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Open data
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Basic information
Entry | Database: PDB / ID: 8pno | ||||||
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Title | The MgF3(H2O) transition state analog complex of E. coli YihX | ||||||
![]() | Alpha-D-glucose 1-phosphate phosphatase YihX | ||||||
![]() | HYDROLASE / phosphatase / HAD superfamily / transition state analog complex | ||||||
Function / homology | ![]() glucose-1-phosphatase / glucose-1-phosphatase activity / manganese ion binding / magnesium ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Baumann, P. / Zappala, D. / Jin, Y. | ||||||
Funding support | ![]()
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![]() | ![]() Title: The MgF3(H2O)- transition state analog complex of E. coli YihX Authors: Baumann, P. / Zappala, D. / Jin, Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 103.6 KB | Display | ![]() |
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PDB format | ![]() | 77.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.8 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 20 KB | Display | |
Data in CIF | ![]() | 28.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 23139.189 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 9 types, 246 molecules ![](data/chem/img/PEG.gif)
![](data/chem/img/KQB.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/IMD.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/KQB.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/IMD.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-PG4 / | #5: Chemical | ChemComp-IMD / | #6: Chemical | #7: Chemical | #8: Chemical | #9: Chemical | #10: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.43 Å3/Da / Density % sol: 71.97 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 20 mg/mL YihX in Tris-HCl 25 mM pH 7.5, NaCl 150 mM, MgCl2 20 mM, NaF 30 mM was mixed 1:1 ratio with precipitant containing MES 55.5 mM, imidazole 44.5 mM pH 6.5, 20% PEG500, 30 mM MgCl2, 30 ...Details: 20 mg/mL YihX in Tris-HCl 25 mM pH 7.5, NaCl 150 mM, MgCl2 20 mM, NaF 30 mM was mixed 1:1 ratio with precipitant containing MES 55.5 mM, imidazole 44.5 mM pH 6.5, 20% PEG500, 30 mM MgCl2, 30 mM CaCl2, 20% glycerol, 10% PEG4000. The crystals are further soaked with the precipitant supplemented with 50 mM MgCl2 and 100 mM NH4F |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Apr 30, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→58.97 Å / Num. obs: 40811 / % possible obs: 100 % / Redundancy: 6.9 % / CC1/2: 0.992 / Net I/σ(I): 5.8 |
Reflection shell | Resolution: 2.2→2.27 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 3532 / CC1/2: 0.664 |
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Processing
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Refinement | Method to determine structure: ![]()
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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 mean: 38.806 Å2
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Refinement step | Cycle: 1 / Resolution: 2.2→59.04 Å
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Refine LS restraints |
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