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Yorodumi- PDB-1av6: VACCINIA METHYLTRANSFERASE VP39 COMPLEXED WITH M7G CAPPED RNA HEX... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1av6 | ||||||
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Title | VACCINIA METHYLTRANSFERASE VP39 COMPLEXED WITH M7G CAPPED RNA HEXAMER AND S-ADENOSYLHOMOCYSTEINE | ||||||
Components |
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Keywords | TRANSFERASE/RNA / SINGLE-STRANDED RNA / METHYLTRANSFERASE / RNA CAP / POLY(A) POLYMERASE / VACCINIA / MRNA PROCESSING / TRANSCRIPTION / COMPLEX (TRANSFERASE-RNA) / TRANSFERASE-RNA complex | ||||||
Function / homology | Function and homology information regulation of mRNA 3'-end processing / 7-methylguanosine mRNA capping / translation elongation factor activity / virion component / methyltransferase cap1 / mRNA (nucleoside-2'-O-)-methyltransferase activity / RNA binding Similarity search - Function | ||||||
Biological species | Vaccinia virus WR | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR / Resolution: 2.8 Å | ||||||
Authors | Hodel, A.E. / Gershon, P.D. / Quiocho, F.A. | ||||||
Citation | Journal: Mol.Cell / Year: 1998 Title: Structural basis for sequence-nonspecific recognition of 5'-capped mRNA by a cap-modifying enzyme. Authors: Hodel, A.E. / Gershon, P.D. / Quiocho, F.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1av6.cif.gz | 77.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1av6.ent.gz | 61.6 KB | Display | PDB format |
PDBx/mmJSON format | 1av6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/av/1av6 ftp://data.pdbj.org/pub/pdb/validation_reports/av/1av6 | HTTPS FTP |
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-Related structure data
Related structure data | 1vptS 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: RNA chain | Mass: 1946.277 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source |
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#2: Protein | Mass: 34573.008 Da / Num. of mol.: 1 / Mutation: C-TERMINAL DELETION OF 26 RESIDUES Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vaccinia virus WR / Genus: Orthopoxvirus / Strain: Western Reserve / Gene: PAPS, VACWR095, F9 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / Keywords: MUTATION:C-TERMINAL DELETION OF 26 RESIDUES / References: UniProt: P07617, methyltransferase cap1 |
#3: Chemical | ChemComp-MGT / |
#4: Chemical | ChemComp-SAH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 56 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8.5 / Details: pH 8.50 | ||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / Details: used to seeding / pH: 7 | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 103 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Aug 15, 1997 / Details: GOBEL MIRROR |
Radiation | Monochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.7→20 Å / Num. obs: 9755 / % possible obs: 92 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Biso Wilson estimate: 27 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 20 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 2 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 6 |
Reflection | *PLUS Highest resolution: 2.7 Å / Lowest resolution: 20 Å / % possible obs: 92 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Num. measured all: 22144 / Biso Wilson estimate: 27 Å2 |
Reflection shell | *PLUS Highest resolution: 2.7 Å / Lowest resolution: 2.8 Å / Redundancy: 2 % / Mean I/σ(I) obs: 6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR Starting model: PDB ENTRY 1VPT Resolution: 2.8→8 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.0001 / Isotropic thermal model: GROUP / Cross valid method: FREE-R / σ(F): 2 Details: SINGLE PHOSPHATE LINKS BETWEEN RESIDUES ARE PHOSPHOROTHIOATE, I.E., M7GPPPG-PS-A-PS-A-PS-A-PS-A-PS-A. PHOSPHOROTHIOLATES ARE LEFT AS PHOSPHATE IN THIS INITIAL DEPOSITION.
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Displacement parameters | Biso mean: 13 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→8 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 8 Å / σ(F): 2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 13 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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