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- PDB-3d6a: Crystal structure of the 2H-phosphatase domain of Sts-2 in comple... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3d6a | ||||||
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Title | Crystal structure of the 2H-phosphatase domain of Sts-2 in complex with tungstate. | ||||||
![]() | Sts-2 protein | ||||||
![]() | HYDROLASE / 2H-phosphatase / PGM domain / tungstate / SH3 domain | ||||||
Function / homology | ![]() negative regulation of T cell receptor signaling pathway / regulation of cytokine production / nuclear speck / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chen, Y. / Carpino, N. / Nassar, N. | ||||||
![]() | ![]() Title: Structural and functional characterization of the 2H-phosphatase domain of Sts-2 reveals an acid-dependent phosphatase activity. Authors: Chen, Y. / Jakoncic, J. / Carpino, N. / Nassar, N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 219.1 KB | Display | ![]() |
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PDB format | ![]() | 177.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3d4iSC ![]() 3db1C 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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1 | ![]()
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2 | ![]()
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3 |
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Unit cell |
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Components
#1: Protein | Mass: 30716.334 Da / Num. of mol.: 4 / Fragment: PGM domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-NA / #4: Chemical | ChemComp-W / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.46 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.2 M Lithium sulfate, 0.1 M Tris-HCl, 5-20 mM Strontium chloride, 20% PEG8000, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 20, 2006 / Details: monochromator |
Radiation | Monochromator: Silicon 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→100 Å / Num. all: 53723 / Num. obs: 53273 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.5 % / Rmerge(I) obs: 0.098 |
Reflection shell | Resolution: 2.25→2.33 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.565 / Mean I/σ(I) obs: 2.5 / % possible all: 97.1 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 3d4i Resolution: 2.25→47.95 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.919 / SU B: 11.188 / SU ML: 0.167 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.348 / ESU R Free: 0.243 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.185 Å2
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Refinement step | Cycle: LAST / Resolution: 2.25→47.95 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.25→2.304 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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