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- PDB-5w7b: Rabbit acyloxyacyl hydrolase (AOAH), proteolytically processed, S... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5w7b | |||||||||
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Title | Rabbit acyloxyacyl hydrolase (AOAH), proteolytically processed, S262A mutant, with LPS | |||||||||
![]() | (Acyloxyacyl hydrolase ...) x 2 | |||||||||
![]() | HYDROLASE / lipopolysaccharide / LPS / GDSL esterase / saposin | |||||||||
Function / homology | ![]() lipopolysaccharide catabolic process / acyloxyacyl hydrolase / acyloxyacyl hydrolase activity / fatty acid metabolic process / cytoplasmic vesicle / calcium ion binding / extracellular region Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Gorelik, A. / Illes, K. / Nagar, B. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of the mammalian lipopolysaccharide detoxifier. Authors: Gorelik, A. / Illes, K. / Nagar, 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 | ![]() | 429.2 KB | Display | ![]() |
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PDB format | ![]() | 365.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 9.1 MB | Display | ![]() |
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Full document | ![]() | 9.2 MB | Display | |
Data in XML | ![]() | 48.6 KB | Display | |
Data in CIF | ![]() | 66.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5w78C ![]() 5w7aC ![]() 5w7cC ![]() 5w7dC ![]() 5w7eC ![]() 5w7fC C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Acyloxyacyl hydrolase ... , 2 types, 4 molecules ABCD
#1: Protein | Mass: 16384.969 Da / Num. of mol.: 2 / Fragment: residues 23-153 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | Mass: 47621.781 Da / Num. of mol.: 2 / Fragment: residues 154-575 / Mutation: S262A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Sugars , 4 types, 8 molecules
#3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Polysaccharide | Source method: isolated from a genetically manipulated source #6: Polysaccharide | Source method: isolated from a genetically manipulated source |
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-Non-polymers , 10 types, 500 molecules ![](data/chem/img/PEG.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/FTT.gif)
![](data/chem/img/MYR.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/FTT.gif)
![](data/chem/img/MYR.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
#7: Chemical | ChemComp-PEG / #8: Chemical | ChemComp-PGE / #9: Chemical | ChemComp-FTT / #10: Chemical | ChemComp-MYR / #11: Chemical | ChemComp-CA / #12: Chemical | #13: Chemical | #14: Chemical | ChemComp-1PE / #15: Chemical | ChemComp-PO4 / #16: Water | ChemComp-HOH / | |
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-Details
Compound details | The authors state that the protein was treated with trypsin, and the exact cut site is unknown but ...The authors state that the protein was treated with trypsin, and the exact cut site is unknown but should be somewhere between K129 and R153. |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.74 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: post-trypsin; 1 mM Triton X-100, 0.333 mM E. coli LPS Ra; 100 mM sodium MES pH 6; 34 % PEG 200; 5 % PEG 3000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Sep 17, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9801 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 106913 / % possible obs: 100 % / Redundancy: 14.6 % / Net I/σ(I): 19.5 |
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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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→44.765 Å
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Refine LS restraints |
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LS refinement shell |
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