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Yorodumi- PDB-1ri2: Structure and mechanism of mRNA cap (guanine N-7) methyltransferase -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ri2 | ||||||
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Title | Structure and mechanism of mRNA cap (guanine N-7) methyltransferase | ||||||
Components | mRNA CAPPING ENZYME | ||||||
Keywords | TRANSFERASE / methyltransferase / rna / cap / m7G / messenger rna cap | ||||||
Function / homology | Function and homology information mRNA (guanine-N7)-methyltransferase / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA binding / nucleus Similarity search - Function | ||||||
Biological species | Encephalitozoon cuniculi (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD, MIR / Resolution: 2.7 Å | ||||||
Authors | Fabrega, C. / Hausmann, S. / Shen, V. / Shuman, S. / Lima, C.D. | ||||||
Citation | Journal: Mol.Cell / Year: 2004 Title: Structure and mechanism of mRNA cap (Guanine-n7) methyltransferase Authors: Fabrega, C. / Hausmann, S. / Shen, V. / Shuman, S. / Lima, C.D. | ||||||
History |
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Remark 600 | HETEROGEN 7mG and ribose are disordered leaving only a GTP modeled in the structure |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ri2.cif.gz | 65.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ri2.ent.gz | 48.6 KB | Display | PDB format |
PDBx/mmJSON format | 1ri2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ri2_validation.pdf.gz | 695.4 KB | Display | wwPDB validaton report |
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Full document | 1ri2_full_validation.pdf.gz | 701.9 KB | Display | |
Data in XML | 1ri2_validation.xml.gz | 12.7 KB | Display | |
Data in CIF | 1ri2_validation.cif.gz | 16.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ri/1ri2 ftp://data.pdbj.org/pub/pdb/validation_reports/ri/1ri2 | HTTPS FTP |
-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: 34823.684 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Encephalitozoon cuniculi (fungus) / Gene: ECU10_0380 / Plasmid: PSUMO-SMT3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: Q8SR66 |
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#2: Chemical | ChemComp-GTG / |
#3: 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: 1.83 Å3/Da / Density % sol: 32.74 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.25 Details: 1.2M Na/K tartrate, 50mM BIS/TRIS, 20mM DTT, pH 6.25, VAPOR DIFFUSION, HANGING DROP, temperature 291K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8 / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 31-ID / Wavelength: 0.979 Å |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Monochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→20 Å / Num. all: 7623 / Num. obs: 6929 / % possible obs: 90.9 % / Observed criterion σ(F): -1 / Observed criterion σ(I): -1 / Biso Wilson estimate: 83.4 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 9 |
Reflection shell | Resolution: 2.7→2.8 Å / % possible all: 80.4 |
Reflection | *PLUS Num. measured all: 38733 |
Reflection shell | *PLUS % possible obs: 80.4 % / Rmerge(I) obs: 0.389 / Mean I/σ(I) obs: 4.8 |
-Processing
Software |
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Refinement | Method to determine structure: SAD, MIR / Resolution: 2.7→19.5 Å / Rfactor Rfree error: 0.016 / Data cutoff high absF: 1504918.56 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 39.4623 Å2 / ksol: 0.300665 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 74.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→19.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.87 Å / Rfactor Rfree error: 0.058 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.7 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.29 / Rfactor Rwork: 0.22 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.42 / Rfactor Rwork: 0.34 |