+
Open data
-
Basic information
Entry | Database: PDB / ID: 5kqp | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Apo-form LMW-PTP | ||||||
![]() | Low molecular weight phosphotyrosine protein phosphatase | ||||||
![]() | ![]() | ||||||
Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wang, J. / Zhang, Z.-Y. / Yu, Z.-H. | ||||||
![]() | ![]() Title: Inhibition of low molecular weight protein tyrosine phosphatase by an induced-fit mechanism. Authors: He, R. / Wang, J. / Yu, Z.H. / Zhang, R.Y. / Liu, S. / Wu, L. / Zhang, Z.Y. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 47 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 30.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 5kqgC ![]() 5kqlC ![]() 5kqmC ![]() 5pntS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 20236.879 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: P24666, ![]() ![]() |
---|---|
#2: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.67 % |
---|---|
Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: Crystals grew under the following condition: 30% PEGME 5000, 0.2 M ammonium sulfate, 100 mM MES buffer, pH=6.5. Then crystal were transferred to buffer containing 30% PEGME 5000, 0.2 M ...Details: Crystals grew under the following condition: 30% PEGME 5000, 0.2 M ammonium sulfate, 100 mM MES buffer, pH=6.5. Then crystal were transferred to buffer containing 30% PEGME 5000, 0.2 M ammonium sulfate, 100 mM Bis-Tris, pH=6.5 to deplete the bound MES. |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 4, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.05→25 Å / Num. obs: 11281 / % possible obs: 99.9 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.102 / Rsym value: 0.102 / Net I/σ(I): 25.5 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure![]() ![]() Starting model: 5PNT Resolution: 2.052→24.029 Å / SU ML: 0.52 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.35
| |||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Bsol: 35.184 Å2 / ksol: 0.354 e/Å3 | |||||||||||||||||||||||||||||||||||
Displacement parameters |
| |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.052→24.029 Å
| |||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||
LS refinement shell |
|