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- PDB-1j97: Phospho-Aspartyl Intermediate Analogue of Phosphoserine phosphatase -
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Open data
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Basic information
Entry | Database: PDB / ID: 1j97 | ||||||
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Title | Phospho-Aspartyl Intermediate Analogue of Phosphoserine phosphatase | ||||||
![]() | Phosphoserine Phosphatase | ||||||
![]() | HYDROLASE / Phosphoserine phosphatase / PSP / phospho-Aspartyl / Beryllium Fluoride / Structural Genomics / BSGC structure funded by NIH / Protein Structure Initiative / PSI / Berkeley Structural Genomics Center | ||||||
Function / homology | ![]() phosphoserine phosphatase / L-phosphoserine phosphatase activity / L-serine biosynthetic process / magnesium ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cho, H. / Wang, W. / Kim, R. / Yokota, H. / Damo, S. / Kim, S.-H. / Wemmer, D. / Kustu, S. / Yan, D. / Berkeley Structural Genomics Center (BSGC) | ||||||
![]() | ![]() Title: BeF(3)(-) acts as a phosphate analog in proteins phosphorylated on aspartate: structure of a BeF(3)(-) complex with phosphoserine phosphatase. Authors: Cho, H. / Wang, W. / Kim, R. / Yokota, H. / Damo, S. / Kim, S.-H. / Wemmer, D. / Kustu, S. / Yan, D. #1: ![]() Title: Crystal Structure of Phosphoserine Phosphatase from Methanococcus jannaschii, a Hyperthermophile, at 1.8 A Resolution Authors: Wang, W. / Kim, R. / Jancarik, J. / Yokota, H. / Kim, S.-H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 98.8 KB | Display | ![]() |
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PDB format | ![]() | 79.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 23699.660 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Plasmid: pET21a / Production host: ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47.04 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 2K MME, sodium phosphate dihydrate, NaF, BeCl2, MgCl2, sodium actate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Details: used microseeding | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 31, 2000 |
Radiation | Monochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→20 Å / Num. all: 71630 / Num. obs: 67186 / % possible obs: 93.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.3 % / Biso Wilson estimate: 14.8 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 16 |
Reflection shell | Resolution: 1.5→1.59 Å / Redundancy: 2 % / Rmerge(I) obs: 0.248 / Mean I/σ(I) obs: 3.3 / % possible all: 86.5 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. measured all: 288900 |
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Processing
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Refinement | Method to determine structure: ![]()
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Refine analyze | Luzzati coordinate error obs: 0.18 Å / Luzzati sigma a obs: 0.02 Å | ||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→15 Å
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.5 Å / Lowest resolution: 15 Å / σ(F): 0 / % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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