystal structure of human methyltransferase-like protein 1 | ||||||
Components | tRNA (guanine-N(7)-)-methyltransferase | ||||||
Keywords | TRANSFERASE / METTL1 / Methyltransferase / S-adenosyl-L-methionine / tRNA processing / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information internal mRNA (guanine-N7-)-methyltransferase activity / tRNA stabilization / tRNA (m7G46) methyltransferase complex / tRNA (guanine-N7)-methylation / RNA (guanine-N7)-methylation / tRNA (guanine46-N7)-methyltransferase / tRNA (guanine(46)-N7)-methyltransferase activity / tRNA methyltransferase complex / tRNA modification in the nucleus and cytosol / tRNA methylation ...internal mRNA (guanine-N7-)-methyltransferase activity / tRNA stabilization / tRNA (m7G46) methyltransferase complex / tRNA (guanine-N7)-methylation / RNA (guanine-N7)-methylation / tRNA (guanine46-N7)-methyltransferase / tRNA (guanine(46)-N7)-methyltransferase activity / tRNA methyltransferase complex / tRNA modification in the nucleus and cytosol / tRNA methylation / tRNA modification / Transferases; Transferring one-carbon groups; Methyltransferases / tRNA binding / nucleolus / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||
Authors | Dong, A. / Zeng, H. / Dobrovetsky, E. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Min, J. / Plotnikov, A.N. ...Dong, A. / Zeng, H. / Dobrovetsky, E. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Min, J. / Plotnikov, A.N. / Wu, H. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of human methyltransferase-like protein 1. Authors: Zeng, H. / Dong, A. / Dobrovetsky, E. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Min, J. / Plotnikov, A.N. / Wu, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ckk.cif.gz | 59.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ckk.ent.gz | 41.6 KB | Display | PDB format |
PDBx/mmJSON format | 3ckk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ck/3ckk ftp://data.pdbj.org/pub/pdb/validation_reports/ck/3ckk | HTTPS FTP |
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-Related structure data
Related structure data | 2vduS S: Starting model for refinement |
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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: 27035.004 Da / Num. of mol.: 1 / Fragment: Residues 32-265 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Tissue: Brain / Gene: METTL1, C12orf1 / Plasmid: p15-tev-lic (derived from pET15) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta-R3 References: UniProt: Q9UBP6, tRNA (guanine46-N7)-methyltransferase |
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#2: Chemical | ChemComp-SAM / |
#3: Chemical | ChemComp-GOL / |
#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: 2.39 Å3/Da / Density % sol: 48.59 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 2.0 M Ammonium sulfate, 2% PEG 400, 0.1 M Na HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0331 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 5, 2008 / Details: Si(111) |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0331 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→100 Å / Num. all: 36869 / Num. obs: 36869 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.2 % / Biso Wilson estimate: 23.1 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 1.55→1.61 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.596 / Mean I/σ(I) obs: 1.78 / Num. unique all: 3389 / Rsym value: 0.596 / % possible all: 91.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2VDU Resolution: 1.55→50 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.559 / SU ML: 0.057 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.078 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.817 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.59 Å / Total num. of bins used: 20
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