[English] 日本語
![](img/lk-miru.gif)
- PDB-7mog: Crystal Structure of Arabidopsis thaliana Plant and Fungi Atypica... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7mog | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of Arabidopsis thaliana Plant and Fungi Atypical Dual Specificity Phosphatase 1(AtPFA-DSP1 ) Cys150Ser in complex with 5-PCF2 Am-InsP5, an analogue of 5-InsP7 | ||||||
![]() | 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 | ![]() | 161.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 127.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 17.9 KB | Display | |
Data in CIF | ![]() | 25.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7modC ![]() 7moeC ![]() 7mofC ![]() 7mohC ![]() 7moiC ![]() 7mojC ![]() 7mokC ![]() 7molC ![]() 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: 19642.770 Da / Num. of mol.: 2 / Mutation: Cys150Ser Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 0.4 M NaCl, 100 mM HEPES pH 7.2, 50 mM beta-mercaptoethanol at 298K (3 ul of 5.5 mg/ml protein plus 1 ul of well buffer in the crystallization drop). The formed crystal was soaked in 30% ...Details: 0.4 M NaCl, 100 mM HEPES pH 7.2, 50 mM beta-mercaptoethanol at 298K (3 ul of 5.5 mg/ml protein plus 1 ul of well buffer in the crystallization drop). The formed crystal was soaked in 30% PEG400, 13mM MgCl2, 33mM NaF, 50 mM beta-mercaptoethanol, 66 mM HEPES, pH 7.2, and 2 mM 5-PCF2Am-InsP5 for 3 days. |
---|
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 22, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 59897 / % possible obs: 100 % / Redundancy: 8.2 % / Rrim(I) all: 0.084 / Net I/σ(I): 23.5 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 8.6 % / Mean I/σ(I) obs: 3.2 / Num. unique obs: 2925 / Rrim(I) all: 0.853 / % 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: 148.5 Å2 / Biso mean: 29.214 Å2 / Biso min: 9.91 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.8→37.61 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.8→1.846 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|