+Open data
-Basic information
Entry | Database: PDB / ID: 4jwj | ||||||
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Title | Crystal structure of scTrm10(84)-SAH complex | ||||||
Components | tRNA (guanine(9)-N1)-methyltransferase | ||||||
Keywords | TRANSFERASE / tRNA MTase domain | ||||||
Function / homology | Function and homology information : / tRNA (guanine) methyltransferase activity / mitochondrial tRNA processing / tRNA (guanine9-N1)-methyltransferase / tRNA (guanosine(9)-N1)-methyltransferase activity / tRNA modification / tRNA methylation / tRNA binding / mitochondrion / nucleoplasm ...: / tRNA (guanine) methyltransferase activity / mitochondrial tRNA processing / tRNA (guanine9-N1)-methyltransferase / tRNA (guanosine(9)-N1)-methyltransferase activity / tRNA modification / tRNA methylation / tRNA binding / mitochondrion / nucleoplasm / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.76 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 | 4jwj.cif.gz | 104.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4jwj.ent.gz | 79 KB | Display | PDB format |
PDBx/mmJSON format | 4jwj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4jwj_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 4jwj_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 4jwj_validation.xml.gz | 21.3 KB | Display | |
Data in CIF | 4jwj_validation.cif.gz | 30.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jw/4jwj ftp://data.pdbj.org/pub/pdb/validation_reports/jw/4jwj | HTTPS FTP |
-Related structure data
Related structure data | 4jwfSC 4jwgC 4jwhC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 23907.439 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 84-276 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: O0926, TRM10, YOL093W / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q12400, tRNA (guanine9-N1)-methyltransferase #2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.04 Å3/Da / Density % sol: 59.58 % / Mosaicity: 0.308 ° |
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Crystal grow | Temperature: 287 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1.5M Lithium sulfate monohydrate, 0.1M BIS-TRIS propane, pH 7.0, 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: May 6, 2012 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.76→50 Å / Num. all: 57042 / Num. obs: 56871 / % possible obs: 99.7 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.066 / Χ2: 1.394 / Net I/σ(I): 14.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | 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: 1.76→37.57 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.933 / WRfactor Rfree: 0.2705 / WRfactor Rwork: 0.2354 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8056 / SU B: 2.824 / SU ML: 0.088 / SU R Cruickshank DPI: 0.1186 / SU Rfree: 0.1169 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.119 / ESU R Free: 0.117 / 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: 76.81 Å2 / Biso mean: 30.2092 Å2 / Biso min: 12.91 Å2
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Refinement step | Cycle: LAST / Resolution: 1.76→37.57 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.761→1.807 Å / Total num. of bins used: 20
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