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Yorodumi- PDB-1j97: Phospho-Aspartyl Intermediate Analogue of Phosphoserine phosphatase -
+Open data
-Basic information
Entry | Database: PDB / ID: 1j97 | ||||||
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Title | Phospho-Aspartyl Intermediate Analogue of Phosphoserine phosphatase | ||||||
Components | Phosphoserine Phosphatase | ||||||
Keywords | 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 | Function and homology information phosphoserine phosphatase / L-phosphoserine phosphatase activity / L-serine biosynthetic process / dephosphorylation / magnesium ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Methanocaldococcus jannaschii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Cho, H. / Wang, W. / Kim, R. / Yokota, H. / Damo, S. / Kim, S.-H. / Wemmer, D. / Kustu, S. / Yan, D. / Berkeley Structural Genomics Center (BSGC) | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2001 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: Journal: Structure / Year: 2001 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1j97.cif.gz | 98.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1j97.ent.gz | 79.9 KB | Display | PDB format |
PDBx/mmJSON format | 1j97.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1j97_validation.pdf.gz | 438.5 KB | Display | wwPDB validaton report |
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Full document | 1j97_full_validation.pdf.gz | 442.3 KB | Display | |
Data in XML | 1j97_validation.xml.gz | 21.5 KB | Display | |
Data in CIF | 1j97_validation.cif.gz | 31.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j9/1j97 ftp://data.pdbj.org/pub/pdb/validation_reports/j9/1j97 | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data | |
Other databases |
-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: 23699.660 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii (archaea) Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)/pSJS1244 / References: UniProt: Q58989, phosphoserine phosphatase #2: Chemical | #3: Chemical | #4: 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: 2.32 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: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9686 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→15 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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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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