+Open data
-Basic information
Entry | Database: PDB / ID: 4lwp | ||||||
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Title | Crystal structure of PRMT6-SAH | ||||||
Components | Arginine N-methyltransferase, putative | ||||||
Keywords | TRANSFERASE / SAM binding domain / arginine methylation | ||||||
Function / homology | Function and homology information protein-arginine C-methyltransferase activity / : / peptidyl-arginine methylation, to asymmetrical-dimethyl arginine / histone arginine N-methyltransferase activity / cytosol Similarity search - Function | ||||||
Biological species | Trypanosoma brucei brucei (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SAD / Resolution: 2.353 Å | ||||||
Authors | Zhu, Y. / Wang, C. / Shi, Y. / Teng, M. | ||||||
Citation | Journal: Plos One / Year: 2014 Title: Crystal Structure of Arginine Methyltransferase 6 from Trypanosoma brucei Authors: Wang, C. / Zhu, Y. / Chen, J. / Li, X. / Peng, J. / Chen, J. / Zou, Y. / Zhang, Z. / Jin, H. / Yang, P. / Wu, J. / Niu, L. / Gong, Q. / Teng, M. / Shi, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4lwp.cif.gz | 142.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4lwp.ent.gz | 111 KB | Display | PDB format |
PDBx/mmJSON format | 4lwp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lw/4lwp ftp://data.pdbj.org/pub/pdb/validation_reports/lw/4lwp | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 41257.465 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1 / Gene: Tb927.5.3960 / Production host: Escherichia coli (E. coli) / References: UniProt: Q57U70 #2: Chemical | ChemComp-IOD / #3: Chemical | #4: Chemical | ChemComp-PGE / | #5: Water | ChemComp-HOH / | |
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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: 2.3 Å3/Da / Density % sol: 46.47 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 100 mM Citrate pH 5.5, 20% PEG3000, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.54 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE |
Radiation | Monochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→50 Å / Num. all: 31830 / Num. obs: 31792 / Biso Wilson estimate: 38.79 Å2 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.353→47.596 Å / Occupancy max: 1 / Occupancy min: 0.43 / FOM work R set: 0.805 / SU ML: 0.31 / σ(F): 1.34 / Phase error: 26.09 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 114.88 Å2 / Biso mean: 28.4894 Å2 / Biso min: 14.63 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.353→47.596 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11
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