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Yorodumi- PDB-7t39: Co-crystal structure of human PRMT9 in complex with MT221 inhibitor -
+Open data
-Basic information
Entry | Database: PDB / ID: 7t39 | ||||||
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Title | Co-crystal structure of human PRMT9 in complex with MT221 inhibitor | ||||||
Components | Protein arginine N-methyltransferase 9 | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / methyltransferase / PRMT9 / SGC / Structural Genomics / Structural Genomics Consortium / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | Function and homology information type II protein arginine methyltransferase / protein-arginine omega-N symmetric methyltransferase activity / protein-arginine N-methyltransferase activity / histone methyltransferase activity / mRNA processing / methylation / chromatin remodeling / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.81 Å | ||||||
Authors | Zeng, H. / Dong, A. / Hutchinson, A. / Seitova, A. / Li, Y. / Gao, Y.D. / Schneider, S. / Siliphaivanh, P. / Sloman, D. / Nicholson, B. ...Zeng, H. / Dong, A. / Hutchinson, A. / Seitova, A. / Li, Y. / Gao, Y.D. / Schneider, S. / Siliphaivanh, P. / Sloman, D. / Nicholson, B. / Fischer, C. / Hicks, J. / Brown, P.J. / Arrowsmith, C.H. / Edwards, A.M. / Halabelian, L. / Structural Genomics Consortium (SGC) | ||||||
Funding support | Canada, 1items
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Citation | Journal: To Be Published Title: Co-crystal structure of human PRMT9 in complex with MT221 inhibitor Authors: Zeng, H. / Dong, A. / Hutchinson, A. / Seitova, A. / Li, Y. / Gao, Y.D. / Schneider, S. / Siliphaivanh, P. / Sloman, D. / Nicholson, B. / Fischer, C. / Hicks, J. / Brown, P.J. / Arrowsmith, ...Authors: Zeng, H. / Dong, A. / Hutchinson, A. / Seitova, A. / Li, Y. / Gao, Y.D. / Schneider, S. / Siliphaivanh, P. / Sloman, D. / Nicholson, B. / Fischer, C. / Hicks, J. / Brown, P.J. / Arrowsmith, C.H. / Edwards, A.M. / Halabelian, L. / Structural Genomics Consortium (SGC) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7t39.cif.gz | 136.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7t39.ent.gz | 99.5 KB | Display | PDB format |
PDBx/mmJSON format | 7t39.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7t39_validation.pdf.gz | 672.8 KB | Display | wwPDB validaton report |
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Full document | 7t39_full_validation.pdf.gz | 674.3 KB | Display | |
Data in XML | 7t39_validation.xml.gz | 22 KB | Display | |
Data in CIF | 7t39_validation.cif.gz | 30.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t3/7t39 ftp://data.pdbj.org/pub/pdb/validation_reports/t3/7t39 | HTTPS FTP |
-Related structure data
Related structure data | 6pdmS 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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Unit cell |
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-Components
#1: Protein | Mass: 80486.297 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PRMT9, PRMT10 / Plasmid: pFBOH-MHL / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: Q6P2P2, type II protein arginine methyltransferase |
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#2: Chemical | ChemComp-EJB / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.78 % / Mosaicity: 0.26 ° |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: 25%(w/v) PEG3350, 0.2M Ammonium Acetate, 0.1M Bis-Tris pH5.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.97741 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 14, 2019 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97741 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.8→50 Å / Num. obs: 16704 / % possible obs: 99.6 % / Redundancy: 14.4 % / Rmerge(I) obs: 0.162 / Rpim(I) all: 0.043 / Rrim(I) all: 0.168 / Χ2: 0.848 / Net I/σ(I): 4 / Num. measured all: 241023 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6PDM Resolution: 2.81→49.06 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.898 / SU B: 19.837 / SU ML: 0.372 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.416 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 121 Å2 / Biso mean: 54.646 Å2 / Biso min: 29.82 Å2
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Refinement step | Cycle: final / Resolution: 2.81→49.06 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.81→2.88 Å / Rfactor Rfree error: 0
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