[English] 日本語
![](img/lk-miru.gif)
- PDB-6x1r: Crystal Structure of Choanoflagellate (Monosiga brevicollis) Dlg1... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6x1r | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of Choanoflagellate (Monosiga brevicollis) Dlg1 PDZ2 (mbDLG-2) in spacegroup P212121 | ||||||
![]() | mbDLG protein | ||||||
![]() | SIGNALING PROTEIN / PDZ / protein-protein interaction / choanoflagellates / Monosiga brevicollis / peptide-binding domain | ||||||
Function / homology | ![]() embryo development / receptor localization to synapse / establishment or maintenance of epithelial cell apical/basal polarity / receptor clustering / cell-cell adhesion / cell junction / neuron projection / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bamonte, H.A. / Amacher, J.F. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Structural characterization and computational analysis of PDZ domains in Monosiga brevicollis. Authors: Gao, M. / Mackley, I.G.P. / Mesbahi-Vasey, S. / Bamonte, H.A. / Struyvenberg, S.A. / Landolt, L. / Pederson, N.J. / Williams, L.I. / Bahl, C.D. / Brooks 3rd, L. / Amacher, J.F. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 35.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 22.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 431.3 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 431.7 KB | Display | |
Data in XML | ![]() | 7.4 KB | Display | |
Data in CIF | ![]() | 9.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6x1nC ![]() 6x1pC ![]() 6x1xC ![]() 6x20C ![]() 6x22C ![]() 6x23C ![]() 2bygS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 10847.223 Da / Num. of mol.: 1 / Fragment: second PDZ domain (UNP residues 93-192) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
---|---|
#2: Chemical | ChemComp-GOL / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.28 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 0.2 M sodium malonate, pH 5, 20% w/v PEG3350 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 12, 2020 | ||||||||||||||||||
Radiation | Monochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength | Wavelength: 0.97741 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 1.3→40.3 Å / Num. obs: 28809 / % possible obs: 99.4 % / Redundancy: 6.04 % / Biso Wilson estimate: 24.3 Å2 / CC1/2: 1 / Rsym value: 0.033 / Net I/σ(I): 24.04 | ||||||||||||||||||
Reflection shell | CC1/2: 0.866 / Diffraction-ID: 1
|
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB entry 2BYG Resolution: 1.3→40.299 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.66 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 75.48 Å2 / Biso mean: 24.4252 Å2 / Biso min: 11.85 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.3→40.299 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
|