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Yorodumi- PDB-8jb3: Structure and allosteric regulation of the inosine 5'-monophospha... -
+Open data
-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 | |||||||||
Components | IMP-specific 5'-nucleotidase 1 | |||||||||
Keywords | HYDROLASE / hydrolysis / phosphatase | |||||||||
Function / homology | Function and homology information nicotinamide riboside biosynthetic process / nicotinic acid riboside biosynthetic process / inosine salvage / IMP-specific 5'-nucleotidase / IMP 5'-nucleotidase activity / nucleotide metabolic process / magnesium ion binding / ATP binding Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.77382458733 Å | |||||||||
Authors | Byun, S.J. / Rhee, S. | |||||||||
Funding support | Korea, Republic Of, 2items
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Citation | Journal: Febs J. / Year: 2024 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8jb3.cif.gz | 128.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8jb3.ent.gz | 78.7 KB | Display | PDB format |
PDBx/mmJSON format | 8jb3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8jb3_validation.pdf.gz | 2.4 MB | Display | wwPDB validaton report |
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Full document | 8jb3_full_validation.pdf.gz | 2.4 MB | Display | |
Data in XML | 8jb3_validation.xml.gz | 18.8 KB | Display | |
Data in CIF | 8jb3_validation.cif.gz | 27 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jb/8jb3 ftp://data.pdbj.org/pub/pdb/validation_reports/jb/8jb3 | HTTPS FTP |
-Related structure data
Related structure data | 8j6hC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-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.) Saccharomyces cerevisiae (brewer's yeast) Strain: BL21(DE3) / Gene: ISN1, YOR155C, O3548 / Variant: DELTA4R / Plasmid: pET41a / Cell line (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): DELTA4R / References: UniProt: Q99312, IMP-specific 5'-nucleotidase |
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-Non-polymers , 5 types, 194 molecules
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97954 Å |
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: 0.97954 Å / Relative weight: 1 |
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 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.77382458733→31.4654581115 Å / SU ML: 0.264342707946 / Cross valid method: FREE R-VALUE / σ(F): 1.32593671838 / Phase error: 31.0746381815
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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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