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- PDB-4fyg: Structural basis for substrate recognition by a novel Legionella ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4fyg | ||||||
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Title | Structural basis for substrate recognition by a novel Legionella phosphoinositide phosphatase | ||||||
![]() | SidF, inhibitor of growth family, member 3 | ||||||
![]() | HYDROLASE / mixed alpha-beta / phosphoinositide phosphatase / phosphoinositides / membrane | ||||||
Function / homology | : / Phosphoinositide phosphatase / phosphatidylinositol phosphate phosphatase activity / membrane / Chem-3PT / 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 | ![]() | 308.9 KB | Display | ![]() |
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PDB format | ![]() | 253 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 744.6 KB | Display | ![]() |
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Full document | ![]() | 765.8 KB | Display | |
Data in XML | ![]() | 29.5 KB | Display | |
Data in CIF | ![]() | 39.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4fyeC ![]() 4fyfSC C: citing same article ( S: Starting model for refinement |
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Similar 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 (UNP Residues 1-760) 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-3PT / ( |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.95 Å3/Da / Density % sol: 58.31 % |
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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 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Feb 4, 2012 / Details: mirrors |
Radiation | Monochromator: Single crystal bender / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9789 Å / Relative weight: 1 |
Reflection | Resolution: 2.82→50 Å / Num. all: 301119 / Num. obs: 24387 / % possible obs: 96.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 12.3 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 28.6 |
Reflection shell | Resolution: 2.82→2.9 Å / % possible all: 78.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 4FYF Resolution: 2.822→36.58 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.91 / SU B: 30.281 / SU ML: 0.272 / Cross valid method: THROUGHOUT / ESU R Free: 0.375 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 70.396 Å2
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Refinement step | Cycle: LAST / Resolution: 2.822→36.58 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.822→2.895 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -2.5584 Å / Origin y: 45.7343 Å / Origin z: 21.9739 Å
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