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- PDB-8p7k: The impact of molecular variants, crystallization conditions and ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8p7k | |||||||||
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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. / Aggawal, 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 | ![]() | 150.6 KB | Display | ![]() |
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PDB format | ![]() | 114.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.1 MB | Display | ![]() |
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Full document | ![]() | 3.1 MB | Display | |
Data in XML | ![]() | 28.5 KB | Display | |
Data in CIF | ![]() | 42.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8p7fC ![]() 8p7hC ![]() 8p7iC ![]() 8p7mC ![]() 8p7nC ![]() 8p7qC ![]() 8p7rC ![]() 8p7sC ![]() 8p7tC ![]() 8p7uC ![]() 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
#1: Protein | Mass: 36756.648 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-ZN / #4: Chemical | #5: 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: 2.2 Å3/Da / Density % sol: 43.97 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 22% Polyacrylic acid 0.02M MgCl2 0.1M HEPES pH=7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 28, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.541 Å / Relative weight: 1 |
Reflection | Resolution: 1.929→32.702 Å / Num. obs: 46379 / % possible obs: 98.69 % / Redundancy: 3.5 % / CC1/2: 0.995 / Rpim(I) all: 0.052 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 1.93→2 Å / Mean I/σ(I) obs: 2.9 / Num. unique obs: 4410 / CC1/2: 0.772 / Rpim(I) all: 0.338 |
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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: 1.929→32.702 Å
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Refine LS restraints |
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LS refinement shell |
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