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- PDB-4o7i: Structural and functional characterization of 3'(2'),5'-bisphosph... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4o7i | |||||||||
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Title | Structural and functional characterization of 3'(2'),5'-bisphosphate nucleotidase1 from Entamoeba histolytica | |||||||||
![]() | 3'(2'),5'-bisphosphate nucleotidase, putative | |||||||||
![]() | HYDROLASE / Li sensitive/Mg dependent Phosphatase / Dephosphorylation | |||||||||
Function / homology | ![]() inositol-1,4-bisphosphate 1-phosphatase / inositol-1,4-bisphosphate 1-phosphatase activity / 3'(2'),5'-bisphosphate nucleotidase / 3'(2'),5'-bisphosphate nucleotidase activity / sulfate assimilation / phosphatidylinositol phosphate biosynthetic process / nucleotide binding / magnesium ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Tarique, K.F. / Rehman, S.A.A. / Gourinath, S. | |||||||||
![]() | ![]() Title: Structural elucidation of a dual-activity PAP phosphatase-1 from Entamoeba histolytica capable of hydrolysing both 3'-phosphoadenosine 5'-phosphate and inositol 1,4-bisphosphate Authors: Faisal Tarique, K. / Arif Abdul Rehman, S. / 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 | ![]() | 135.5 KB | Display | ![]() |
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PDB format | ![]() | 105.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 439.9 KB | Display | ![]() |
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Full document | ![]() | 442.5 KB | Display | |
Data in XML | ![]() | 14.3 KB | Display | |
Data in CIF | ![]() | 19.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4hxvC ![]() 1qgxS S: Starting model for refinement C: citing same article ( |
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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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Unit cell |
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Components
#1: Protein | Mass: 36154.023 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: C4M4T9, 3'(2'),5'-bisphosphate nucleotidase |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-PO4 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.36 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 28% PEG 4000, 200mM lithium acetate, 5mM magnesium chloride, 5mM adenosine monophospahte, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 10, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. all: 17183 / Num. obs: 16255 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.2 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 3.7 / Num. unique all: 1648 / % possible all: 93.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1QGX Resolution: 2.11→50 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.922 / SU B: 10.827 / SU ML: 0.143 / Cross valid method: THROUGHOUT / ESU R: 0.265 / ESU R Free: 0.201 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.42 Å2
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Refine analyze | Luzzati coordinate error obs: 0.2803 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.11→50 Å
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Refine LS restraints |
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