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Open data
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Basic information
Entry | Database: PDB / ID: 1jsz | ||||||
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Title | Crystal Structure Analysis of N7,9-dimethylguanine-VP39 complex | ||||||
![]() | VP39 | ||||||
![]() | TRANSFERASE / VP39 / mRNA Cap-binding protein / methyltransferase | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Hu, G. / Oguro, A. / Gershon, P.D. / Quiocho, F.A. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 77.2 KB | Display | ![]() |
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PDB format | ![]() | 56.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 723.5 KB | Display | ![]() |
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Full document | ![]() | 729.3 KB | Display | |
Data in XML | ![]() | 15.1 KB | Display | |
Data in CIF | ![]() | 21.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 35921.438 Da / Num. of mol.: 1 / Fragment: residues 1-307 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P07617, polynucleotide adenylyltransferase |
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#2: Chemical | ChemComp-SAH / |
#3: Chemical | ChemComp-NDM / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.88 % | ||||||||||||||||||||||||
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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: ![]() |
Detector | Type: SIEMENS / Detector: CCD / Date: Jan 1, 1999 / 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: 1.93→50 Å / Num. all: 23277 / Num. obs: 22339 / % possible obs: 73.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 1.93→1.99 Å / % possible all: 50 |
Reflection | *PLUS Rmerge(I) obs: 0.081 |
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Processing
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Refinement | Method to determine structure: ![]()
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Refinement step | Cycle: LAST / Resolution: 1.93→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.93→1.99 Å / Rfactor Rfree error: 0.012
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Refinement | *PLUS % reflection Rfree: 10 % / Rfactor all: 0.224 / Rfactor obs: 0.214 / Rfactor Rfree: 0.252 / Rfactor Rwork: 0.21 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.36 / Rfactor Rwork: 0.32 |