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Yorodumi- PDB-3b3g: The 2.4 A crystal structure of the apo catalytic domain of coacti... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3b3g | ||||||
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Title | The 2.4 A crystal structure of the apo catalytic domain of coactivator-associated arginine methyl transferase I(CARM1,140-480). | ||||||
Components | Histone-arginine methyltransferase CARM1 | ||||||
Keywords | TRANSFERASE / PROTEIN ARGININE METHYLTRANSFERASE / CATALYTIC DOMAIN / Chromatin regulator / mRNA processing / mRNA splicing / Nucleus / S-adenosyl-L-methionine / Transcription / Transcription regulation | ||||||
Function / homology | Function and homology information RMTs methylate histone arginines / Estrogen-dependent gene expression / Regulation of lipid metabolism by PPARalpha / histone H3R26 methyltransferase activity / Cytoprotection by HMOX1 / regulation of growth plate cartilage chondrocyte proliferation / histone H3R17 methyltransferase activity / endochondral bone morphogenesis / histone H3R2 methyltransferase activity / type I protein arginine methyltransferase ...RMTs methylate histone arginines / Estrogen-dependent gene expression / Regulation of lipid metabolism by PPARalpha / histone H3R26 methyltransferase activity / Cytoprotection by HMOX1 / regulation of growth plate cartilage chondrocyte proliferation / histone H3R17 methyltransferase activity / endochondral bone morphogenesis / histone H3R2 methyltransferase activity / type I protein arginine methyltransferase / negative regulation of dendrite development / protein-arginine omega-N asymmetric methyltransferase activity / histone arginine N-methyltransferase activity / protein methyltransferase activity / regulation of intracellular estrogen receptor signaling pathway / replication fork reversal / protein-arginine N-methyltransferase activity / positive regulation of epithelial cell apoptotic process / positive regulation of fat cell differentiation / histone methyltransferase activity / positive regulation of transcription by RNA polymerase I / nuclear replication fork / estrogen receptor signaling pathway / nuclear receptor-mediated steroid hormone signaling pathway / protein localization to chromatin / lysine-acetylated histone binding / response to cAMP / RNA splicing / nuclear receptor coactivator activity / RNA polymerase II transcription regulator complex / mRNA processing / DNA-binding transcription factor binding / methylation / transcription coactivator activity / transcription cis-regulatory region binding / cell population proliferation / chromatin remodeling / positive regulation of cell population proliferation / regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / protein homodimerization activity / protein-containing complex / nucleoplasm / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Troffer-Charlier, N. / Cura, V. / Hassenboehler, P. / Moras, D. / Cavarelli, J. | ||||||
Citation | Journal: Embo J. / Year: 2007 Title: Functional insights from structures of coactivator-associated arginine methyltransferase 1 domains. Authors: Troffer-Charlier, N. / Cura, V. / Hassenboehler, P. / Moras, D. / Cavarelli, J. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2007 Title: Expression, purification, crystallization and preliminary crystallographic study of isolated modules of the mouse coactivator-associated arginine methyltransferase 1. Authors: Troffer-Charlier, N. / Cura, V. / Hassenboehler, P. / Moras, D. / Cavarelli, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3b3g.cif.gz | 137.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3b3g.ent.gz | 108.2 KB | Display | PDB format |
PDBx/mmJSON format | 3b3g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b3/3b3g ftp://data.pdbj.org/pub/pdb/validation_reports/b3/3b3g | 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
#1: Protein | Mass: 38774.160 Da / Num. of mol.: 2 / Fragment: Catalytic Domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Carm1, Prmt4 / Production host: unidentified baculovirus / Strain (production host): SF9 References: UniProt: Q4AE70, EC: 2.1.1.125, Transferases; Transferring one-carbon groups; Methyltransferases #2: 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: 2.42 Å3/Da / Density % sol: 49.13 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 19% PEG 3350, 0.15M sodium malate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 297K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 15, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.4→29.49 Å / Num. all: 30000 / Num. obs: 28039 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 49.9 Å2 / Rmerge(I) obs: 0.045 / Rsym value: 0.045 / Net I/σ(I): 20.8 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 4 % / Rmerge(I) obs: 0.177 / Mean I/σ(I) obs: 6.8 / Num. unique all: 2791 / Rsym value: 0.177 / % possible all: 98.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→29.49 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.902 / SU B: 17.845 / SU ML: 0.197 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.432 / ESU R Free: 0.281 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 44.711 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→29.49 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.462 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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