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Yorodumi- PDB-2yd4: Crystal structure of the N-terminal Ig1-2 module of Chicken Recep... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2yd4 | ||||||
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Title | Crystal structure of the N-terminal Ig1-2 module of Chicken Receptor Protein Tyrosine Phosphatase Sigma | ||||||
Components | PROTEIN-TYROSINE PHOSPHATASE CRYPALPHA1 ISOFORM | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information negative regulation of collateral sprouting / negative regulation of axon regeneration / negative regulation of dendritic spine development / synaptic membrane adhesion / negative regulation of axon extension / heparan sulfate proteoglycan binding / peptidyl-tyrosine dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / postsynaptic density membrane ...negative regulation of collateral sprouting / negative regulation of axon regeneration / negative regulation of dendritic spine development / synaptic membrane adhesion / negative regulation of axon extension / heparan sulfate proteoglycan binding / peptidyl-tyrosine dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / postsynaptic density membrane / synaptic vesicle membrane / heparin binding / growth cone / perikaryon / axon / protein homodimerization activity / plasma membrane Similarity search - Function | ||||||
Biological species | GALLUS GALLUS (chicken) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.65 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 | 2yd4.cif.gz | 99.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2yd4.ent.gz | 81.2 KB | Display | PDB format |
PDBx/mmJSON format | 2yd4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yd/2yd4 ftp://data.pdbj.org/pub/pdb/validation_reports/yd/2yd4 | HTTPS FTP |
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-Related structure data
Related structure data | 2yd1C 2yd2C 2yd3C 2yd5C 2yd6C 2yd7C 2yd8C 2yd9C 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 on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 23156.998 Da / Num. of mol.: 1 / Fragment: IG1-2, RESIDUES 29-226 Source method: isolated from a genetically manipulated source Source: (gene. exp.) GALLUS GALLUS (chicken) / Cell line (production host): HEK293T / Production host: HOMO SAPIENS (human) References: UniProt: Q90815, UniProt: F1NWE3*PLUS, protein-tyrosine-phosphatase |
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-Non-polymers , 5 types, 284 molecules
#2: Chemical | ChemComp-CL / | ||||
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#3: Chemical | ChemComp-PGE / | ||||
#4: Chemical | #5: Chemical | ChemComp-SO4 / | #6: Water | ChemComp-HOH / | |
-Details
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. |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 57 % Description: THE STRUCTURE WAS DETERMINED BY SAD ANALYSIS USING DATA COLLECTED FROM A SELENOMETHIONINE LABELLED PROTEIN CRYSTAL WHICH DIFFRACTED TO 3.1A |
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Crystal grow | pH: 9.6 / Details: 20% W/V PEG 8000, 0.1M CHES, PH 9.6 . |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9763 |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→74 Å / Num. obs: 31882 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 26 % / Biso Wilson estimate: 17.51 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 26.2 |
Reflection shell | Resolution: 1.65→1.7 Å / Redundancy: 18.6 % / Rmerge(I) obs: 0.88 / Mean I/σ(I) obs: 4.2 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 1.65→74.07 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.951 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.09 / ESU R Free: 0.087 / 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: 18.706 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→74.07 Å
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