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- PDB-8p7u: The impact of molecular variants, crystallization conditions and ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8p7u | |||||||||
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Title | The impact of molecular variants, crystallization conditions and space group on structure-ligand complexes: A case study on Bacterial Phosphotriesterase Variants and complexes | |||||||||
![]() | Parathion hydrolase | |||||||||
![]() | HYDROLASE | |||||||||
Function / homology | ![]() aryldialkylphosphatase / aryldialkylphosphatase activity / catabolic process / zinc ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Dym, O. / Aggarwal, N. / Ashani, Y. / Albeck, S. / Unger, T. / Hamer Rogotner, S. / Silman, I. / Sussman, J.L. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: The impact of molecular variants, crystallization conditions and the space group on ligand-protein complexes: a case study on bacterial phosphotriesterase. Authors: Dym, O. / Aggarwal, N. / Ashani, Y. / Leader, H. / Albeck, S. / Unger, T. / Hamer-Rogotner, S. / Silman, I. / Tawfik, D.S. / Sussman, J.L. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 90.5 KB | Display | ![]() |
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PDB format | ![]() | 63.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.6 MB | Display | ![]() |
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Full document | ![]() | 3.6 MB | Display | |
Data in XML | ![]() | 18 KB | Display | |
Data in CIF | ![]() | 27.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8p7fC ![]() 8p7hC ![]() 8p7iC ![]() 8p7kC ![]() 8p7mC ![]() 8p7nC ![]() 8p7qC ![]() 8p7rC ![]() 8p7sC ![]() 8p7tC ![]() 8p7vC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 35747.582 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 7 types, 370 molecules ![](data/chem/img/FMT.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/X3T.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/E8N.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/X3T.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/E8N.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-FMT / | ||||||||||
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#3: Chemical | #4: Chemical | ChemComp-X3T / | #5: Chemical | #6: Chemical | ChemComp-E8N / | #7: Chemical | ChemComp-SO4 / | #8: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.18 Å3/Da / Density % sol: 61.28 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 1.5M (NH4)2SO4 12% Glycerol 0.1M Tris pH=8.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 7, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.27242 Å / Relative weight: 1 |
Reflection | Resolution: 1.376→18.12 Å / Num. obs: 96151 / % possible obs: 99.15 % / Redundancy: 6.5 % / CC1/2: 0.992 / Rpim(I) all: 0.05118 / Net I/σ(I): 6.87 |
Reflection shell | Resolution: 1.38→1.42 Å / Num. unique obs: 9438 / CC1/2: 0.776 / Rpim(I) all: 0.274 / % possible all: 98.7 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.38→18.12 Å
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Refine LS restraints |
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LS refinement shell |
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