+Open data
-Basic information
Entry | Database: PDB / ID: 4jwg | ||||||
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Title | Crystal structure of spTrm10(74) | ||||||
Components | tRNA (guanine(9)-N1)-methyltransferase | ||||||
Keywords | TRANSFERASE / tRNA MTase domain | ||||||
Function / homology | Function and homology information tRNA (guanine9-N1)-methyltransferase / tRNA (guanosine(9)-N1)-methyltransferase activity / tRNA N1-guanine methylation / tRNA binding / nucleolus / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Schizosaccharomyces pombe (fission yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å | ||||||
Authors | Yan, W. / Shao, Z. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2014 Title: Crystal structure of tRNA m1G9 methyltransferase Trm10: insight into the catalytic mechanism and recognition of tRNA substrate. Authors: Shao, Z. / Yan, W. / Peng, J. / Zuo, X. / Zou, Y. / Li, F. / Gong, D. / Ma, R. / Wu, J. / Shi, Y. / Zhang, Z. / Teng, M. / Li, X. / Gong, Q. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4jwg.cif.gz | 55 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4jwg.ent.gz | 37.1 KB | Display | PDB format |
PDBx/mmJSON format | 4jwg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jw/4jwg ftp://data.pdbj.org/pub/pdb/validation_reports/jw/4jwg | HTTPS FTP |
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-Related structure data
Related structure data | 4jwfSC 4jwhC 4jwjC 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: 25319.107 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 74-281 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast) Strain: 972 / ATCC 24843 / Gene: SPAC6B12.09, trm10 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: O14214, tRNA (guanine9-N1)-methyltransferase | ||
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#2: Chemical | #3: 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: 2.15 Å3/Da / Density % sol: 42.76 % / Mosaicity: 1.087 ° |
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Crystal grow | Temperature: 287 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 15% PEG 6000, 0.1M Na acetate, pH 5.0, vapor diffusion, hanging drop, temperature 287K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Dec 2, 2011 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.5→50 Å / Num. all: 7886 / Num. obs: 7871 / % possible obs: 99.8 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 7 % / Rmerge(I) obs: 0.09 / Χ2: 1.243 / Net I/σ(I): 11.9 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Rfactor: 60.39 / Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4JWF Resolution: 2.5→41.48 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.881 / WRfactor Rfree: 0.2936 / WRfactor Rwork: 0.2196 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.7744 / SU B: 11.382 / SU ML: 0.252 / SU R Cruickshank DPI: 0.5957 / SU Rfree: 0.3291 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.596 / ESU R Free: 0.329 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
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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 max: 75.46 Å2 / Biso mean: 45.7657 Å2 / Biso min: 21.01 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→41.48 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.565 Å / Total num. of bins used: 20
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