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- PDB-8yib: Staphylococcus aureus lipase -PSA complex - covalent bonding state -
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Open data
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Basic information
Entry | Database: PDB / ID: 8yib | ||||||
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Title | Staphylococcus aureus lipase -PSA complex - covalent bonding state | ||||||
![]() | Lipase 2 | ||||||
![]() | HYDROLASE / Lipase | ||||||
Function / homology | ![]() triacylglycerol lipase / triacylglycerol lipase activity / lipid catabolic process / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kitadokoro, J. / Kamitani, S. / Kitadokoro, K. | ||||||
Funding support | 1items
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![]() | ![]() Title: Crystal structure of Staphylococcus aureus lipase complex with unsaturated petroselinic acid. Authors: Kitadokoro, J. / Kamitani, S. / Okuno, Y. / Hikima, T. / Yamamoto, M. / Hirokawa, T. / Kitadokoro, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 176.4 KB | Display | ![]() |
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PDB format | ![]() | 137.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 34.2 KB | Display | |
Data in CIF | ![]() | 46.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8k7pC ![]() 8k7qC 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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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 45797.391 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: E68Q WAS GENETIC VARIANT / Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 14 types, 181 molecules ![](data/chem/img/FMT.gif)
![](data/chem/img/OCA.gif)
![](data/chem/img/PPI.gif)
![](data/chem/img/ACY.gif)
![](data/chem/img/4I1.gif)
![](data/chem/img/BUA.gif)
![](data/chem/img/DAO.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/6NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/OCA.gif)
![](data/chem/img/PPI.gif)
![](data/chem/img/ACY.gif)
![](data/chem/img/4I1.gif)
![](data/chem/img/BUA.gif)
![](data/chem/img/DAO.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/6NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-FMT / #3: Chemical | ChemComp-OCA / #4: Chemical | ChemComp-PPI / | #5: Chemical | ChemComp-ACY / | #6: Chemical | #7: Chemical | #8: Chemical | ChemComp-DAO / #9: Chemical | #10: Chemical | #11: Chemical | ChemComp-MG / | #12: Chemical | ChemComp-GOL / #13: Chemical | #14: Chemical | ChemComp-CL / #15: 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: 5.94 Å3/Da / Density % sol: 79.3 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: Sodium Formate, Acetate |
-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: Feb 9, 2023 |
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.27→50 Å / Num. obs: 195118 / % possible obs: 99.9 % / Redundancy: 6.29 % / CC1/2: 0.999 / Rrim(I) all: 0.084 / Net I/σ(I): 13.31 |
Reflection shell | Resolution: 2.27→2.41 Å / Redundancy: 5.87 % / Num. unique obs: 31379 / CC1/2: 0.515 / % possible all: 99.2 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 64.924 Å2
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Refinement step | Cycle: 1 / Resolution: 2.27→48.29 Å
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Refine LS restraints |
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