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Open data
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Basic information
Entry | Database: PDB / ID: 7qow | ||||||
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Title | Crystal structure of Vibrio alkaline phosphatase in 1.0 M NaCl | ||||||
![]() | Alkaline phosphatase | ||||||
![]() | HYDROLASE / Phosphatase / Chloride | ||||||
Function / homology | ![]() alkaline phosphatase activity / dephosphorylation / periplasmic space / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Markusson, S. / Hjorleifsson, J.G. / Kursula, P. / Asgeirsson, B. | ||||||
Funding support | 1items
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![]() | ![]() Title: Structural Characterization of Functionally Important Chloride Binding Sites in the Marine Vibrio Alkaline Phosphatase. Authors: Markusson, S. / Hjorleifsson, J.G. / Kursula, P. / Asgeirsson, B. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 748.6 KB | Display | ![]() |
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PDB format | ![]() | 514 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2 MB | Display | ![]() |
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Full document | ![]() | 2 MB | Display | |
Data in XML | ![]() | 47.2 KB | Display | |
Data in CIF | ![]() | 72.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7qp8C ![]() 7yzzC ![]() 7z00C ![]() 3e2dS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
Experimental dataset #1 | Data reference: ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 58616.484 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 7 types, 1146 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-MG / #4: Chemical | #5: Chemical | ChemComp-EDO / #6: Chemical | #7: Chemical | ChemComp-TRS / | #8: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.4 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 28% PEG3350, 1.0 M NaCl, 0.1 M Tris pH 7.0. Grown from seed crystals grown in 28% PEG3350, 0.8 M NaCl, 0.1 M Tris pH 7.0. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 9, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→43 Å / Num. obs: 1999077 / % possible obs: 95.9 % / Redundancy: 6.55 % / Biso Wilson estimate: 16.81 Å2 / CC1/2: 1 / Rrim(I) all: 0.052 / Net I/σ(I): 17.21 |
Reflection shell | Resolution: 1.2→1.27 Å / Redundancy: 4.77 % / Mean I/σ(I) obs: 0.79 / Num. unique obs: 198148 / CC1/2: 0.3 / Rrim(I) all: 1.83 / % possible all: 80.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3E2D Resolution: 1.2→43 Å / SU ML: 0.1381 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.8208 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 Details: Anisotropic refinement of all atoms, excluding hydrogens.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.06 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.2→43 Å
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Refine LS restraints |
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LS refinement shell |
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