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- PDB-5wt1: Pyrococcus abyssi methyltransferase PaTrm5a bound by SAH and cogn... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5wt1 | ||||||
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Title | Pyrococcus abyssi methyltransferase PaTrm5a bound by SAH and cognate tRNA | ||||||
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![]() | TRANSFERASE/RNA / methyltransferase / Trm5a / wyosine hypermodification / TRANSFERASE-RNA complex | ||||||
Function / homology | ![]() tRNA N1-guanine methylation / tRNA (guanine37-N1)-methyltransferase / tRNA (guanine(37)-N1)-methyltransferase activity / tRNA methylation / Transferases; Transferring one-carbon groups; Methyltransferases / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Xie, W. / Wang, C. / Jia, Q. | ||||||
![]() | ![]() Title: Structural insight into the methyltransfer mechanism of the bifunctional Trm5. Authors: Wang, C. / Jia, Q. / Zeng, J. / Chen, R. / Xie, W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 215.9 KB | Display | ![]() |
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PDB format | ![]() | 164.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1008.9 KB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 31 KB | Display | |
Data in CIF | ![]() | 43.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5wt3C ![]() 2zznS C: citing same article ( S: Starting model for refinement |
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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: 38545.062 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: GE5 / Orsay / Gene: trm5a, PYRAB01130, PAB2272 / Production host: ![]() ![]() References: UniProt: Q9V2G1, tRNA (guanine37-N1)-methyltransferase #2: RNA chain | Mass: 24551.658 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 45% MPD, 100 mM MES (pH 6.5), 200 mM NH4OAc |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 2, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99 Å / Relative weight: 1 |
Reflection | Resolution: 2.598→50 Å / Num. obs: 40587 / % possible obs: 99.5 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.911 / Mean I/σ(I) obs: 1.7 / CC1/2: 0.739 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2ZZN Resolution: 2.598→40.217 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.31 / 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: 2.598→40.217 Å
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Refine LS restraints |
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LS refinement shell |
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