[English] 日本語
Yorodumi- PDB-1l8o: Molecular basis for the local conformational rearrangement of hum... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1l8o | ||||||
---|---|---|---|---|---|---|---|
Title | Molecular basis for the local conformational rearrangement of human phosphoserine phosphatase | ||||||
Components | L-3-phosphoserine phosphatase | ||||||
Keywords | HYDROLASE / phosphatase / conformational rearrangement | ||||||
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: 2.8 Å | ||||||
Authors | Kim, H.Y. / Heo, Y.S. / Kim, J.H. / Park, M.H. / Moon, J. / Park, S.Y. / Lee, T.G. / Jeon, Y.H. / Ro, S. / Hwang, K.Y. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2002 Title: Molecular basis for the local conformational rearrangement of human phosphoserine phosphatase Authors: Kim, H.Y. / Heo, Y.S. / Kim, J.H. / Park, M.H. / Moon, J. / Kim, E. / Kwon, D. / Yoon, J. / Shin, D. / Jeong, E.J. / Park, S.Y. / Lee, T.G. / Jeon, Y.H. / Ro, S. / Cho, J.M. / Hwang, K.Y. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1l8o.cif.gz | 93.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1l8o.ent.gz | 76.5 KB | Display | PDB format |
PDBx/mmJSON format | 1l8o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l8/1l8o ftp://data.pdbj.org/pub/pdb/validation_reports/l8/1l8o | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Details | The biological assembly is a dimer in the asymmetric unit. |
-Components
#1: Protein | Mass: 25086.713 Da / Num. of mol.: 2 / Mutation: L164F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / References: UniProt: P78330, phosphoserine phosphatase #2: Chemical | #3: Chemical | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.14 % | ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: PEG 6000, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ / pH: 5 | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 6B / Wavelength: 1.1 Å |
Detector | Type: MACSCIENCE / Detector: IMAGE PLATE / Date: Jul 20, 2001 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→20 Å / Num. all: 53399 / Num. obs: 52545 / % possible obs: 98.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 35.4 Å2 |
Reflection shell | Resolution: 2.8→2.98 Å / % possible all: 87.7 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. obs: 11843 / Num. measured all: 52545 / Rmerge(I) obs: 0.059 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→19.34 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 834055.67 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 15.5317 Å2 / ksol: 0.265167 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.1 Å2
| |||||||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→19.34 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 2.8→2.98 Å / Rfactor Rfree error: 0.042 / Total num. of bins used: 6
| |||||||||||||||||||||||||
Xplor file |
| |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 500 Å / Num. reflection obs: 10343 / % reflection Rfree: 7 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
|