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Yorodumi- PDB-6wog: Diphosphoinositol polyphosphate phosphohydrolase 1 (DIPP1/NUDT3) ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6wog | ||||||
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Title | Diphosphoinositol polyphosphate phosphohydrolase 1 (DIPP1/NUDT3) in complex with 5-methylenebisphosphonate inositol pentakisphosphate (5-PCP-IP5) | ||||||
Components | Diphosphoinositol polyphosphate phosphohydrolase 1 | ||||||
Keywords | HYDROLASE / phosphatase / nudix / catalysis mechanism / Substrate Specificity / inositol / inositol pyrophosphate | ||||||
Function / homology | Function and homology information diphosphoinositol polyphosphate catabolic process / inositol diphosphate pentakisphosphate diphosphatase activity / inositol-3,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 5-diphosphatase activity / inositol diphosphate tetrakisphosphate diphosphatase activity / inositol-5-diphosphate-1,2,3,4,6-pentakisphosphate diphosphatase activity / endopolyphosphatase / diadenosine polyphosphate catabolic process / 5'-(N7-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase / endopolyphosphatase activity / bis(5'-adenosyl)-hexaphosphatase activity ...diphosphoinositol polyphosphate catabolic process / inositol diphosphate pentakisphosphate diphosphatase activity / inositol-3,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 5-diphosphatase activity / inositol diphosphate tetrakisphosphate diphosphatase activity / inositol-5-diphosphate-1,2,3,4,6-pentakisphosphate diphosphatase activity / endopolyphosphatase / diadenosine polyphosphate catabolic process / 5'-(N7-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase / endopolyphosphatase activity / bis(5'-adenosyl)-hexaphosphatase activity / bis(5'-adenosyl)-pentaphosphatase activity / diphosphoinositol polyphosphate metabolic process / RNA decapping / diadenosine pentaphosphate catabolic process / diadenosine hexaphosphate catabolic process / adenosine 5'-(hexahydrogen pentaphosphate) catabolic process / diphosphoinositol-polyphosphate diphosphatase / diphosphoinositol-polyphosphate diphosphatase activity / 5'-(N(7)-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase activity / diadenosine hexaphosphate hydrolase (ATP-forming) / Synthesis of pyrophosphates in the cytosol / 5'-(N7-methylguanosine 5'-triphospho)-[mRNA] hydrolase / 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity / cell-cell signaling / manganese ion binding / magnesium ion binding / zinc ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.5 Å | ||||||
Authors | Zong, G.N. / Wang, H.C. / Shears, S.B. | ||||||
Funding support | United States, 1items
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Citation | Journal: Faseb J. / Year: 2021 Title: New structural insights reveal an expanded reaction cycle for inositol pyrophosphate hydrolysis by human DIPP1. Authors: Zong, G. / Jork, N. / Hostachy, S. / Fiedler, D. / Jessen, H.J. / Shears, S.B. / Wang, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6wog.cif.gz | 79.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6wog.ent.gz | 56.4 KB | Display | PDB format |
PDBx/mmJSON format | 6wog.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wo/6wog ftp://data.pdbj.org/pub/pdb/validation_reports/wo/6wog | HTTPS FTP |
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-Related structure data
Related structure data | 6wo7C 6wo8C 6wo9C 6woaC 6wobC 6wocC 6wodC 6woeC 6wofC 6wohC 6woiC 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: 19542.922 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NUDT3, DIPP, DIPP1 / Production host: Escherichia coli (E. coli) References: UniProt: O95989, diphosphoinositol-polyphosphate diphosphatase, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides |
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#2: Chemical | ChemComp-5A3 / |
#3: Chemical | ChemComp-SO4 / |
#4: 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: 2.13 Å3/Da / Density % sol: 42.36 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 200 mM Li2SO4, 18% (w/v) PEG 8000, 5% (v/v) isopropanol, 100mM NaAc, pH 4.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Jun 7, 2019 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.5→50 Å / Num. obs: 27490 / % possible obs: 99.3 % / Redundancy: 8 % / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.017 / Rrim(I) all: 0.049 / Χ2: 0.983 / Net I/σ(I): 13.5 / Num. measured all: 218627 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.5→27.7 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.527 / SU ML: 0.042 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.071 / ESU R Free: 0.065 / 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: 73.8 Å2 / Biso mean: 17.211 Å2 / Biso min: 7.17 Å2
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Refinement step | Cycle: final / Resolution: 1.5→27.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.539 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 5.9456 Å / Origin y: 7.3464 Å / Origin z: 13.7001 Å
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