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Yorodumi- PDB-5w7c: Human acyloxyacyl hydrolase (AOAH), proteolytically processed, S2... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5w7c | |||||||||
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Title | Human acyloxyacyl hydrolase (AOAH), proteolytically processed, S263A mutant, with LPS | |||||||||
Components | (Acyloxyacyl hydrolase) x 2 | |||||||||
Keywords | HYDROLASE / lipopolysaccharide / LPS / GDSL esterase / saposin | |||||||||
Function / homology | Function and homology information lipopolysaccharide catabolic process / acyloxyacyl hydrolase / acyloxyacyl hydrolase activity / fatty acid metabolic process / negative regulation of inflammatory response / cytoplasmic vesicle / intracellular membrane-bounded organelle / calcium ion binding / extracellular region Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 Å | |||||||||
Authors | Gorelik, A. / Illes, K. / Nagar, B. | |||||||||
Funding support | Canada, 1items
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Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5w7c.cif.gz | 416.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5w7c.ent.gz | 352.1 KB | Display | PDB format |
PDBx/mmJSON format | 5w7c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w7/5w7c ftp://data.pdbj.org/pub/pdb/validation_reports/w7/5w7c | HTTPS FTP |
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-Related structure data
Related structure data | 5w78C 5w7aC 5w7bC 5w7dC 5w7eC 5w7fC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 2 types, 4 molecules ABCD
#1: Protein | Mass: 15831.375 Da / Num. of mol.: 2 / Fragment: N-terminal residues 24-152 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AOAH / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P28039, acyloxyacyl hydrolase #2: Protein | Mass: 48170.438 Da / Num. of mol.: 2 / Fragment: C-terminal residues 153-575 / Mutation: S263A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AOAH / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P28039, acyloxyacyl hydrolase |
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-Sugars , 2 types, 8 molecules
#3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #4: Sugar | ChemComp-NAG / |
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-Non-polymers , 4 types, 309 molecules
#5: Chemical | ChemComp-FTT / #6: Chemical | ChemComp-CA / #7: Chemical | #8: Water | ChemComp-HOH / | |
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-Details
Compound details | The authors state that the protein was proteolytically cleaved likely between residues 152-153. |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.78 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: post-chymotrypsin; 1mM Triton X-100, 0.333 mM E. coli LPS Ra; 200 mM ammonium chloride, 100 mM sodium acetate pH 5.3, 20 % PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97243 Å |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: May 23, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97243 Å / Relative weight: 1 |
Reflection | Resolution: 2.23→50 Å / Num. obs: 61346 / % possible obs: 100 % / Redundancy: 13.6 % / Net I/σ(I): 9.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.23→44.816 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 27.08 / Stereochemistry target values: ML
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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: 2.23→44.816 Å
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Refine LS restraints |
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LS refinement shell |
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