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Yorodumi- PDB-7aul: Yeast Diphosphoinositol Polyphosphate Phosphohydrolase DDP1 in co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7aul | ||||||
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Title | Yeast Diphosphoinositol Polyphosphate Phosphohydrolase DDP1 in complex with 5-InsP7 in presence of Mg | ||||||
Components | Diphosphoinositol polyphosphate phosphohydrolase DDP1 | ||||||
Keywords | HYDROLASE / Inositol / PP-InsP / Pyrophosphatase / Polyphosphate / Diadenosine polyphosphate / DDP1 / Nudix | ||||||
Function / homology | Function and homology information diadenosine hexaphosphate hydrolase (AMP-forming) / Synthesis of pyrophosphates in the cytosol / polyphosphate catabolic process / endopolyphosphatase / diadenosine polyphosphate catabolic process / endopolyphosphatase activity / bis(5'-adenosyl)-hexaphosphatase activity / diphosphoinositol polyphosphate metabolic process / diadenosine pentaphosphate catabolic process / diadenosine hexaphosphate catabolic process ...diadenosine hexaphosphate hydrolase (AMP-forming) / Synthesis of pyrophosphates in the cytosol / polyphosphate catabolic process / endopolyphosphatase / diadenosine polyphosphate catabolic process / endopolyphosphatase activity / bis(5'-adenosyl)-hexaphosphatase activity / diphosphoinositol polyphosphate metabolic process / diadenosine pentaphosphate catabolic process / diadenosine hexaphosphate catabolic process / adenosine 5'-(hexahydrogen pentaphosphate) catabolic process / phosphodiesterase decapping endonuclease activity / diphosphoinositol-polyphosphate diphosphatase / diphosphoinositol-polyphosphate diphosphatase activity / bis(5'-adenosyl)-pentaphosphatase activity / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.85 Å | ||||||
Authors | Marquez-Monino, M.A. / Gonzalez, B. | ||||||
Funding support | Spain, 1items
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Citation | Journal: Sci Adv / Year: 2021 Title: Multiple substrate recognition by yeast diadenosine and diphosphoinositol polyphosphate phosphohydrolase through phosphate clamping. Authors: Marquez-Monino, M.A. / Ortega-Garcia, R. / Shipton, M.L. / Franco-Echevarria, E. / Riley, A.M. / Sanz-Aparicio, J. / Potter, B.V.L. / Gonzalez, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7aul.cif.gz | 53.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7aul.ent.gz | 37 KB | Display | PDB format |
PDBx/mmJSON format | 7aul.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7aul_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 7aul_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 7aul_validation.xml.gz | 9.7 KB | Display | |
Data in CIF | 7aul_validation.cif.gz | 12.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/au/7aul ftp://data.pdbj.org/pub/pdb/validation_reports/au/7aul | HTTPS FTP |
-Related structure data
Related structure data | 7auiC 7aujC 7aukSC 7aumC 7aunC 7auoC 7aupC 7auqC 7aurC 7ausC 7autC 7auuC C: citing same article (ref.) 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 21812.713 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: GGS is a rest of purification linker, protein starts in MGK. Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: DDP1, YOR163W, O3575 / Plasmid: pKLSLt / Production host: Escherichia coli (E. coli) / Strain (production host): Rossetta2(DE3) References: UniProt: Q99321, diphosphoinositol-polyphosphate diphosphatase, diadenosine hexaphosphate hydrolase (AMP-forming) |
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#2: Chemical | ChemComp-I7P / ( |
#3: Chemical | ChemComp-ACT / |
#4: Chemical | ChemComp-MG / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.14 % / Description: Hexagonal prism |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 25% PEG 3350, 0.1 M Sodium acetate pH 4.5, 0.1 M NaCl, 5 mM Magnesium chloride. Protein buffer: 20 mM Tris pH 8.0, 150 mM NaCl, 1 mM DTT, 5 mM 5-InsP7. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 16, 2020 / Details: KB focusing mirrors |
Radiation | Monochromator: Si(111) channel-cut, cryocooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97926 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→47.99 Å / Num. obs: 18607 / % possible obs: 100 % / Redundancy: 15.2 % / Biso Wilson estimate: 32.802 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.021 / Net I/σ(I): 17.9 |
Reflection shell | Resolution: 1.85→1.89 Å / Redundancy: 13.6 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 1124 / CC1/2: 0.914 / Rpim(I) all: 0.183 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 7AUK Resolution: 1.85→46.69 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.927 / SU B: 4.38 / SU ML: 0.132 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.175 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 122.81 Å2 / Biso mean: 46.413 Å2 / Biso min: 24.25 Å2
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Refinement step | Cycle: final / Resolution: 1.85→46.69 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.898 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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