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Yorodumi- PDB-4bpc: Structure of the Catalytic Domain of Protein Tyrosine Phosphatase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4bpc | ||||||
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Title | Structure of the Catalytic Domain of Protein Tyrosine Phosphatase Sigma in the Sulfenic Acid Form | ||||||
Components | RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE S | ||||||
Keywords | HYDROLASE / PROTEOGLYCAN / REDOX REGULATION | ||||||
Function / homology | Function and homology information negative regulation of toll-like receptor 9 signaling pathway / Signaling by NTRK3 (TRKC) / trans-synaptic signaling / negative regulation of interferon-alpha production / chondroitin sulfate binding / Receptor-type tyrosine-protein phosphatases / negative regulation of collateral sprouting / negative regulation of axon regeneration / establishment of endothelial intestinal barrier / negative regulation of dendritic spine development ...negative regulation of toll-like receptor 9 signaling pathway / Signaling by NTRK3 (TRKC) / trans-synaptic signaling / negative regulation of interferon-alpha production / chondroitin sulfate binding / Receptor-type tyrosine-protein phosphatases / negative regulation of collateral sprouting / negative regulation of axon regeneration / establishment of endothelial intestinal barrier / negative regulation of dendritic spine development / synaptic membrane adhesion / regulation of postsynaptic density assembly / negative regulation of axon extension / Synaptic adhesion-like molecules / corpus callosum development / negative regulation of interferon-beta production / heparan sulfate proteoglycan binding / spinal cord development / phosphoprotein phosphatase activity / peptidyl-tyrosine dephosphorylation / ECM proteoglycans / protein dephosphorylation / cerebellum development / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / hippocampus development / postsynaptic density membrane / Schaffer collateral - CA1 synapse / modulation of chemical synaptic transmission / cerebral cortex development / synaptic vesicle membrane / negative regulation of neuron projection development / presynaptic membrane / heparin binding / growth cone / perikaryon / axon / glutamatergic synapse / extracellular exosome / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Jeon, T.J. / Chien, P.N. / Chun, H.J. / Ryu, S.E. | ||||||
Citation | Journal: Mol.Cells / Year: 2013 Title: Structure of the Catalytic Domain of Protein Tyrosine Phosphatase Sigma in the Sulfenic Acid Form Authors: Jeon, T.J. / Chien, P.N. / Chun, H.J. / Ryu, S.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4bpc.cif.gz | 132.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bpc.ent.gz | 101.3 KB | Display | PDB format |
PDBx/mmJSON format | 4bpc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bp/4bpc ftp://data.pdbj.org/pub/pdb/validation_reports/bp/4bpc | HTTPS FTP |
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-Related structure data
Related structure data | 2fh7S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 66932.555 Da / Num. of mol.: 1 Fragment: CYTOPLASMIC PHOSPHATASE DOMAINS, RESIDUES 1367-1948 Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q13332, protein-tyrosine-phosphatase |
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#2: Water | ChemComp-HOH / |
Sequence details | SEQUENCE BASED ON NCBI: NM_002850.2. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 49.96 % / Description: NONE |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.8M SUCCINIC ACID, PH 7.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 30, 2012 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 36574 / % possible obs: 98.2 % / Observed criterion σ(I): 7.9 / Redundancy: 5.7 % / Rmerge(I) obs: 0.06 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 4 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 7.4 / % possible all: 95.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2FH7 Resolution: 2.1→37.56 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.945 / SU B: 4.783 / SU ML: 0.127 / Cross valid method: THROUGHOUT / ESU R: 0.217 / ESU R Free: 0.179 / 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: 51.252 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→37.56 Å
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