+Open data
-Basic information
Entry | Database: PDB / ID: 5wwq | |||||||||||||||
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Title | Crystal structure of human NSun6 | |||||||||||||||
Components | Putative methyltransferase NSUN6 | |||||||||||||||
Keywords | TRANSFERASE / RNA modification / m5C methyltransferase / NSun | |||||||||||||||
Function / homology | Function and homology information tRNA C5-cytosine methylation / tRNA (cytidine-5-)-methyltransferase activity / tRNA modification in the nucleus and cytosol / RNA methylation / tRNA methylation / tRNA modification / Transferases; Transferring one-carbon groups; Methyltransferases / tRNA binding / cytosol / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.815 Å | |||||||||||||||
Authors | Liu, R.J. / Long, T. / Wang, E.D. | |||||||||||||||
Funding support | China, 4items
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Citation | Journal: Nucleic Acids Res. / Year: 2017 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5wwq.cif.gz | 345.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5wwq.ent.gz | 286.9 KB | Display | PDB format |
PDBx/mmJSON format | 5wwq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ww/5wwq ftp://data.pdbj.org/pub/pdb/validation_reports/ww/5wwq | HTTPS FTP |
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-Related structure data
Related structure data | 5wwrC 5wwsC 5wwtC 1j2bS 2yxlS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER
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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.) Homo sapiens (human) / Gene: NSUN6, NOPD1 Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others) References: UniProt: Q8TEA1, Transferases; Transferring one-carbon groups; Methyltransferases |
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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: 2.49 Å3/Da / Density % sol: 50.62 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion / pH: 8.6 Details: 2% Dioxane, 0.1M Bicine, 18% (w/v) PEG 8000, 10 mM Yttrium(III) chloride hexahydrate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97852 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 25, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97852 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 26419 / % possible obs: 97.6 % / Redundancy: 24.5 % / Net I/σ(I): 15.9 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1J2B, 2yxl Resolution: 2.815→37.406 Å / SU ML: 0.32 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 24.95
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 129.41 Å2 / Biso mean: 54.2703 Å2 / Biso min: 19.15 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.815→37.406 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: 9
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Refinement TLS params. | Method: refined / Origin x: 54.3381 Å / Origin y: 33.7716 Å / Origin z: 135.1311 Å
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Refinement TLS group |
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