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- PDB-1l7m: HIGH RESOLUTION LIGANDED STRUCTURE OF PHOSPHOSERINE PHOSPHATASE (... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1l7m | ||||||
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Title | HIGH RESOLUTION LIGANDED STRUCTURE OF PHOSPHOSERINE PHOSPHATASE (PI COMPLEX) | ||||||
![]() | Phosphoserine Phosphatase | ||||||
![]() | HYDROLASE / Rossmann Fold / four-Helix bundle / b-hairpin / 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 / dephosphorylation / magnesium ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wang, W. / Cho, H.S. / Kim, R. / Jancarik, J. / Yokota, H. / Nguyen, H.H. / Grigoriev, I.V. / Wemmer, D.E. / Kim, S.H. / Berkeley Structural Genomics Center (BSGC) | ||||||
![]() | ![]() Title: Structural characterization of the reaction pathway in phosphoserine phosphatase: crystallographic "snapshots" of intermediate states. Authors: Wang, W. / Cho, H.S. / Kim, R. / Jancarik, J. / Yokota, H. / Nguyen, H.H. / Grigoriev, I.V. / Wemmer, D.E. / 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 | ![]() | 105.9 KB | Display | ![]() |
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PDB format | ![]() | 80.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 433.5 KB | Display | ![]() |
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Full document | ![]() | 438.6 KB | Display | |
Data in XML | ![]() | 22.1 KB | Display | |
Data in CIF | ![]() | 32.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1l7nC ![]() 1l7oC ![]() 1l7pC ![]() 1f5sS S: Starting model for refinement C: citing same article ( |
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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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 23775.346 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: MJ1594 / Plasmid: pET21a / Production host: ![]() ![]() #2: Chemical | ChemComp-PO4 / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 53.74 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 22% PEG 200 MME, 0.2M SODIUM PHOSPHATE, 0.1M ACETATE BUFFER, 5mM MgCl2, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 25K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / Details: Wang, W., (2001) Struct. Fold. Des., 9, 65. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 3, 2000 |
Radiation | Monochromator: ALS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.48→30 Å / Num. all: 70604 / Num. obs: 70604 / % possible obs: 0.989 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 13.9 Å2 / Rsym value: 0.035 / Net I/σ(I): 36 |
Reflection shell | Resolution: 1.48→1.5 Å / Mean I/σ(I) obs: 3.4 / Num. unique all: 3547 / Rsym value: 0.335 / % possible all: 0.974 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. obs: 72554 / % possible obs: 98.9 % / Rmerge(I) obs: 0.035 |
Reflection shell | *PLUS % possible obs: 97.4 % / Num. unique obs: 3547 / Rmerge(I) obs: 0.335 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1F5S Resolution: 1.48→15 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: CNS
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Displacement parameters | Biso mean: 13.96 Å2
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Refinement step | Cycle: LAST / Resolution: 1.48→15 Å
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Refinement | *PLUS Lowest resolution: 15 Å / % reflection Rfree: 10 % / Rfactor obs: 0.202 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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