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Yorodumi- PDB-1j4x: HUMAN VH1-RELATED DUAL-SPECIFICITY PHOSPHATASE C124S MUTANT-PEPTI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1j4x | |||||||||
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Title | HUMAN VH1-RELATED DUAL-SPECIFICITY PHOSPHATASE C124S MUTANT-PEPTIDE COMPLEX | |||||||||
Components |
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Keywords | HYDROLASE / PROTEIN DUAL-SPECIFICITY PHOSPHATASE | |||||||||
Function / homology | Function and homology information MAP kinase phosphatase activity / negative regulation of chemotaxis / negative regulation of T cell activation / protein tyrosine/serine/threonine phosphatase activity / positive regulation of focal adhesion disassembly / negative regulation of JNK cascade / ERKs are inactivated / regulation of focal adhesion assembly / negative regulation of T cell receptor signaling pathway / negative regulation of MAPK cascade ...MAP kinase phosphatase activity / negative regulation of chemotaxis / negative regulation of T cell activation / protein tyrosine/serine/threonine phosphatase activity / positive regulation of focal adhesion disassembly / negative regulation of JNK cascade / ERKs are inactivated / regulation of focal adhesion assembly / negative regulation of T cell receptor signaling pathway / negative regulation of MAPK cascade / myosin phosphatase activity / peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity / protein-serine/threonine phosphatase / negative regulation of epidermal growth factor receptor signaling pathway / phosphatase activity / immunological synapse / peptidyl-tyrosine dephosphorylation / dephosphorylation / cellular response to epidermal growth factor stimulus / cytoskeletal protein binding / positive regulation of mitotic cell cycle / negative regulation of cell migration / protein tyrosine kinase binding / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / negative regulation of ERK1 and ERK2 cascade / receptor tyrosine kinase binding / protein kinase binding / nucleoplasm / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 2.75 Å | |||||||||
Authors | Schumacher, M.A. / Todd, J.L. / Tanner, K.G. / Denu, J.M. | |||||||||
Citation | Journal: Biochemistry / Year: 2002 Title: Structural basis for the recognition of a bisphosphorylated MAP kinase peptide by human VHR protein Phosphatase. Authors: Schumacher, M.A. / Todd, J.L. / Rice, A.E. / Tanner, K.G. / Denu, J.M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1j4x.cif.gz | 52 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1j4x.ent.gz | 36.4 KB | Display | PDB format |
PDBx/mmJSON format | 1j4x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j4/1j4x ftp://data.pdbj.org/pub/pdb/validation_reports/j4/1j4x | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 20354.012 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PT7-7-VHR / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P51452, protein-tyrosine-phosphatase |
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#2: Protein/peptide | Mass: 1414.283 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: 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: 2.23 Å3/Da / Density % sol: 44.76 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG 4000, ISOPROPANOL, pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 5.6 / Method: vapor diffusion | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 20, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→30 Å / Num. obs: 9234 / % possible obs: 90 % / Observed criterion σ(I): 0 / Redundancy: 1.5 % / Biso Wilson estimate: 45 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 17.1 |
Reflection shell | Resolution: 2.75→2.9 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.29 / % possible all: 80 |
Reflection | *PLUS Highest resolution: 2.75 Å / Lowest resolution: 10 Å / Num. measured all: 16753 |
-Processing
Software |
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Refinement | Method to determine structure: molecular replacement / Resolution: 2.75→10 Å / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
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Refinement step | Cycle: LAST / Resolution: 2.75→10 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 10 Å / % reflection Rfree: 10 % / Rfactor all: 0.192 / Rfactor obs: 0.188 / Rfactor Rfree: 0.264 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |