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Yorodumi- PDB-1i9t: CRYSTAL STRUCTURE OF THE OXIDIZED RNA TRIPHOSPHATASE DOMAIN OF MO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1i9t | ||||||
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Title | CRYSTAL STRUCTURE OF THE OXIDIZED RNA TRIPHOSPHATASE DOMAIN OF MOUSE MRNA CAPPING ENZYME | ||||||
Components | MRNA CAPPING ENZYMEMRNA guanylyltransferase | ||||||
Keywords | HYDROLASE / RNA triphosphatase domain / mRNA capping enzyme / cysteine sulfenic acid | ||||||
Function / homology | Function and homology information RNA Pol II CTD phosphorylation and interaction with CE / mRNA Capping / RNA guanylyltransferase activity / inorganic triphosphate phosphatase activity / mRNA 5'-triphosphate monophosphatase activity / mRNA 5'-phosphatase / polynucleotide 5'-phosphatase activity / protein tyrosine/serine/threonine phosphatase activity / 7-methylguanosine mRNA capping / RNA processing ...RNA Pol II CTD phosphorylation and interaction with CE / mRNA Capping / RNA guanylyltransferase activity / inorganic triphosphate phosphatase activity / mRNA 5'-triphosphate monophosphatase activity / mRNA 5'-phosphatase / polynucleotide 5'-phosphatase activity / protein tyrosine/serine/threonine phosphatase activity / 7-methylguanosine mRNA capping / RNA processing / dephosphorylation / mRNA guanylyltransferase activity / mRNA guanylyltransferase / GTP binding / ATP binding / nucleus Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Changela, A. / Ho, C.K. / Martins, A. / Shuman, S. / Mondragon, A. | ||||||
Citation | Journal: EMBO J. / Year: 2001 Title: Structure and mechanism of the RNA triphosphatase component of mammalian mRNA capping enzyme. Authors: Changela, A. / Ho, C.K. / Martins, A. / Shuman, S. / Mondragon, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1i9t.cif.gz | 60.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1i9t.ent.gz | 41.8 KB | Display | PDB format |
PDBx/mmJSON format | 1i9t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i9/1i9t ftp://data.pdbj.org/pub/pdb/validation_reports/i9/1i9t | HTTPS FTP |
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-Related structure data
Related structure data | 1i9sSC S: Starting model for refinement C: citing same article (ref.) |
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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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3 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 24335.631 Da / Num. of mol.: 1 / Fragment: TPASE DOMAIN (RESIDUES 1-210) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PET16B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O55236, polynucleotide 5'-phosphatase |
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-Non-polymers , 5 types, 220 molecules
#2: Chemical | ChemComp-SO4 / | ||
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#3: Chemical | ChemComp-CAC / | ||
#4: Chemical | ChemComp-MG / | ||
#5: Chemical | #6: 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: 2.26 Å3/Da / Density % sol: 45.47 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 15% isopropanol, 50mM sodium cacodylate (pH 6.5), 25mM magnesium chloride, 25mM ammonium sulfate , VAPOR DIFFUSION, HANGING DROP, temperature 283K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 10 ℃ | ||||||||||||||||||||||||||||||||||||
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: APS / Beamline: 5ID-B / Wavelength: 1.20374 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Aug 28, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.20374 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→27 Å / Num. all: 145070 / Num. obs: 24075 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Biso Wilson estimate: 17.9 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 6 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 1.7→1.74 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.155 / Mean I/σ(I) obs: 4.9 / Num. unique all: 1749 / Rsym value: 12 / % possible all: 96.5 |
Reflection | *PLUS Lowest resolution: 27 Å / Num. measured all: 145070 / Rmerge(I) obs: 0.07 |
Reflection shell | *PLUS % possible obs: 96.5 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1I9S Resolution: 1.7→27 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.7→27 Å
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LS refinement shell | Resolution: 1.7→1.79 Å
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 27 Å / σ(F): 0 / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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