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Yorodumi- PDB-4hsg: Crystal structure of human PRMT3 in complex with an allosteric in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4hsg | ||||||
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Title | Crystal structure of human PRMT3 in complex with an allosteric inhibitor (PRMT3- KTD) | ||||||
Components | PRMT3 protein | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / PRMT3 / allosteric inhibitor / Structural Genomics / Structural Genomics Consortium / SGC / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | Function and homology information protein-arginine omega-N monomethyltransferase activity / negative regulation of retinoic acid biosynthetic process / type I protein arginine methyltransferase / protein-arginine omega-N asymmetric methyltransferase activity / protein-arginine N-methyltransferase activity / histone methyltransferase activity / Protein methylation / negative regulation of protein ubiquitination / methyltransferase activity / RMTs methylate histone arginines ...protein-arginine omega-N monomethyltransferase activity / negative regulation of retinoic acid biosynthetic process / type I protein arginine methyltransferase / protein-arginine omega-N asymmetric methyltransferase activity / protein-arginine N-methyltransferase activity / histone methyltransferase activity / Protein methylation / negative regulation of protein ubiquitination / methyltransferase activity / RMTs methylate histone arginines / ribosome binding / methylation / chromatin remodeling / nucleus / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Dobrovetsky, E. / Dong, A. / Liu, F. / Li, F. / Tempel, W. / Siarheyeva, A. / Hajian, T. / Smil, D. / Bountra, C. / Arrowsmith, C.H. ...Dobrovetsky, E. / Dong, A. / Liu, F. / Li, F. / Tempel, W. / Siarheyeva, A. / Hajian, T. / Smil, D. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Brown, P.J. / Schapira, M. / Jin, J. / Vedadi, M. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: J. Med. Chem. / Year: 2013 Title: Exploiting an allosteric binding site of PRMT3 yields potent and selective inhibitors. Authors: Liu, F. / Li, F. / Ma, A. / Dobrovetsky, E. / Dong, A. / Gao, C. / Korboukh, I. / Liu, J. / Smil, D. / Brown, P.J. / Frye, S.V. / Arrowsmith, C.H. / Schapira, M. / Vedadi, M. / Jin, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4hsg.cif.gz | 78 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4hsg.ent.gz | 55.7 KB | Display | PDB format |
PDBx/mmJSON format | 4hsg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4hsg_validation.pdf.gz | 685.7 KB | Display | wwPDB validaton report |
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Full document | 4hsg_full_validation.pdf.gz | 685.8 KB | Display | |
Data in XML | 4hsg_validation.xml.gz | 13.7 KB | Display | |
Data in CIF | 4hsg_validation.cif.gz | 19.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hs/4hsg ftp://data.pdbj.org/pub/pdb/validation_reports/hs/4hsg | HTTPS FTP |
-Related structure data
Related structure data | 3smqS 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: 38281.914 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PRMT3 / Plasmid: pET28-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-V2R-PRAR2 / References: UniProt: Q8WUV3, UniProt: O60678*PLUS | ||
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#2: Chemical | ChemComp-KTD / | ||
#3: Chemical | ChemComp-UNX / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 56.42 % |
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Crystal grow | Temperature: 291 K / pH: 7.5 Details: 25% PEG 3350, 0.2 M Lithium Sulfate, 0.1 M Hepes pH7.5, vapor diffusion hanging drop, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 18, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97926 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 20339 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 9.7 % / Biso Wilson estimate: 45.7 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 25.7 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 9.9 % / Rmerge(I) obs: 0.847 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3SMQ Resolution: 2.3→48.07 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.949 / Occupancy max: 1 / Occupancy min: 0.01 / SU B: 5.513 / SU ML: 0.133 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.231 / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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 mean: 39.87 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→48.07 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.36 Å / Total num. of bins used: 20
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