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- PDB-6m1x: Crystal structure of Phosphoserine Phosphatase in complex with 3-... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6m1x | ||||||
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Title | Crystal structure of Phosphoserine Phosphatase in complex with 3-Phosphoglyceric Acid from Entamoeba histolytica | ||||||
![]() | Phosphoglycerate mutase family protein | ||||||
![]() | CYTOSOLIC PROTEIN / Phosphoserine Phosphatase / 3-Phosphoglyceric Acid / complex | ||||||
Function / homology | ![]() intramolecular phosphotransferase activity / phosphatase activity / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Kumari, P. / Gourinath, S. | ||||||
Funding support | 1items
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![]() | ![]() Title: Structural analysis of EhPSP in complex with 3-phosphoglyceric acid from Entamoeba histolytica reveals a basis for its lack of phosphoglycerate mutase activity. Authors: Kumari, P. / Vijayan, R. / Gourinath, S. #1: ![]() Title: Structural and functional characterisation of phosphoserine phosphatase, that plays critical role in the oxidative stress response in the parasite Entamoeba histolytica. Authors: Kumari, P. / Babuta, M. / Bhattacharya, A. / Gourinath, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 160.5 KB | Display | ![]() |
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PDB format | ![]() | 125.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 29.7 KB | Display | |
Data in CIF | ![]() | 40.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5zkkS S: Starting model for refinement |
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Similar structure data |
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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: 23771.080 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: 3-Phosphoglyceric Acid / Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.62 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop Details: 0.1 M MMT buffer pH-4.0, PEG-1500 (20%), 0.2 M Ammonium sulphate |
-Data collection
Diffraction | Mean temperature: 82 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 9, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.48→88.87 Å / Num. obs: 33163 / % possible obs: 96.1 % / Redundancy: 4.1 % / CC1/2: 1 / Net I/σ(I): 10.83 |
Reflection shell | Resolution: 2.48→2.59 Å / Rmerge(I) obs: 0.506 / Num. unique obs: 3206 / CC1/2: 0.843 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5ZKK Resolution: 2.48→88.87 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.93 / SU B: 12.453 / SU ML: 0.254 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R: 0.526 / ESU R Free: 0.287 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 114.35 Å2 / Biso mean: 54.274 Å2 / Biso min: 25.47 Å2
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Refinement step | Cycle: final / Resolution: 2.48→88.87 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.48→2.541 Å / Rfactor Rfree error: 0
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