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- PDB-7qp8: Crystal structure of Vibrio alkaline phosphatase with bound HEPES -
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Open data
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Basic information
Entry | Database: PDB / ID: 7qp8 | ||||||
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Title | Crystal structure of Vibrio alkaline phosphatase with bound HEPES | ||||||
![]() | Alkaline phosphatase | ||||||
![]() | HYDROLASE / Phosphatase / HEPES | ||||||
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. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 723.3 KB | Display | ![]() |
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PDB format | ![]() | 496 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 45.6 KB | Display | |
Data in CIF | ![]() | 68 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7qowC ![]() 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, 852 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/15P.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/15P.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-15P / | #5: Chemical | #6: Chemical | ChemComp-EPE / #7: Chemical | #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: 1.51 Å3/Da / Density % sol: 45.6 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 23% PEG3350, 0.4 M NaCl and 0.1 M HEPES pH 7.5, 10 mg/mL protein. Crystal dehydrated in the mother liquior with PEG3350 increased to 30% prior to data collection |
-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: Jun 21, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→44.1 Å / Num. obs: 517701 / % possible obs: 79.6 % / Redundancy: 5.88 % / Biso Wilson estimate: 26.46 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.0092 / Net I/σ(I): 12.14 |
Reflection shell | Resolution: 1.7→1.74 Å / Mean I/σ(I) obs: 0.76 / Num. unique obs: 7929 / CC1/2: 0.375 / Rrim(I) all: 1.671 / % possible all: 29.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3E2D Resolution: 1.7→44.1 Å / SU ML: 0.1799 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.1408 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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: 33.6 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→44.1 Å
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Refine LS restraints |
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LS refinement shell |
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