+Open data
-Basic information
Entry | Database: PDB / ID: 4lwo | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of PRMT6 | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.203 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4lwo.cif.gz | 265.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4lwo.ent.gz | 212.9 KB | Display | PDB format |
PDBx/mmJSON format | 4lwo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4lwo_validation.pdf.gz | 451.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4lwo_full_validation.pdf.gz | 461.7 KB | Display | |
Data in XML | 4lwo_validation.xml.gz | 46.4 KB | Display | |
Data in CIF | 4lwo_validation.cif.gz | 65.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lw/4lwo ftp://data.pdbj.org/pub/pdb/validation_reports/lw/4lwo | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 41257.465 Da / Num. of mol.: 4 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: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.93 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 100mM Citrate pH 5.5, 20% PEG 3000, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 298 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 0.9792 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: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. all: 77167 / Num. obs: 77126 / Biso Wilson estimate: 34.29 Å2 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.203→44.035 Å / Occupancy max: 1 / Occupancy min: 0.41 / FOM work R set: 0.8029 / SU ML: 0.28 / σ(F): 1.36 / Phase error: 27.09 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 90.13 Å2 / Biso mean: 37.5116 Å2 / Biso min: 13.42 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.203→44.035 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 28
|