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Yorodumi- PDB-2yd8: Crystal structure of the N-terminal Ig1-2 module of Human Recepto... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2yd8 | |||||||||
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Title | Crystal structure of the N-terminal Ig1-2 module of Human Receptor Protein Tyrosine Phosphatase LAR in complex with sucrose octasulphate | |||||||||
Components | RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE F | |||||||||
Keywords | HYDROLASE / RPTPF | |||||||||
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: 2.05 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 | 2yd8.cif.gz | 93.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2yd8.ent.gz | 69.9 KB | Display | PDB format |
PDBx/mmJSON format | 2yd8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yd/2yd8 ftp://data.pdbj.org/pub/pdb/validation_reports/yd/2yd8 | HTTPS FTP |
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-Related structure data
Related structure data | 2yd1C 2yd2C 2yd3C 2yd4SC 2yd5C 2yd6C 2yd7C 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: Sugar | ChemComp-YYJ / |
#3: Water | ChemComp-HOH / |
Nonpolymer details | SUCROSE OCTASULPHATE (SCR): THE SIX-MEMBERED RING OF SUCROSE OCTASULPHATE IS DISORDERED AND ...SUCROSE OCTASULPHA |
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: 2.75 Å3/Da / Density % sol: 56 % / Description: NONE |
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Crystal grow | pH: 6 / Details: 0.1 M MES, 30% PEG 6000, PH 6.0 . |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9763 |
Detector | Type: ADSC CCD / 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: 2.05→40 Å / Num. obs: 16614 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 9.9 % / Biso Wilson estimate: 32.14 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 24.7 |
Reflection shell | Resolution: 2.05→2.12 Å / Redundancy: 10 % / Rmerge(I) obs: 0.94 / Mean I/σ(I) obs: 2.7 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2YD4 Resolution: 2.05→39.384 Å / SU ML: 0.22 / σ(F): 0 / Phase error: 24.1 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.675 Å2 / ksol: 0.286 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.34 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→39.384 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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