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Yorodumi- PDB-4pbx: Crystal structure of the six N-terminal domains of human receptor... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4pbx | ||||||||||||||||||
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Title | Crystal structure of the six N-terminal domains of human receptor protein tyrosine phosphatase sigma | ||||||||||||||||||
Components | Receptor-type tyrosine-protein phosphatase S | ||||||||||||||||||
Keywords | HYDROLASE / Signaling protein / Synapse Cell signalling Cell surface receptor | ||||||||||||||||||
Function / homology | Function and homology information negative regulation of toll-like receptor 9 signaling pathway / trans-synaptic signaling / Signaling by NTRK3 (TRKC) / 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 / trans-synaptic signaling / Signaling by NTRK3 (TRKC) / 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 / regulation of postsynaptic density assembly / synaptic membrane adhesion / negative regulation of axon extension / corpus callosum development / Synaptic adhesion-like molecules / negative regulation of interferon-beta production / heparan sulfate proteoglycan binding / spinal cord development / phosphoprotein phosphatase activity / peptidyl-tyrosine dephosphorylation / ECM proteoglycans / protein dephosphorylation / protein-tyrosine-phosphatase / cerebellum development / protein tyrosine phosphatase activity / hippocampus development / postsynaptic density membrane / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / cerebral cortex development / synaptic vesicle membrane / negative regulation of neuron projection development / heparin binding / presynaptic membrane / 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: 3.15 Å | ||||||||||||||||||
Authors | Coles, C.H. / Mitakidis, N. / Zhang, P. / Elegheert, J. / Lu, W. / Stoker, A.W. / Nakagawa, T. / Craig, A.M. / Jones, E.Y. / Aricescu, A.R. | ||||||||||||||||||
Funding support | United Kingdom, 5items
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Citation | Journal: Nat Commun / Year: 2014 Title: Structural basis for extracellular cis and trans RPTP sigma signal competition in synaptogenesis. Authors: Coles, C.H. / Mitakidis, N. / Zhang, P. / Elegheert, J. / Lu, W. / Stoker, A.W. / Nakagawa, T. / Craig, A.M. / Jones, E.Y. / Aricescu, A.R. | ||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4pbx.cif.gz | 239.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4pbx.ent.gz | 194 KB | Display | PDB format |
PDBx/mmJSON format | 4pbx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4pbx_validation.pdf.gz | 451.6 KB | Display | wwPDB validaton report |
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Full document | 4pbx_full_validation.pdf.gz | 454.1 KB | Display | |
Data in XML | 4pbx_validation.xml.gz | 20.7 KB | Display | |
Data in CIF | 4pbx_validation.cif.gz | 27.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pb/4pbx ftp://data.pdbj.org/pub/pdb/validation_reports/pb/4pbx | HTTPS FTP |
-Related structure data
Related structure data | 4pbvC 4pbwC 2djuS 2yd3S 2yd4S 2yd9S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 64344.035 Da / Num. of mol.: 1 / Fragment: Residues 30-588 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PTPRS / Plasmid: pHLsec / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q13332, protein-tyrosine-phosphatase | ||
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#2: Sugar | Compound details | The sample sequence matches to isoform 6 of UniProt Q13332 | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 5.87 Å3/Da / Density % sol: 79.04 % |
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Crystal grow | Temperature: 293.5 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 10 % PEG 400, 0.01 M magnesium chloride, 0.1 M potassium chloride, 0.05 M MES pH 6.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9788 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 8, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9788 Å / Relative weight: 1 |
Reflection | Resolution: 3.15→99.4 Å / Num. obs: 25619 / % possible obs: 95.6 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 17.8 |
Reflection shell | Resolution: 3.15→3.23 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.991 / Mean I/σ(I) obs: 2.1 / % possible all: 96.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2YD3, 2YD4, 2YD9, 2DJU Resolution: 3.15→172.15 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.9 / SU B: 42.451 / SU ML: 0.312 / Cross valid method: THROUGHOUT / ESU R: 0.622 / ESU R Free: 0.369 / 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: 120.828 Å2
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Refinement step | Cycle: 1 / Resolution: 3.15→172.15 Å
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Refine LS restraints |
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