+Open data
-Basic information
Entry | Database: PDB / ID: 6hyj | |||||||||
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Title | PSPH Human phosphoserine phosphatase | |||||||||
Components | Phosphoserine phosphatase | |||||||||
Keywords | HYDROLASE / phosphoserine phosphatase / homo sapiens | |||||||||
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 / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.929 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6hyj.cif.gz | 105.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6hyj.ent.gz | 80.2 KB | Display | PDB format |
PDBx/mmJSON format | 6hyj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6hyj_validation.pdf.gz | 474.6 KB | Display | wwPDB validaton report |
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Full document | 6hyj_full_validation.pdf.gz | 494 KB | Display | |
Data in XML | 6hyj_validation.xml.gz | 22 KB | Display | |
Data in CIF | 6hyj_validation.cif.gz | 30.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hy/6hyj ftp://data.pdbj.org/pub/pdb/validation_reports/hy/6hyj | HTTPS FTP |
-Related structure data
Related structure data | 6hyyC 6q6jC 1nnlS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 24923.584 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PSPH / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P78330, phosphoserine phosphatase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-SER / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 50.09 % |
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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 |
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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: 1.929→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 |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
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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
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13
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