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- PDB-4fye: Crystal structure of a Legionella phosphoinositide phosphatase, SidF -
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Open data
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Basic information
Entry | Database: PDB / ID: 4fye | ||||||
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Title | Crystal structure of a Legionella phosphoinositide phosphatase, SidF | ||||||
![]() | SidF, inhibitor of growth family, member 3 | ||||||
![]() | HYDROLASE / mixed alpha-beta / phosphatase / phosphoinositides / membrane | ||||||
Function / homology | : / Phosphoinositide phosphatase / phosphatidylinositol phosphate phosphatase activity / membrane / PHOSPHATE ION / SidF, inhibitor of growth family, member 3![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hsu, F.S. / Zhu, W. / Brennan, L. / Tao, L. / Luo, Z.Q. / Mao, Y. | ||||||
![]() | ![]() Title: Structural basis for substrate recognition by a unique Legionella phosphoinositide phosphatase. Authors: Hsu, F. / Zhu, W. / Brennan, L. / Tao, L. / Luo, Z.Q. / Mao, 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 | ![]() | 301.5 KB | Display | ![]() |
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PDB format | ![]() | 247.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 448 KB | Display | ![]() |
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Full document | ![]() | 474.1 KB | Display | |
Data in XML | ![]() | 28.7 KB | Display | |
Data in CIF | ![]() | 39.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 86191.359 Da / Num. of mol.: 1 / Fragment: N-terminal phosphatase domain of SidF / Mutation: C645S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: lpg2584, sidF / Plasmid: PET28a / Production host: ![]() ![]() References: UniProt: Q5ZSD5, phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase |
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#2: Chemical | ChemComp-PO4 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.02 Å3/Da / Density % sol: 59.21 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.1 M Tris-HCl pH8.0, 10% PEG3350, and 10% ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 1, 2012 / Details: Mirrors |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9789 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→84.767 Å / Num. obs: 40455 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 14.8 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 27.3 |
Reflection shell | Resolution: 2.4→2.49 Å / % possible all: 99.9 |
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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: 67.922 Å2
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Refinement step | Cycle: LAST / Resolution: 2.413→84.767 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.413→2.475 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -1.8238 Å / Origin y: 45.7536 Å / Origin z: 22.3393 Å
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