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Yorodumi- PDB-4jak: Crystal structure of tRNA (Um34/Cm34) methyltransferase TrmL from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4jak | ||||||
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Title | Crystal structure of tRNA (Um34/Cm34) methyltransferase TrmL from Escherichia coli | ||||||
Components | tRNA (cytidine(34)-2'-O)-methyltransferase | ||||||
Keywords | TRANSFERASE / SPOUT / tRNA modification / methyltransferase / deep trefoil knot / SAM binding / methylation | ||||||
Function / homology | Function and homology information wobble position cytosine ribose methylation / wobble position uridine ribose methylation / tRNA (uracil-2'-O-)-methyltransferase activity / tRNA (cytidine34-2'-O)-methyltransferase / S-adenosylmethionine-dependent methyltransferase activity / protein homodimerization activity / RNA binding / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Liu, R.J. / Zhou, M. / Wang, E.D. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2013 Title: The tRNA recognition mechanism of the minimalist SPOUT methyltransferase, TrmL Authors: Liu, R.J. / Zhou, M. / Fang, Z.P. / Wang, M. / Zhou, X.L. / Wang, E.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4jak.cif.gz | 78.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4jak.ent.gz | 57.9 KB | Display | PDB format |
PDBx/mmJSON format | 4jak.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4jak_validation.pdf.gz | 430 KB | Display | wwPDB validaton report |
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Full document | 4jak_full_validation.pdf.gz | 433.1 KB | Display | |
Data in XML | 4jak_validation.xml.gz | 15.3 KB | Display | |
Data in CIF | 4jak_validation.cif.gz | 21.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ja/4jak ftp://data.pdbj.org/pub/pdb/validation_reports/ja/4jak | HTTPS FTP |
-Related structure data
Related structure data | 4jalC 1j85S C: citing same article (ref.) 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: 18832.369 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: trmL, yibK, b3606, JW3581 / Production host: Escherichia coli (E. coli) References: UniProt: P0AGJ7, tRNA (cytidine34-2'-O)-methyltransferase #2: 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: 4.36 Å3/Da / Density % sol: 71.81 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 20% polyethylene glycol (PEG) 3350, 0.1M HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 3, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 43047 / Num. obs: 42546 / % possible obs: 98.8 % |
Reflection shell | Resolution: 2→2.07 Å / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1J85 Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.958 / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.107 / 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: 41.285 Å2
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Refinement step | Cycle: LAST / Resolution: 2→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.998→2.05 Å / Total num. of bins used: 20
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