- PDB-6yxh: Cryogenic human alkaline ceramidase 3 (ACER3) at 2.6 A resolution... -
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Basic information
Entry
Database: PDB / ID: 6yxh
Title
Cryogenic human alkaline ceramidase 3 (ACER3) at 2.6 A resolution determined by Serial Crystallography (SSX) using CrystalDirect
Components
Alkaline ceramidase 3
Keywords
MEMBRANE PROTEIN / Alkaline ceramidase / ACER3 / serial synchrotron crystallography / SSX / CrystalDirect / LCP crystallisation / in meso / HTX facility / Membrane proteins
Function / homology
Function and homology information
: / phytosphingosine biosynthetic process / : / ceramidase / N-acylsphingosine amidohydrolase activity / : / ceramide catabolic process / regulation of programmed cell death / sphingosine biosynthetic process / sphingolipid biosynthetic process ...: / phytosphingosine biosynthetic process / : / ceramidase / N-acylsphingosine amidohydrolase activity / : / ceramide catabolic process / regulation of programmed cell death / sphingosine biosynthetic process / sphingolipid biosynthetic process / Sphingolipid de novo biosynthesis / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / myelination / inflammatory response / Golgi membrane / calcium ion binding / positive regulation of cell population proliferation / endoplasmic reticulum membrane / zinc ion binding / membrane Similarity search - Function
Mass: 40491.059 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ACER3, APHC, PHCA / Production host: Spodoptera frugiperda / Variant (production host): BOLD-2017 References: UniProt: Q9NUN7, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides, ceramidase
Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O
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Details
Has ligand of interest
Y
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 3.45 Å3/Da / Density % sol: 64.3 %
Crystal grow
Temperature: 293 K / Method: lipidic cubic phase Details: 30 or 50 nl bolus overlaid with 600 nl precipitant solution in CrystalDirect plate-2. 41% PEG 400, 100 mM HEPES pH 7.5, 75 mM magnesium sulfate and 5% DMSO. Crystallisation experiments were ...Details: 30 or 50 nl bolus overlaid with 600 nl precipitant solution in CrystalDirect plate-2. 41% PEG 400, 100 mM HEPES pH 7.5, 75 mM magnesium sulfate and 5% DMSO. Crystallisation experiments were carried out at the HTX facility of EMBL Grenoble. LCP bolus were harvested automatically at cryogenic condition using CrystalDirect technology.
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Data collection
Diffraction
Mean temperature: 100 K / Serial crystal experiment: Y
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