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- PDB-8dhj: Crystal structure of Clostridioides difficile Protein Tyrosine Ph... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8dhj | ||||||
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Title | Crystal structure of Clostridioides difficile Protein Tyrosine Phosphatase at pH 7.5 | ||||||
![]() | TYR_PHOSPHATASE_2 domain-containing protein | ||||||
![]() | HYDROLASE / phosphatase | ||||||
Function / homology | Tyrosine/serine-protein phosphatase IphP-type / Tyrosine phosphatase family / phosphoprotein phosphatase activity / dephosphorylation / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / Tyrosine specific protein phosphatases domain-containing protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lountos, G.T. / Tropea, J.E. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of Clostridioides difficile Protein Tyrosine Phosphatase at pH 7.5 Authors: Lountos, G.T. / Tropea, J.E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 222 KB | Display | ![]() |
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PDB format | ![]() | 175.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 977.1 KB | Display | ![]() |
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Full document | ![]() | 978.9 KB | Display | |
Data in XML | ![]() | 24.8 KB | Display | |
Data in CIF | ![]() | 37.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1ywfS 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 28969.008 Da / Num. of mol.: 2 Mutation: First three glycine residues are non-native, remnants of linker Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Plasmid: pJT510 / Production host: ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-CL / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.83 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M HEPES pH 7.5, 0.2 magnesium chloride, 25% (w/v) polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Jun 18, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.48→50 Å / Num. obs: 82376 / % possible obs: 98.8 % / Redundancy: 2.6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.035 / Net I/σ(I): 19.5 |
Reflection shell | Resolution: 1.48→1.5 Å / Rmerge(I) obs: 0.531 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4129 / CC1/2: 0.679 / Rpim(I) all: 0.41 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1YWF Resolution: 1.483→36.229 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 18.67 / 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: 129.47 Å2 / Biso mean: 21.2777 Å2 / Biso min: 5.77 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.483→36.229 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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