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Yorodumi- PDB-4n49: Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase 1 Protein ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4n49 | ||||||
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Title | Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase 1 Protein in complex with m7GpppG and SAM | ||||||
Components | Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase 1 | ||||||
Keywords | TRANSFERASE / methyltransferase / mRNA cap methylation / mRNA | ||||||
Function / homology | Function and homology information : / : / 7-methylguanosine mRNA capping / methyltransferase cap1 / mRNA (nucleoside-2'-O-)-methyltransferase activity / nucleic acid binding / intracellular membrane-bounded organelle / nucleoplasm / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Smietanski, M. / Werener, M. / Purta, E. / Kaminska, K.H. / Stepinski, J. / Darzynkiewicz, E. / Nowotny, M. / Bujnicki, J.M. | ||||||
Citation | Journal: Nat Commun / Year: 2014 Title: Structural analysis of human 2'-O-ribose methyltransferases involved in mRNA cap structure formation. Authors: Smietanski, M. / Werner, M. / Purta, E. / Kaminska, K.H. / Stepinski, J. / Darzynkiewicz, E. / Nowotny, M. / Bujnicki, J.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4n49.cif.gz | 112.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4n49.ent.gz | 82.4 KB | Display | PDB format |
PDBx/mmJSON format | 4n49.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n4/4n49 ftp://data.pdbj.org/pub/pdb/validation_reports/n4/4n49 | HTTPS FTP |
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-Related structure data
Related structure data | 4n48C 4n4aSC 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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Unit cell |
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-Components
#1: Protein | Mass: 48935.754 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FTSJD2, KIAA0082, MTR1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8N1G2, methyltransferase cap1 |
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#2: Chemical | ChemComp-SAM / |
#3: Chemical | ChemComp-MGT / |
#4: Chemical | ChemComp-NA / |
#5: 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: 2.4 Å3/Da / Density % sol: 48.81 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 6.5 Details: 30% PEG 3350, 100 mM Bis-Tris [pH 6.5], and 100 mM NaBr, VAPOR DIFFUSION, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 22, 2011 |
Radiation | Monochromator: Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→46.8 Å / Num. all: 36471 / Num. obs: 36369 / % possible obs: 99.7 % / Observed criterion σ(F): 2.1 / Observed criterion σ(I): 2.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4N4A Resolution: 1.9→46.8 Å / SU ML: 0.22 / σ(F): 2 / Phase error: 19.85 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→46.8 Å
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Refine LS restraints |
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LS refinement shell |
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