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- PDB-6qe6: Structure of M. capricolum TrmK in complex with the natural cofac... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6qe6 | ||||||
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Title | Structure of M. capricolum TrmK in complex with the natural cofactor product S-adenosyl-homocysteine (SAH) | ||||||
![]() | tRNA (Adenine(22)-N(1))-methyltransferase | ||||||
![]() | TRANSFERASE / RNA MTases / methyltransferase / m6A / transition state analogue / inhibitor / RNA binding / TrmK / RlmJ / m1A / structure. | ||||||
Function / homology | tRNA (adenine22-N1)-methyltransferase / tRNA methyltransferase TrmK / tRNA (adenine(22)-N(1))-methyltransferase / : / S-adenosyl-L-methionine-dependent methyltransferase superfamily / S-ADENOSYL-L-HOMOCYSTEINE / tRNA (Adenine(22)-N(1))-methyltransferase![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Oerum, S. / Catala, M. / Atdjian, C. / Brachet, F. / Ponchon, L. / Barraud, P. / Iannazzo, L. / Droogmans, L. / Braud, E. / Etheve-Quelquejeu, M. / Tisne, C. | ||||||
![]() | ![]() Title: Bisubstrate analogues as structural tools to investigate m6A methyltransferase active sites. Authors: Oerum, S. / Catala, M. / Atdjian, C. / Brachet, F. / Ponchon, L. / Barraud, P. / Iannazzo, L. / Droogmans, L. / Braud, E. / Etheve-Quelquejeu, M. / Tisne, C. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 110.5 KB | Display | ![]() |
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PDB format | ![]() | 83.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 947.1 KB | Display | ![]() |
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Full document | ![]() | 949.5 KB | Display | |
Data in XML | ![]() | 19.8 KB | Display | |
Data in CIF | ![]() | 28 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6qdxC ![]() 6qe0C ![]() 6qe5C ![]() 4blvS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 28510.572 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: trmK, MCGM508_03695 / Production host: ![]() ![]() References: UniProt: A0A0C3A3T0, tRNA (adenine22-N1)-methyltransferase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.75 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 0.2 M Li2SO4, 0.1 M HEPES pH 7.5, 25% (w/v) PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Jun 13, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87313 Å / Relative weight: 1 |
Reflection | Resolution: 2.36→42.91 Å / Num. obs: 24468 / % possible obs: 99.75 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.2719 / Net I/σ(I): 5.47 |
Reflection shell | Resolution: 2.36→2.44 Å |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4BLV Resolution: 2.36→42.909 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.71 / 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: 2.36→42.909 Å
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Refine LS restraints |
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LS refinement shell |
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