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Yorodumi- PDB-7auo: Yeast Diphosphoinositol Polyphosphate Phosphohydrolase DDP1 in co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7auo | ||||||
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Title | Yeast Diphosphoinositol Polyphosphate Phosphohydrolase DDP1 in complex with PA-InsP8 | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.65 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 | 7auo.cif.gz | 80.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7auo.ent.gz | 60.4 KB | Display | PDB format |
PDBx/mmJSON format | 7auo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7auo_validation.pdf.gz | 818.2 KB | Display | wwPDB validaton report |
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Full document | 7auo_full_validation.pdf.gz | 819.6 KB | Display | |
Data in XML | 7auo_validation.xml.gz | 7.8 KB | Display | |
Data in CIF | 7auo_validation.cif.gz | 9.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/au/7auo ftp://data.pdbj.org/pub/pdb/validation_reports/au/7auo | HTTPS FTP |
-Related structure data
Related structure data | 7auiSC 7aujC 7aukC 7aulC 7aumC 7aunC 7aupC 7auqC 7aurC 7ausC 7autC 7auuC S: Starting model for refinement C: citing same article (ref.) |
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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
#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-4WY / {[( |
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: 2.25 Å3/Da / Density % sol: 45.36 % / Description: Bipyramid |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 25% PEG 6000, 0.1 M Sodium acetate pH 5.0, 0.1 M NaCl. Protein:precipitant ratio 2:1. Protein buffer: 20 mM Tris pH 8.0, 150 mM NaCl, 1 mM DTT, 10 mM PA-InsP8. |
-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: Feb 28, 2019 / 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: 2.65→45.87 Å / Num. obs: 6055 / % possible obs: 99.8 % / Redundancy: 18 % / Biso Wilson estimate: 80.07 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.014 / Net I/σ(I): 25.1 |
Reflection shell | Resolution: 2.65→2.78 Å / Redundancy: 19.1 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 5.3 / Num. unique obs: 799 / CC1/2: 0.972 / Rpim(I) all: 0.152 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7AUI Resolution: 2.65→45.87 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.925 / SU B: 44.843 / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.826 / ESU R Free: 0.342 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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: 181.42 Å2 / Biso mean: 106.396 Å2 / Biso min: 78.94 Å2
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Refinement step | Cycle: final / Resolution: 2.65→45.87 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.651→2.719 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 16.7699 Å / Origin y: -19.4254 Å / Origin z: -1.2799 Å
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