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- PDB-8jb3: Structure and allosteric regulation of the inosine 5'-monophospha... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8jb3 | |||||||||
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Title | Structure and allosteric regulation of the inosine 5'-monophosphate-specific phosphatase ISN1 from Saccharomyces cerevisiae | |||||||||
![]() | IMP-specific 5'-nucleotidase 1 | |||||||||
![]() | ![]() ![]() ![]() | |||||||||
Function / homology | ![]() nicotinamide riboside biosynthetic process / nicotinic acid riboside biosynthetic process / inosine salvage / IMP-specific 5'-nucleotidase / ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Byun, S.J. / Rhee, S. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure, cooperativity and inhibition of the inosine 5'-monophosphate-specific phosphatase from Saccharomyces cerevisiae. Authors: Byun, S. / Park, C. / Suh, J.Y. / Witte, C.P. / Rhee, S. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 128.8 KB | Display | ![]() |
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PDB format | ![]() | 78.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8j6hC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 52335.164 Da / Num. of mol.: 1 / Mutation: D172A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Strain: BL21(DE3) / Gene: ISN1, YOR155C, O3548 / Variant: DELTA4R / Plasmid: pET41a / Cell line (production host): Escherichia coli / Production host: ![]() ![]() ![]() |
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-Non-polymers , 5 types, 194 molecules ![](data/chem/img/NOS.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/IMP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/IMP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-NOS / ![]() | ||
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#3: Chemical | ChemComp-PO4 / ![]() | ||
#4: Chemical | ChemComp-IMP / ![]() | ||
#5: Chemical | #6: Water | ChemComp-HOH / | ![]() |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.54 Å3/Da / Density % sol: 65.29 % |
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Crystal grow![]() | Temperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 0.7 M ammonium dihydrogen phosphate, 0.07 M sodium citrate (pH 5.6), 30% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 11, 2020 |
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.75→50 Å / Num. obs: 72288 / % possible obs: 99.9 % / Redundancy: 13.6 % / Biso Wilson estimate: 33.3265142755 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.09 / Net I/σ(I): 19.3 |
Reflection shell | Resolution: 1.75→1.81 Å / Num. unique obs: 7534 / CC1/2: 0.38 |
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Processing
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Refinement | Method to determine structure![]() ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.3334018587 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.77382458733→31.4654581115 Å
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Refine LS restraints |
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LS refinement shell |
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