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Yorodumi- PDB-9dj9: HUMAN VH1-RELATED DUAL-SPECIFICITY PHOSPHATASE (VHR) in distinct ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 9dj9 | |||||||||
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Title | HUMAN VH1-RELATED DUAL-SPECIFICITY PHOSPHATASE (VHR) in distinct apo form | |||||||||
Components | Dual specificity protein phosphatase 3 | |||||||||
Keywords | HYDROLASE / Phosphatase | |||||||||
Function / homology | Function and homology information MAP kinase phosphatase activity / negative regulation of chemotaxis / protein tyrosine/serine/threonine phosphatase activity / negative regulation of T cell activation / positive regulation of focal adhesion disassembly / negative regulation of JNK cascade / ERKs are inactivated / regulation of focal adhesion assembly / myosin phosphatase activity / negative regulation of T cell receptor signaling pathway ...MAP kinase phosphatase activity / negative regulation of chemotaxis / protein tyrosine/serine/threonine phosphatase activity / negative regulation of T cell activation / positive regulation of focal adhesion disassembly / negative regulation of JNK cascade / ERKs are inactivated / regulation of focal adhesion assembly / myosin phosphatase activity / negative regulation of T cell receptor signaling pathway / peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity / protein-serine/threonine phosphatase / dephosphorylation / negative regulation of epidermal growth factor receptor signaling pathway / phosphatase activity / immunological synapse / peptidyl-tyrosine dephosphorylation / negative regulation of MAPK cascade / cellular response to epidermal growth factor stimulus / cytoskeletal protein binding / positive regulation of mitotic cell cycle / protein-tyrosine-phosphatase / protein tyrosine kinase binding / negative regulation of cell migration / protein tyrosine phosphatase activity / receptor tyrosine kinase binding / negative regulation of ERK1 and ERK2 cascade / protein kinase binding / nucleoplasm / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.924 Å | |||||||||
Authors | Keedy, D.A. / Lemberikman, A.M. / Isiorho, E.A. / Aleshin, A.E. / Wu, J. / Lambert, L.J. / Cosford, N.D.P. / Tautz, L. | |||||||||
Funding support | United States, 2items
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Citation | Journal: To Be Published Title: Fragment Screening Platform and Discovery of Novel Fragment Binders of the VHR Phosphatase, a Drug Target for Sepsis and Septic Shock Authors: Wu, J. / Baranowski, M.R. / Aleshin, A.E. / Lambert, L.J. / Isiorho, E.A. / Lemberikman, A.M. / Keedy, D.A. / Cosford, N.D.P. / Tautz, L. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9dj9.cif.gz | 59.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9dj9.ent.gz | 34.2 KB | Display | PDB format |
PDBx/mmJSON format | 9dj9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9dj9_validation.pdf.gz | 422.2 KB | Display | wwPDB validaton report |
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Full document | 9dj9_full_validation.pdf.gz | 423.6 KB | Display | |
Data in XML | 9dj9_validation.xml.gz | 10.5 KB | Display | |
Data in CIF | 9dj9_validation.cif.gz | 13.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dj/9dj9 ftp://data.pdbj.org/pub/pdb/validation_reports/dj/9dj9 | HTTPS FTP |
-Related structure data
Related structure data | 8tk5C 8tk6C C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 20984.732 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DUSP3, VHR / Production host: Escherichia coli (E. coli) References: UniProt: P51452, protein-serine/threonine phosphatase, protein-tyrosine-phosphatase |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.23 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop Details: Protein in 50 mM TRIS-Cl pH 8.5, 1 mM TCEP, 0.5 mM EDTA was mixed with the precipitant solution (100 mM Bis-Tris pH 6.5, 50 mM NH4F, 26.7% (w/v) PEG-4000) and equilibrated against the precipitant solution. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 11, 2024 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9201 Å / Relative weight: 1 |
Reflection | Resolution: 1.924→34.318 Å / Num. obs: 12987 / % possible obs: 98.2 % / Redundancy: 3 % / Biso Wilson estimate: 27.1 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.135 / Rpim(I) all: 0.091 / Rrim(I) all: 0.163 / Net I/σ(I): 5.7 |
Reflection shell | Resolution: 1.924→1.958 Å / Redundancy: 3.1 % / Rmerge(I) obs: 1.561 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 656 / CC1/2: 0.341 / Rpim(I) all: 1.042 / Rrim(I) all: 1.884 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.924→34.318 Å / SU ML: 0.2646 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.4917 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||
Displacement parameters | Biso mean: 33.3 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.924→34.318 Å
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LS refinement shell | Resolution: 1.924→2.411 Å
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