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Yorodumi- PDB-5e72: Crystal structure of the archaeal tRNA m2G/m22G10 methyltransfera... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5.0E+72 | |||||||||
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Title | Crystal structure of the archaeal tRNA m2G/m22G10 methyltransferase (aTrm11) in complex with S-adenosyl-L-methionine (SAM) from Thermococcus kodakarensis | |||||||||
Components | N2, N2-dimethylguanosine tRNA methyltransferase | |||||||||
Keywords | TRANSFERASE / tRNA methyltransferase / SAM | |||||||||
Function / homology | Function and homology information tRNA (guanine) methyltransferase activity / : / tRNA methylation / RNA binding Similarity search - Function | |||||||||
Biological species | Thermococcus kodakarensis (archaea) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / molecular replacement / Resolution: 1.739 Å | |||||||||
Authors | Hirata, A. | |||||||||
Funding support | Japan, 2items
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Citation | Journal: Nucleic Acids Res. / Year: 2016 Title: Structural and functional analyses of the archaeal tRNA m2G/m22G10 methyltransferase aTrm11 provide mechanistic insights into site specificity of a tRNA methyltransferase that contains common RNA-binding modules. Authors: Hirata, A. / Nishiyama, S. / Tamura, T. / Yamauchi, A. / Hori, H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5e72.cif.gz | 82.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5e72.ent.gz | 63.7 KB | Display | PDB format |
PDBx/mmJSON format | 5e72.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e7/5e72 ftp://data.pdbj.org/pub/pdb/validation_reports/e7/5e72 | HTTPS FTP |
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-Related 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: 39300.129 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (archaea) Strain: ATCC BAA-918 / JCM 12380 / KOD1 / Gene: TK0981 / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (DE3) / References: UniProt: Q5JID5 |
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#2: Chemical | ChemComp-SAM / |
#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: 2.19 Å3/Da / Density % sol: 43.84 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 4.5M NaCl, 0.1M Tris-HCl |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 13, 2013 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.739→50 Å / Num. obs: 36188 / % possible obs: 99.7 % / Redundancy: 5.1 % / Biso Wilson estimate: 18.83 Å2 / Rmerge(I) obs: 0.043 / Χ2: 1.376 / Net I/av σ(I): 41.572 / Net I/σ(I): 16.9 / Num. measured all: 185983 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.739→32.674 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.72 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 57.47 Å2 / Biso mean: 22.2948 Å2 / Biso min: 3.83 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.739→32.674 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13
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