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Yorodumi- PDB-2hv9: Encephalitozoon cuniculi mRNA Cap (Guanine-N7) Methyltransferase ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2hv9 | ||||||
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Title | Encephalitozoon cuniculi mRNA Cap (Guanine-N7) Methyltransferase in complex with sinefungin | ||||||
Components | mRNA cap guanine-N7 methyltransferase | ||||||
Keywords | TRANSFERASE / MRNA / CAP / METHYLTRANSFERASE / INHIBITOR | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Lima, C.D. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2006 Title: Mutational Analysis of Encephalitozoon cuniculi mRNA Cap (Guanine-N7) Methyltransferase, Structure of the Enzyme Bound to Sinefungin, and Evidence That Cap Methyltransferase Is the Target of ...Title: Mutational Analysis of Encephalitozoon cuniculi mRNA Cap (Guanine-N7) Methyltransferase, Structure of the Enzyme Bound to Sinefungin, and Evidence That Cap Methyltransferase Is the Target of Sinefungin's Antifungal Activity Authors: Zheng, S. / Hausmann, S. / Liu, Q. / Ghosh, A. / Schwer, B. / Lima, C.D. / Shuman, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2hv9.cif.gz | 66.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2hv9.ent.gz | 48.2 KB | Display | PDB format |
PDBx/mmJSON format | 2hv9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hv/2hv9 ftp://data.pdbj.org/pub/pdb/validation_reports/hv/2hv9 | HTTPS FTP |
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-Related structure data
Related structure data | 1z3cS 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: 34823.684 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Encephalitozoon cuniculi (fungus) / Gene: Ecm1 / Plasmid: pSMT3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) CP(RIL) References: UniProt: Q8SR66, mRNA (guanine-N7)-methyltransferase |
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#2: Chemical | ChemComp-SFG / |
#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: 1.89 Å3/Da / Density % sol: 34.99 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.25 Details: 1.2 M SODIUM/POTASSIUM TARTRATE, 0.05 M bis(2-hydroxyethyl)amino-tris(hydroxy-methyl)methane, 0.02 M DTT, pH 6.25, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 10, 2005 / Details: confocal osmic multilayer (blue) |
Radiation | Monochromator: osmic multilayer optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→39 Å / Num. obs: 8580 / % possible obs: 98.1 % / Observed criterion σ(F): -0.5 / Observed criterion σ(I): -0.5 / Redundancy: 4 % / Biso Wilson estimate: 38.1 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.426 / Mean I/σ(I) obs: 2.6 / Num. unique all: 8444 / % possible all: 96.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1z3c Resolution: 2.6→39.36 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 231070.09 / 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: 55.0347 Å2 / ksol: 0.386028 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→39.36 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.69 Å / Rfactor Rfree error: 0.056 / Total num. of bins used: 10
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Xplor file |
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