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Yorodumi- PDB-1ori: Structure of the predominant protein arginine methyltransferase PRMT1 -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ori | ||||||
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Title | Structure of the predominant protein arginine methyltransferase PRMT1 | ||||||
Components | Protein arginine N-methyltransferase 1 | ||||||
Keywords | TRANSFERASE / protein arginine methylation AdoMet-dependent methylation | ||||||
Function / homology | Function and homology information snoRNP binding / peptidyl-arginine omega-N-methylation / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / RMTs methylate histone arginines / Estrogen-dependent gene expression / peptidyl-arginine methylation, to asymmetrical-dimethyl arginine / positive regulation of hemoglobin biosynthetic process / Extra-nuclear estrogen signaling / protein-arginine omega-N monomethyltransferase activity / N-methyltransferase activity ...snoRNP binding / peptidyl-arginine omega-N-methylation / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / RMTs methylate histone arginines / Estrogen-dependent gene expression / peptidyl-arginine methylation, to asymmetrical-dimethyl arginine / positive regulation of hemoglobin biosynthetic process / Extra-nuclear estrogen signaling / protein-arginine omega-N monomethyltransferase activity / N-methyltransferase activity / regulation of BMP signaling pathway / histone H4R3 methyltransferase activity / type I protein arginine methyltransferase / protein-arginine omega-N asymmetric methyltransferase activity / regulation of megakaryocyte differentiation / protein methyltransferase activity / protein methylation / methylosome / protein-arginine N-methyltransferase activity / negative regulation of JNK cascade / S-adenosylmethionine-dependent methyltransferase activity / S-adenosyl-L-methionine binding / cardiac muscle tissue development / methyl-CpG binding / positive regulation of p38MAPK cascade / mitogen-activated protein kinase p38 binding / histone methyltransferase activity / negative regulation of megakaryocyte differentiation / RNA splicing / positive regulation of translation / positive regulation of erythrocyte differentiation / liver regeneration / protein homooligomerization / neuron projection development / in utero embryonic development / positive regulation of cell population proliferation / enzyme binding / protein-containing complex / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Zhang, X. / Cheng, X. | ||||||
Citation | Journal: Structure / Year: 2003 Title: Structure of the Predominant Protein Arginine Methyltransferase PRMT1 and Analysis of its Binding to Substrate Peptides Authors: Zhang, X. / Cheng, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ori.cif.gz | 81.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ori.ent.gz | 59.3 KB | Display | PDB format |
PDBx/mmJSON format | 1ori.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/or/1ori ftp://data.pdbj.org/pub/pdb/validation_reports/or/1ori | HTTPS FTP |
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-Related structure data
Related structure data | 1or8C 1orhC 1f3lS C: citing same article (ref.) 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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 39627.297 Da / Num. of mol.: 1 / Fragment: M11 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: HRMT1L2 OR PRMT1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q63009, EC: 2.1.1.125 | ||
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#2: Chemical | ChemComp-SAH / | ||
#3: Chemical | Num. of mol.: 2 / Source method: obtained synthetically #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: 3.57 Å3/Da / Density % sol: 65.51 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.7 Details: ammonium phosphate, pH 4.7, VAPOR DIFFUSION, HANGING DROP, temperature 289K | ||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 31, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→25 Å / Num. all: 20200 / Num. obs: 20200 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.07 % / Biso Wilson estimate: 34.5 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 19.2 |
Reflection shell | Resolution: 2.5→2.54 Å / Rmerge(I) obs: 0.213 / Mean I/σ(I) obs: 6.7 / Num. unique all: 952 / % possible all: 96.2 |
Reflection | *PLUS Highest resolution: 2.5 Å / Num. measured all: 102483 / Rmerge(I) obs: 0.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1F3L Resolution: 2.5→24.18 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: BULK SOLVENT MODEL USED
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Displacement parameters | Biso mean: 38.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→24.18 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.61 Å / Rfactor Rfree error: 0.028
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Refinement | *PLUS | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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