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Open data
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Basic information
Entry | Database: PDB / ID: 5d2u | ||||||
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Title | Crystal structure of tPphA Variant - H39A | ||||||
![]() | Protein serin-threonin phosphatase | ||||||
![]() | METAL BINDING PROTEIN / PP2C type phosphatase | ||||||
Function / homology | ![]() negative regulation of stress-activated MAPK cascade / protein serine/threonine phosphatase activity / protein-serine/threonine phosphatase / negative regulation of canonical NF-kappaB signal transduction / positive regulation of canonical Wnt signaling pathway / positive regulation of canonical NF-kappaB signal transduction / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Su, J. | ||||||
![]() | ![]() Title: Structural and Biochemical Characterization of a Cyanobacterial PP2C Phosphatase Reveals Insights into Catalytic Mechanism and Substrate Recognition Authors: Si, Y. / Yuan, Y. / Wang, Y. / Gao, J. / Hu, Y. / Feng, S. / Su, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 63.8 KB | Display | ![]() |
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PDB format | ![]() | 44.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 431.8 KB | Display | ![]() |
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Full document | ![]() | 433.5 KB | Display | |
Data in XML | ![]() | 11.9 KB | Display | |
Data in CIF | ![]() | 16.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5itiC ![]() 2xzvS S: Starting model for refinement C: citing same article ( |
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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: 26952.182 Da / Num. of mol.: 1 / Mutation: H39A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: BP-1 / Gene: tlr2243 / Production host: ![]() ![]() | ||
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#2: Chemical | ChemComp-CA / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.26 % |
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Crystal grow | Temperature: 298 K / Method: batch mode Details: 100mM Tris-HCl, pH 7.4, 200mM CaCl2, 26%(v/v) PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 1, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→19.23 Å / Num. obs: 105414 / % possible obs: 99.8 % / Redundancy: 6.2 % / Net I/σ(I): 19 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2XZV Resolution: 1.8→19.23 Å / SU ML: 0.24 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 29 / Stereochemistry target values: ML
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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 max: 93.14 Å2 / Biso mean: 37.4581 Å2 / Biso min: 16.93 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.8→19.23 Å
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