+Open data
-Basic information
Entry | Database: PDB / ID: 2yx1 | ||||||
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Title | Crystal structure of M.jannaschii tRNA m1G37 methyltransferase | ||||||
Components | Hypothetical protein MJ0883 | ||||||
Keywords | TRANSFERASE / methyl transferase / trna modification enzyme | ||||||
Function / homology | Function and homology information tRNA methyltransferase activity / tRNA N1-guanine methylation / tRNA (guanine37-N1)-methyltransferase / tRNA (guanine(37)-N1)-methyltransferase activity / tRNA methylation / cytoplasm Similarity search - Function | ||||||
Biological species | Methanocaldococcus jannaschii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å | ||||||
Authors | Goto-Ito, S. / Ito, T. / Ishii, R. / Bessho, Y. / Yokoyama, S. | ||||||
Citation | Journal: Proteins / Year: 2008 Title: Crystal structure of archaeal tRNA(m(1)G37)methyltransferase aTrm5. Authors: Goto-Ito, S. / Ito, T. / Ishii, R. / Muto, Y. / Bessho, Y. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2yx1.cif.gz | 142.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2yx1.ent.gz | 119 KB | Display | PDB format |
PDBx/mmJSON format | 2yx1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yx/2yx1 ftp://data.pdbj.org/pub/pdb/validation_reports/yx/2yx1 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 39259.527 Da / Num. of mol.: 2 / Fragment: 2.1.1.31 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii (archaea) Plasmid: pET28c / Production host: Escherichia coli (E. coli) / References: UniProt: Q58293 #2: Chemical | ChemComp-ZN / #3: Chemical | #4: 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: 2.39 Å3/Da / Density % sol: 48.49 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.2M sodium cacodylate, 7.5% PEG 3350, 5% PEGMME 550, 0.02M Hepes pH 7.50, 0.002M zinc sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 0.97934, 0.97942, 0.96418 | ||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 5, 2006 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.2→50 Å / Num. obs: 36694 / % possible obs: 96.8 % / Biso Wilson estimate: 28 Å2 / Rsym value: 0.105 / Net I/σ(I): 21.9 | ||||||||||||
Reflection shell | Resolution: 2.2→2.24 Å / % possible obs: 72.6 % / Rmerge(I) obs: 0.504 / Mean I/σ(I) obs: 1.8 / % possible all: 72.6 |
-Processing
Software | Name: CNS / Version: 1.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MAD / Resolution: 2.2→47.9 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1279276.81 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 49.6419 Å2 / ksol: 0.337142 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→47.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
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Xplor file |
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