[English] 日本語
![](img/lk-miru.gif)
- PDB-6tpt: Crystal structures of FNIII domain three and four of the human le... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6tpt | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structures of FNIII domain three and four of the human leucocyte common antigen-related protein, LAR | |||||||||
![]() | Receptor-type tyrosine-protein phosphatase F | |||||||||
![]() | CELL ADHESION / Fibronectin type-III / adhesion protein | |||||||||
Function / homology | ![]() 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 / cell adhesion molecule binding ...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 / cell adhesion molecule binding / Insulin receptor recycling / protein-tyrosine-phosphatase / negative regulation of receptor binding / protein tyrosine phosphatase activity / cell migration / heparin binding / receptor complex / cell adhesion / neuron projection / neuronal cell body / protein-containing complex binding / extracellular exosome / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Vilstrup, J.P. / Thirup, S.S. / Simonsen, A. / Birkefeldt, T. / Strandbygaard, D. | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() Title: Crystal and solution structures of fragments of the human leucocyte common antigen-related protein. Authors: Vilstrup, J. / Simonsen, A. / Birkefeldt, T. / Strandbygard, D. / Lyngso, J. / Pedersen, J.S. / Thirup, S. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 95.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 70.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 416.1 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 417.2 KB | Display | |
Data in XML | ![]() | 8.8 KB | Display | |
Data in CIF | ![]() | 10.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6tpuC ![]() 6tpvC ![]() 6tpwC ![]() 2edxS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 21902.213 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.16 Å3/Da / Density % sol: 61.08 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 6.5 Details: 0.2 M Sodium fluoride, 0.1 M Bis-tris propane pH 6.5, and 20% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 23, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→28 Å / Num. obs: 5225 / % possible obs: 99.3 % / Redundancy: 12.2 % / CC1/2: 0.998 / Net I/σ(I): 14.98 |
Reflection shell | Resolution: 3.2→3.3 Å / Num. unique obs: 493 / CC1/2: 0.937 |
-
Processing
Software |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 2EDX Resolution: 3.2→28 Å / Cross valid method: FREE R-VALUE
| ||||||||||||||||||||||||
Displacement parameters | Biso mean: 150.21 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.2→28 Å
| ||||||||||||||||||||||||
Refine LS restraints |
|