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Open data
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Basic information
Entry | Database: PDB / ID: 5wwr | ||||||
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Title | Crystal structure of human NSun6/tRNA/SFG | ||||||
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![]() | TRANSFERASE/RNA / RNA modification / m5C methyltransferase / NSun / TRANSFERASE-RNA complex | ||||||
Function / homology | ![]() tRNA C5-cytosine methylation / tRNA (cytidine-5-)-methyltransferase activity / tRNA modification in the nucleus and cytosol / RNA methylation / tRNA modification / tRNA methylation / Transferases; Transferring one-carbon groups; Methyltransferases / tRNA binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Liu, R.J. / Long, T. / Wang, E.D. | ||||||
![]() | ![]() Title: Structural basis for substrate binding and catalytic mechanism of a human RNA:m5C methyltransferase NSun6 Authors: Liu, R.J. / Long, T. / Li, J. / Li, H. / Wang, E.D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 268 KB | Display | ![]() |
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PDB format | ![]() | 209.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 948.7 KB | Display | ![]() |
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Full document | ![]() | 948.7 KB | Display | |
Data in XML | ![]() | 36.5 KB | Display | |
Data in CIF | ![]() | 50 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5wwqSC ![]() 5wwsC ![]() 5wwtC ![]() 2du3S 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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Components
#1: Protein | Mass: 52905.230 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() References: UniProt: Q8TEA1, Transferases; Transferring one-carbon groups; Methyltransferases #2: RNA chain | Mass: 24173.365 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ![]() #3: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.18 Å3/Da / Density % sol: 70.56 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion / pH: 8.5 / Details: 0.1 M SPG, 25% (w/v) PEG 1500, 50 mM NaF |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 14, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97776 Å / Relative weight: 1 |
Reflection | Resolution: 3.096→50 Å / Num. obs: 45890 / % possible obs: 98.2 % / Redundancy: 6.7 % / Biso Wilson estimate: 61.73 Å2 / Net I/σ(I): 19.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5WWQ, 2DU3 Resolution: 3.096→42.892 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.81
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 179.41 Å2 / Biso mean: 55.2541 Å2 / Biso min: 8.94 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.096→42.892 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13
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