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- PDB-8joz: Crystal structure of CmoM from E. coli complexed with sinefungin ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8joz | ||||||
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Title | Crystal structure of CmoM from E. coli complexed with sinefungin and cellularly expressed tRNA Ser | ||||||
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![]() | TRANSFERASE/RNA / Methyltransferase / tRNA post-transcriptional modification / CmoM mcmo5U / TRANSFERASE-RNA complex / TRANSFERASE | ||||||
Function / homology | ![]() tRNA (5-carboxymethoxyuridine(34)-5-O)-methyltransferase activity / tRNA wobble uridine modification / tRNA methylation / Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yoo, J. / Kim, J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis for the selective methylation of 5-carboxymethoxyuridine in tRNA modification. Authors: Yoo, J. / Lee, J. / Kim, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 135.3 KB | Display | ![]() |
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PDB format | ![]() | 94.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.5 MB | Display | ![]() |
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Full document | ![]() | 3.5 MB | Display | |
Data in XML | ![]() | 18.8 KB | Display | |
Data in CIF | ![]() | 28.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 32199.889 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P36566, Transferases; Transferring one-carbon groups; Methyltransferases | ||||
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#2: RNA chain | Mass: 28648.268 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||
#3: Chemical | ChemComp-SFG / | ||||
#4: Chemical | ChemComp-MG / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.98 Å3/Da / Density % sol: 58.79 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 0.04 M Magnesium acetate tetrahydrate, 0.05 M Sodium cacodylate trihydrate pH 6.0, 30% v/v (+/-)-2-Methyl-2,4-pentanediol |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: LN2 / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 29, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.22→40.74 Å / Num. obs: 38928 / % possible obs: 99.94 % / Redundancy: 35.6 % / CC1/2: 0.999 / Net I/σ(I): 16.92 |
Reflection shell | Resolution: 2.22→2.3 Å / Num. unique obs: 3750 / CC1/2: 0.658 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.22→40.74 Å
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Refine LS restraints |
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LS refinement shell |
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