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Yorodumi- PDB-7btn: Crystal structure of human inorganic pyrophosphatase with metal ions -
+Open data
-Basic information
Entry | Database: PDB / ID: 7btn | ||||||
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Title | Crystal structure of human inorganic pyrophosphatase with metal ions | ||||||
Components | Inorganic pyrophosphatase | ||||||
Keywords | HYDROLASE / Complex / Monomer | ||||||
Function / homology | Function and homology information Pyrophosphate hydrolysis / inorganic diphosphatase / Cytosolic tRNA aminoacylation / inorganic diphosphate phosphatase activity / phosphate-containing compound metabolic process / magnesium ion binding / extracellular exosome / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.382 Å | ||||||
Authors | Hu, F. / Huang, Z. / Li, L. | ||||||
Funding support | China, 1items
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Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2020 Title: Structural and biochemical characterization of inorganic pyrophosphatase from Homo sapiens. Authors: Hu, F. / Huang, Z. / Zheng, S. / Wu, Q. / Chen, Y. / Lin, H. / Huang, W. / Li, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7btn.cif.gz | 72.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7btn.ent.gz | 50.6 KB | Display | PDB format |
PDBx/mmJSON format | 7btn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7btn_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 7btn_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 7btn_validation.xml.gz | 12.7 KB | Display | |
Data in CIF | 7btn_validation.cif.gz | 16.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bt/7btn ftp://data.pdbj.org/pub/pdb/validation_reports/bt/7btn | HTTPS FTP |
-Related structure data
Related structure data | 7cmoC 1m38S 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: 35110.676 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PPA1, IOPPP, PP / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q15181, inorganic diphosphatase | ||||
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#2: Chemical | #3: 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: 2.79 Å3/Da / Density % sol: 55.91 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / Details: 20% PEG4000, 50mM magnesium acetate, pH 5.5 |
-Data collection
Diffraction | Mean temperature: 200 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.987 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 17, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 2.382→19.771 Å / Num. obs: 14729 / % possible obs: 99.6005 % / Redundancy: 1.71 % / CC1/2: 0.998 / Net I/σ(I): 1.71 |
Reflection shell | Resolution: 2.382→2.467 Å / CC1/2: 0.998 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1M38 Resolution: 2.382→19.771 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 21.09
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 97.12 Å2 / Biso mean: 39.8589 Å2 / Biso min: 19.27 Å2 | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.382→19.771 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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