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Yorodumi- PDB-6q56: Crystal structure of the B. subtilis M1A22 tRNA methyltransferase TrmK -
+Open data
-Basic information
Entry | Database: PDB / ID: 6q56 | ||||||
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Title | Crystal structure of the B. subtilis M1A22 tRNA methyltransferase TrmK | ||||||
Components | tRNA (adenine(22)-N(1))-methyltransferase | ||||||
Keywords | RNA BINDING PROTEIN / methyltransferase / tRNA methyltransferase | ||||||
Function / homology | Function and homology information tRNA (adenine22-N1)-methyltransferase / : / tRNA methylation / cytoplasm Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Degut, C. / Roovers, M. / Barraud, P. / Brachet, F. / Feller, A. / Larue, V. / Al Refaii, A. / Caillet, J. / Droogmans, L. / Tisne, C. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2019 Title: Structural characterization of B. subtilis m1A22 tRNA methyltransferase TrmK: insights into tRNA recognition. Authors: Degut, C. / Roovers, M. / Barraud, P. / Brachet, F. / Feller, A. / Larue, V. / Al Refaii, A. / Caillet, J. / Droogmans, L. / Tisne, C. #1: Journal: Biomol NMR Assign / Year: 2016 Title: Backbone resonance assignments of the m1A22 tRNA methyltransferase TrmK from Bacillus subtilis. Authors: Degut, C. / Barraud, P. / Larue, V. / Tisne, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6q56.cif.gz | 193.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6q56.ent.gz | 155.3 KB | Display | PDB format |
PDBx/mmJSON format | 6q56.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q5/6q56 ftp://data.pdbj.org/pub/pdb/validation_reports/q5/6q56 | HTTPS FTP |
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-Related structure data
Related structure data | 3ku1S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 26165.803 Da / Num. of mol.: 4 / Mutation: C35S C152S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria) Gene: trmK, yqfN, BSU25180 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P54471, tRNA (adenine22-N1)-methyltransferase #2: Chemical | ChemComp-NI / #3: 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: 2.05 Å3/Da / Density % sol: 40 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 0.2 M ammonium acetate 0.1 M sodium acetate trihydrate pH 5 30% w/v polyethylene glycol 4000 8% 2-Methyl-2,4-pentanediol |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 30, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9334 Å / Relative weight: 1 |
Reflection | Resolution: 1.98→46.24 Å / Num. obs: 57747 / % possible obs: 100 % / Redundancy: 3.8 % / Biso Wilson estimate: 32.71 Å2 / Rmerge(I) obs: 0.2108 / Net I/σ(I): 12 |
Reflection shell | Resolution: 1.98→2.175 Å / Redundancy: 3.8 % / Rmerge(I) obs: 1.451 / Mean I/σ(I) obs: 1.11 / Num. unique obs: 4968 / CC1/2: 0.227 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3KU1 Resolution: 2→46.239 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.87 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→46.239 Å
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Refine LS restraints |
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LS refinement shell |
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