+Open data
-Basic information
Entry | Database: PDB / ID: 6hyy | ||||||
---|---|---|---|---|---|---|---|
Title | Human phosphoserine phosphatase with serine and phosphate | ||||||
Components | Phosphoserine phosphatase | ||||||
Keywords | HYDROLASE / Human phosphoserine phosphatase | ||||||
Function / homology | Function and homology information phosphoserine phosphatase / Serine biosynthesis / L-phosphoserine phosphatase activity / L-serine metabolic process / L-serine biosynthetic process / response to testosterone / response to mechanical stimulus / dephosphorylation / response to nutrient levels / in utero embryonic development ...phosphoserine phosphatase / Serine biosynthesis / L-phosphoserine phosphatase activity / L-serine metabolic process / L-serine biosynthetic process / response to testosterone / response to mechanical stimulus / dephosphorylation / response to nutrient levels / in utero embryonic development / magnesium ion binding / protein homodimerization activity / identical protein binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.566 Å | ||||||
Authors | Wouters, J. / Haufroid, M. / Mirgaux, M. | ||||||
Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2019 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: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6hyy.cif.gz | 108.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6hyy.ent.gz | 82 KB | Display | PDB format |
PDBx/mmJSON format | 6hyy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hy/6hyy ftp://data.pdbj.org/pub/pdb/validation_reports/hy/6hyy | HTTPS FTP |
---|
-Related structure data
Related structure data | 6hyjC 6q6jC 1nnlS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 24583.121 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PSPH / Plasmid: PET-28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P78330, phosphoserine phosphatase |
---|
-Non-polymers , 5 types, 352 molecules
#2: Chemical | #3: Chemical | ChemComp-MG / | #4: Chemical | ChemComp-SER / | #5: Chemical | ChemComp-CA / | #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.06 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.05 M CaCl2; 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: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å |
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: 1.566→38.947 Å / Num. obs: 69622 / % possible obs: 99.25 % / Redundancy: 2 % / Biso Wilson estimate: 25.93 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.01387 / Rpim(I) all: 0.01387 / Rrim(I) all: 0.01962 / Net I/σ(I): 22.3 |
Reflection shell | Resolution: 1.566→1.622 Å / Redundancy: 2 % / Rmerge(I) obs: 0.2437 / Num. unique obs: 6498 / CC1/2: 0.897 / Rpim(I) all: 0.2437 / Rrim(I) all: 0.3447 / % possible all: 93.82 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1NNL Resolution: 1.566→38.947 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 22.2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 111.19 Å2 / Biso mean: 35.0199 Å2 / Biso min: 15.66 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.566→38.947 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 25
|