+Open data
-Basic information
Entry | Database: PDB / ID: 1jte | ||||||
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Title | Crystal Structure Analysis of VP39 F180W mutant | ||||||
Components | VP39 | ||||||
Keywords | TRANSFERASE / VP39 / mRNA Cap-binding protein / methyltransferase / mutant | ||||||
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 | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2 Å | ||||||
Authors | Hu, G. / Oguro, A. / Gershon, P.D. / Quiocho, F.A. | ||||||
Citation | Journal: Biochemistry / Year: 2002 Title: The "cap-binding slot" of an mRNA cap-binding protein: quantitative effects of aromatic side chain choice in the double-stacking sandwich with cap. Authors: Hu, G. / Oguro, A. / Li, C. / 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 | 1jte.cif.gz | 67.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jte.ent.gz | 53.4 KB | Display | PDB format |
PDBx/mmJSON format | 1jte.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jt/1jte ftp://data.pdbj.org/pub/pdb/validation_reports/jt/1jte | HTTPS FTP |
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-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: 35960.473 Da / Num. of mol.: 1 / Fragment: residues 1-307 / Mutation: F180W Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vaccinia virus / Genus: Orthopoxvirus / Plasmid: pPG177 / Production host: Escherichia coli (E. coli) References: UniProt: P07617, polynucleotide adenylyltransferase |
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#2: Chemical | ChemComp-SAH / |
#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: 2.83 Å3/Da / Density % sol: 56.47 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: PEG 8000, sodium citrate, ammonium sulphate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K | ||||||||||||||||||||||||
Crystal grow | *PLUS Method: unknownDetails: Hodel, A.E., (1996) Cell(Cambridge,Mass.), 85, 247. | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: SIEMENS / Detector: CCD / Date: Nov 2, 1998 / Details: mirrors |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 23580 / Num. obs: 23570 / % possible obs: 87.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 2→2.09 Å / % possible all: 50 |
Reflection | *PLUS Rmerge(I) obs: 0.07 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2→8 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.09 Å / Rfactor Rfree error: 0.01
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Refinement | *PLUS % reflection Rfree: 10 % / Rfactor all: 0.245 / Rfactor obs: 0.242 / Rfactor Rfree: 0.285 / Rfactor Rwork: 0.232 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2 Å / Rfactor Rfree: 0.33 / Rfactor Rwork: 0.28 |