+
Open data
-
Basic information
Entry | Database: PDB / ID: 6hyj | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | PSPH Human phosphoserine phosphatase | |||||||||
![]() | Phosphoserine phosphatase | |||||||||
![]() | HYDROLASE / phosphoserine phosphatase / homo sapiens | |||||||||
Function / homology | ![]() phosphoserine phosphatase / Serine biosynthesis / L-phosphoserine phosphatase activity / L-serine metabolic process / L-serine biosynthetic process / response to testosterone / response to mechanical stimulus / response to nutrient levels / in utero embryonic development / magnesium ion binding ...phosphoserine phosphatase / Serine biosynthesis / L-phosphoserine phosphatase activity / L-serine metabolic process / L-serine biosynthetic process / response to testosterone / response to mechanical stimulus / response to nutrient levels / in utero embryonic development / magnesium ion binding / protein homodimerization activity / identical protein binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Wouters, J. / Haufroid, M. / Mirgaux, M. | |||||||||
![]() | ![]() Title: Crystal structures and snapshots along the reaction pathway of human phosphoserine phosphatase. Authors: Haufroid, M. / Mirgaux, M. / Leherte, L. / Wouters, J. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 105.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 80.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 6hyyC ![]() 6q6jC ![]() 1nnlS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 24923.584 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-SER / | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 50.09 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: CaCl2 0.15 M; sodium cacodylate 0.1 M pH 6.5; PEG 2000 20% |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 5, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 1.929→34.23 Å / Num. obs: 36957 / % possible obs: 98.66 % / Redundancy: 2 % / Biso Wilson estimate: 43.32 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.02987 / Rpim(I) all: 0.02987 / Rrim(I) all: 0.04224 / Net I/σ(I): 11.27 |
Reflection shell | Resolution: 1.929→1.998 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.5529 / Mean I/σ(I) obs: 0.96 / Num. unique obs: 3228 / CC1/2: 0.589 / Rpim(I) all: 0.5529 / Rrim(I) all: 0.7819 / % possible all: 87.57 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 1NNL Resolution: 1.929→34.23 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.8
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 111.65 Å2 / Biso mean: 48.8391 Å2 / Biso min: 23.74 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.929→34.23 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13
|