[English] 日本語
![](img/lk-miru.gif)
- PDB-7mol: Crystal Structure of Arabidopsis thaliana Plant and Fungi Atypica... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7mol | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of Arabidopsis thaliana Plant and Fungi Atypical Dual Specificity Phosphatase 1(AtPFA-DSP1 ) in complex with phosphate in conformation B (Pi(B)) | ||||||
![]() | Tyrosine-protein phosphatase DSP1 | ||||||
![]() | HYDROLASE / inositol / inositol pyrophosphate / TRANSFERASE / cell-signaling / phosphatase / substrate recognition / reaction mechanism / intermediate / phosphate / metaphosphate / molecular dynamic simulation / self-activation / catalytic water | ||||||
Function / homology | ![]() phosphatase activity / dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wang, H. / Shears, S.B. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: A structural expose of noncanonical molecular reactivity within the protein tyrosine phosphatase WPD loop. Authors: Wang, H. / Perera, L. / Jork, N. / Zong, G. / Riley, A.M. / Potter, B.V.L. / Jessen, H.J. / Shears, S.B. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 159.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 131.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 957.3 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 962.1 KB | Display | |
Data in XML | ![]() | 18.9 KB | Display | |
Data in CIF | ![]() | 27.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7modC ![]() 7moeC ![]() 7mofC ![]() 7mogC ![]() 7mohC ![]() 7moiC ![]() 7mojC ![]() 7mokC ![]() 7momC C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||||||
2 | ![]()
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-
Components
#1: Protein | Mass: 19658.834 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 4.48 Å3/Da / Density % sol: 72.52 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 0.4 M NaCl, 100 mM HEPES pH 7.2 at 298K (3 ul of 4.5 mg/ml protein plus 1 ul of well buffer in the crystallization drop). |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 6, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 50701 / % possible obs: 100 % / Redundancy: 11.3 % / Rrim(I) all: 0.097 / Net I/σ(I): 27.5 |
Reflection shell | Resolution: 1.9→1.93 Å / Rmerge(I) obs: 0.94 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 2516 / % possible all: 100 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 max: 134.46 Å2 / Biso mean: 25.493 Å2 / Biso min: 10.05 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.9→39.35 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.9→1.949 Å / Rfactor Rfree error: 0
|