[English] 日本語
![](img/lk-miru.gif)
- PDB-2yd1: Crystal structure of the N-terminal Ig1-2 module of Drosophila Re... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 2yd1 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the N-terminal Ig1-2 module of Drosophila Receptor Protein Tyrosine Phosphatase DLAR | ||||||
![]() | TYROSINE-PROTEIN PHOSPHATASE LAR | ||||||
![]() | HYDROLASE | ||||||
Function / homology | ![]() centripetally migrating follicle cell migration / negative regulation of homophilic cell adhesion / Receptor-type tyrosine-protein phosphatases / positive regulation of plasma membrane bounded cell projection assembly / Insulin receptor recycling / NCAM signaling for neurite out-growth / Other semaphorin interactions / R7 cell development / Synaptic adhesion-like molecules / RAF/MAP kinase cascade ...centripetally migrating follicle cell migration / negative regulation of homophilic cell adhesion / Receptor-type tyrosine-protein phosphatases / positive regulation of plasma membrane bounded cell projection assembly / Insulin receptor recycling / NCAM signaling for neurite out-growth / Other semaphorin interactions / R7 cell development / Synaptic adhesion-like molecules / RAF/MAP kinase cascade / photoreceptor cell morphogenesis / regulation of axon extension involved in axon guidance / SAM domain binding / axon target recognition / hematopoietic stem cell homeostasis / Neutrophil degranulation / transmembrane receptor protein tyrosine phosphatase activity / synaptic assembly at neuromuscular junction / axon extension / motor neuron axon guidance / positive regulation of filopodium assembly / retinal ganglion cell axon guidance / oogenesis / cell leading edge / peptidyl-tyrosine dephosphorylation / negative regulation of insulin receptor signaling pathway / protein-tyrosine-phosphatase / basal plasma membrane / protein tyrosine phosphatase activity / axon guidance / insulin receptor binding / nervous system development / heparin binding / spermatogenesis / receptor complex / cell adhesion / axon / focal adhesion / cell surface Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | 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. | ||||||
![]() | ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 91.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 68.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 430.5 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 431.1 KB | Display | |
Data in XML | ![]() | 10.4 KB | Display | |
Data in CIF | ![]() | 14.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2yd2C ![]() 2yd3C ![]() 2yd4SC ![]() 2yd5C ![]() 2yd6C ![]() 2yd7C ![]() 2yd8C ![]() 2yd9C C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 23247.146 Da / Num. of mol.: 1 / Fragment: IG1-2, RESIDUES 33-232 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|---|
#2: Chemical | ChemComp-GLY / |
#3: 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) ARE DERIVED FROM THE PHLSEC VECTOR |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 1.83 Å3/Da / Density % sol: 34 % / Description: NONE |
---|---|
Crystal grow | pH: 5 Details: 25% W/V PEG 1500, 0.1M SPG SYSTEM, 35MM AMMONIUM SULPHATE, PH 5.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 16271 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Biso Wilson estimate: 20.29 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 19.6 |
Reflection shell | Resolution: 1.8→1.85 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 3.1 / % possible all: 100 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2YD4 Resolution: 1.8→47.175 Å / SU ML: 0.21 / σ(F): 0 / Phase error: 25.46 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40 Å2 / ksol: 0.376 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.96 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→47.175 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|