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Yorodumi- PDB-2yd5: Crystal structure of the N-terminal Ig1-2 module of Human Recepto... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2yd5 | ||||||
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Title | Crystal structure of the N-terminal Ig1-2 module of Human Receptor Protein Tyrosine Phosphatase LAR | ||||||
Components | RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE F | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information chondroitin sulfate proteoglycan binding / cell surface receptor protein tyrosine phosphatase signaling pathway / neuron projection regeneration / Receptor-type tyrosine-protein phosphatases / synaptic membrane adhesion / transmembrane receptor protein tyrosine phosphatase activity / Synaptic adhesion-like molecules / regulation of axon regeneration / peptidyl-tyrosine dephosphorylation / Insulin receptor recycling ...chondroitin sulfate proteoglycan binding / cell surface receptor protein tyrosine phosphatase signaling pathway / neuron projection regeneration / Receptor-type tyrosine-protein phosphatases / synaptic membrane adhesion / transmembrane receptor protein tyrosine phosphatase activity / Synaptic adhesion-like molecules / regulation of axon regeneration / peptidyl-tyrosine dephosphorylation / Insulin receptor recycling / cell adhesion molecule binding / protein-tyrosine-phosphatase / negative regulation of receptor binding / protein tyrosine phosphatase activity / cell migration / heparin binding / cell adhesion / neuron projection / neuronal cell body / protein-containing complex binding / extracellular exosome / plasma membrane Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Coles, C.H. / Shen, Y. / Tenney, A.P. / Siebold, C. / Sutton, G.C. / Lu, W. / Gallagher, J.T. / Jones, E.Y. / Flanagan, J.G. / Aricescu, A.R. | ||||||
Citation | Journal: Science / Year: 2011 Title: Proteoglycan-Specific Molecular Switch for Rptp Sigma Clustering and Neuronal Extension. Authors: Coles, C.H. / Shen, Y. / Tenney, A.P. / Siebold, C. / Sutton, G.C. / Lu, W. / Gallagher, J.T. / Jones, E.Y. / Flanagan, J.G. / 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 | 2yd5.cif.gz | 90.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2yd5.ent.gz | 68.4 KB | Display | PDB format |
PDBx/mmJSON format | 2yd5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yd/2yd5 ftp://data.pdbj.org/pub/pdb/validation_reports/yd/2yd5 | HTTPS FTP |
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-Related structure data
Related structure data | 2yd1C 2yd2C 2yd3C 2yd4SC 2yd6C 2yd7C 2yd8C 2yd9C C: citing same article (ref.) S: Starting model for refinement |
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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: 23380.301 Da / Num. of mol.: 1 / Fragment: IG1-2, RESIDUES 29-231 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): HEK293T / Production host: HOMO SAPIENS (human) / References: UniProt: P10586, protein-tyrosine-phosphatase |
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#2: Water | ChemComp-HOH / |
Sequence details | THE N-TERMINAL THREE AMINO ACID RESIDUES (ETG) AND THE C- TERMINAL NINE AMINO ACID RESIDUES ...THE N-TERMINAL THREE AMINO ACID RESIDUES (ETG) AND THE C- TERMINAL NINE AMINO ACID RESIDUES (GTKHHHHHH) DERIVE FROM THE PHLSEC VECTOR. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 52 % / Description: NONE |
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Crystal grow | pH: 5.6 Details: 0.1 M SODIUM ACETATE TRIHYDRATE, 20% ISOPROPANOL, 20% (W/V) PEG 4000, 0.25 MM HEPARIN DP10, PH 5.6 . |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9765 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9765 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→48 Å / Num. obs: 12272 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 10.7 % / Biso Wilson estimate: 33.23 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 19.1 |
Reflection shell | Resolution: 2.2→2.26 Å / Redundancy: 10.6 % / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 3.6 / % possible all: 98.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2YD4 Resolution: 2.2→38.475 Å / SU ML: 0.26 / σ(F): 0 / Phase error: 21.72 / Stereochemistry target values: ML Details: THE SIDECHAIN OF ARG228 IS DISORDERED AND IS NOT INCLUDED IN THE CRYSTAL STRUCTURE.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40 Å2 / ksol: 0.349 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.13 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→38.475 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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