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- PDB-5e9w: Crystal structure of mRNA cap guanine-N7 methyltransferase obtain... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5e9w | ||||||
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Title | Crystal structure of mRNA cap guanine-N7 methyltransferase obtained by limited proteolysis | ||||||
![]() | mRNA cap guanine-N7 methyltransferase | ||||||
![]() | TRANSFERASE / mRNA capping | ||||||
Function / homology | ![]() mRNA capping enzyme complex / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / mRNA Capping / 7-methylguanosine mRNA capping / cellular response to leukemia inhibitory factor / fibrillar center / mRNA (guanine-N7)-methyltransferase / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / receptor complex ...mRNA capping enzyme complex / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / mRNA Capping / 7-methylguanosine mRNA capping / cellular response to leukemia inhibitory factor / fibrillar center / mRNA (guanine-N7)-methyltransferase / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / receptor complex / RNA binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Petit, P. / Cowling, V.H. | ||||||
![]() | ![]() Title: Molecular basis of RNA guanine-7 methyltransferase (RNMT) activation by RAM. Authors: Varshney, D. / Petit, A.P. / Bueren-Calabuig, J.A. / Jansen, C. / Fletcher, D.A. / Peggie, M. / Weidlich, S. / Scullion, P. / Pisliakov, A.V. / Cowling, V.H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 463.3 KB | Display | ![]() |
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PDB format | ![]() | 380.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 44 KB | Display | |
Data in CIF | ![]() | 61 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5e8jC ![]() 5e9jC ![]() 3bgvS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 36716.160 Da / Num. of mol.: 4 / Fragment: UNP residues 165-476 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: O43148, mRNA (guanine-N7)-methyltransferase #2: Chemical | ChemComp-SAH / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.87 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: MES pH 6.5 and 25% PEG 4000, 1/5000 thermolysin |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 14, 2014 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.28→29.58 Å / Num. obs: 57298 / % possible obs: 97 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.08 / Rsym value: 0.07 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 2.28→2.41 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 3.9 / % possible all: 97.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3BGV Resolution: 2.283→29.578 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.64 / 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: 2.283→29.578 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 58.1387 Å / Origin y: 64.3557 Å / Origin z: 62.7484 Å
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Refinement TLS group | Selection details: all |