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- PDB-7sdb: Structure of the PTP-like myo-inositol phosphatase from Legionell... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7sdb | ||||||
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Title | Structure of the PTP-like myo-inositol phosphatase from Legionella pneumophila str. Paris in complex with myo-inositol hexakisphosphate | ||||||
![]() | Myo-inositol phosphohydrolase | ||||||
![]() | HYDROLASE / Phytase / PTP fold / myo-inositol phosphate / effector protein | ||||||
Function / homology | dephosphorylation / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Protein-tyrosine phosphatase-like / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / INOSITOL HEXAKISPHOSPHATE / Tyrosine phosphatase II superfamily protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Cleland, C.P. / Mosimann, S.C. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of the PTP-like myo-inositol phosphatase from Legionella pneumophila str. Paris in complex with myo-inositol hexakisphosphate Authors: Cleland, C.P. / Mosimann, S.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 162.9 KB | Display | ![]() |
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PDB format | ![]() | 102.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 932.5 KB | Display | ![]() |
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Full document | ![]() | 933.7 KB | Display | |
Data in XML | ![]() | 16.9 KB | Display | |
Data in CIF | ![]() | 26.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4tvvS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 36026.867 Da / Num. of mol.: 1 / Mutation: C231S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: hopD2, NCTC12000_03020 / Plasmid: pET28b / Production host: ![]() ![]() References: UniProt: A0A378K9X8, protein-tyrosine-phosphatase |
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#2: Chemical | ChemComp-IHP / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 51.96 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: 100 mM Tris HCl (7.4), 12% PEG 4000, 40 mM magnesium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SEALED TUBE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.5418 Å |
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jul 16, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→24.08 Å / Num. obs: 25244 / % possible obs: 97.5 % / Redundancy: 3.5 % / Biso Wilson estimate: 15.14 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 17.81 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.198 / Num. unique obs: 2528 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4TVV Resolution: 2→24.08 Å / SU ML: 0.1607 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.754 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.02 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→24.08 Å
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Refine LS restraints |
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LS refinement shell |
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