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- PDB-5vr6: Structure of Human Sts-1 histidine phosphatase domain with sulfat... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5vr6 | ||||||
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Title | Structure of Human Sts-1 histidine phosphatase domain with sulfate bound | ||||||
![]() | Ubiquitin-associated and SH3 domain-containing protein B | ||||||
![]() | HYDROLASE / T-Cell Receptor / histidine phosphatase / protein tyrosine phosphatase / Zap-70 | ||||||
Function / homology | ![]() regulation of osteoclast differentiation / collagen-activated tyrosine kinase receptor signaling pathway / negative regulation of platelet aggregation / regulation of release of sequestered calcium ion into cytosol / negative regulation of bone resorption / negative regulation of osteoclast differentiation / negative regulation of signal transduction / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / phosphoprotein binding ...regulation of osteoclast differentiation / collagen-activated tyrosine kinase receptor signaling pathway / negative regulation of platelet aggregation / regulation of release of sequestered calcium ion into cytosol / negative regulation of bone resorption / negative regulation of osteoclast differentiation / negative regulation of signal transduction / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / phosphoprotein binding / platelet aggregation / ubiquitin protein ligase binding / identical protein binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Zhou, W. / Yin, Y. / Weinheimer, A.W. / Kaur, N. / Carpino, N. / French, J.B. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural and Functional Characterization of the Histidine Phosphatase Domains of Human Sts-1 and Sts-2. Authors: Zhou, W. / Yin, Y. / Weinheimer, A.S. / Kaur, N. / Carpino, N. / French, J.B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 125.7 KB | Display | ![]() |
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PDB format | ![]() | 96.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 448.1 KB | Display | ![]() |
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Full document | ![]() | 449.1 KB | Display | |
Data in XML | ![]() | 23.9 KB | Display | |
Data in CIF | ![]() | 34.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5w5gC ![]() 5wdiC ![]() 2h0qS 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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Unit cell |
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Components
#1: Protein | Mass: 29981.387 Da / Num. of mol.: 2 / Fragment: UNP Residues 384-649 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.39 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 22 - 25% PEG 2000 MME 200 mM Ammonium Sulfate 0.1 M Sodium Acetate PH range: 5 - 5.75 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 13, 2016 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.87→50 Å / Num. obs: 41518 / % possible obs: 94.4 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.037 / Rrim(I) all: 0.086 / Χ2: 0.601 / Net I/σ(I): 4.9 / Num. measured all: 211226 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2H0Q Resolution: 1.87→50 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.931 / SU B: 4.354 / SU ML: 0.125 / Cross valid method: THROUGHOUT / ESU R: 0.175 / ESU R Free: 0.159 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.628 Å2
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Refinement step | Cycle: 1 / Resolution: 1.87→50 Å
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Refine LS restraints |
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