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Yorodumi- PDB-1ri5: Structure and mechanism of mRNA cap (guanine N-7) methyltransferase -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ri5 | ||||||
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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 / Structural Genomics / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC | ||||||
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: 2.1 Å | ||||||
Authors | Fabrega, C. / Hausmann, S. / Shen, V. / Shuman, S. / Lima, C.D. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
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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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ri5.cif.gz | 66.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ri5.ent.gz | 49.5 KB | Display | PDB format |
PDBx/mmJSON format | 1ri5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ri5_validation.pdf.gz | 425.8 KB | Display | wwPDB validaton report |
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Full document | 1ri5_full_validation.pdf.gz | 432 KB | Display | |
Data in XML | 1ri5_validation.xml.gz | 13.2 KB | Display | |
Data in CIF | 1ri5_validation.cif.gz | 18.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ri/1ri5 ftp://data.pdbj.org/pub/pdb/validation_reports/ri/1ri5 | HTTPS FTP |
-Related structure data
Related structure data | 1ri1C 1ri2C 1ri3C 1ri4C C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-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: 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: 1.9 Å3/Da / Density % sol: 35.29 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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: 2.05→20 Å / Num. all: 17150 / Num. obs: 16224 / % possible obs: 94.6 % / Observed criterion σ(F): -1 / Observed criterion σ(I): -1 / Biso Wilson estimate: 35.6 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 16.4 |
Reflection shell | Resolution: 2.05→2.15 Å / % possible all: 89 |
Reflection | *PLUS Num. measured all: 151528 |
Reflection shell | *PLUS % possible obs: 89 % / Rmerge(I) obs: 0.193 / Mean I/σ(I) obs: 6.5 |
-Processing
Software |
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Refinement | Method to determine structure: SAD, MIR / Resolution: 2.1→19.73 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1707195.19 / 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: 61.3136 Å2 / ksol: 0.420799 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→19.73 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.26 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.32 / Rfactor Rwork: 0.27 |