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Yorodumi- PDB-5a7f: Comparison of the structure and activity of glycosylated and agly... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5a7f | ||||||
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Title | Comparison of the structure and activity of glycosylated and aglycosylated Human Carboxylesterase 1 | ||||||
Components | LIVER CARBOXYLESTERASE 1Carboxylesterase 1 | ||||||
Keywords | HYDROLASE / ESTERASE | ||||||
Function / homology | Function and homology information cholesterol ester hydrolysis involved in cholesterol transport / methylumbelliferyl-acetate deacetylase / methylumbelliferyl-acetate deacetylase activity / methyl indole-3-acetate esterase activity / sterol esterase / sterol esterase activity / medium-chain fatty acid metabolic process / regulation of bile acid secretion / positive regulation of cholesterol metabolic process / Physiological factors ...cholesterol ester hydrolysis involved in cholesterol transport / methylumbelliferyl-acetate deacetylase / methylumbelliferyl-acetate deacetylase activity / methyl indole-3-acetate esterase activity / sterol esterase / sterol esterase activity / medium-chain fatty acid metabolic process / regulation of bile acid secretion / positive regulation of cholesterol metabolic process / Physiological factors / carboxylesterase / carboxylesterase activity / reverse cholesterol transport / cellular response to cholesterol / regulation of bile acid biosynthetic process / triglyceride lipase activity / carboxylic ester hydrolase activity / Phase I - Functionalization of compounds / Aspirin ADME / cholesterol biosynthetic process / negative regulation of cholesterol storage / positive regulation of cholesterol efflux / cellular response to low-density lipoprotein particle stimulus / angiotensin maturation / Metabolism of Angiotensinogen to Angiotensins / lipid catabolic process / cholesterol metabolic process / epithelial cell differentiation / xenobiotic metabolic process / lipid droplet / cholesterol homeostasis / response to toxic substance / endoplasmic reticulum lumen / endoplasmic reticulum / extracellular space / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å | ||||||
Authors | Arena de Souza, V. / Scott, D.J. / Charlton, M. / Walsh, M.A. / Owen, R.J. | ||||||
Citation | Journal: Plos One / Year: 2015 Title: Comparison of the Structure and Activity of Glycosylated and Aglycosylated Human Carboxylesterase 1. Authors: Arena De Souza, V. / Scott, D.J. / Nettleship, J.E. / Rahman, N. / Charlton, M.H. / Walsh, M.A. / Owens, R.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5a7f.cif.gz | 220.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5a7f.ent.gz | 177.2 KB | Display | PDB format |
PDBx/mmJSON format | 5a7f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a7/5a7f ftp://data.pdbj.org/pub/pdb/validation_reports/a7/5a7f | HTTPS FTP |
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-Related structure data
Related structure data | 5a7gC 5a7hC 2h7cS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 58672.227 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 21-553 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Cell line: HEK 323 / Organ: LIVER / Plasmid: POPINTTG / Cell line (production host): HEK 323 / Production host: HOMO SAPIENS (human) References: UniProt: P23141-3, UniProt: P23141*PLUS, carboxylesterase, carboxylesterase, methylumbelliferyl-acetate deacetylase | ||||
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#2: Sugar | ChemComp-NAG / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Nonpolymer details | N-ACETYL-D-GLUCOSAMIN | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.8 % / Description: NONE |
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Crystal grow | Temperature: 293 K / pH: 6.5 Details: CRYSTALS WERE GROWN AT 20C IN 0.1 M MES/IMIDAZOLE, PH 6.5 CONTAINING 0.03 M EACH OF DIETHYLENE GLYCOL, TRIETHYLENE GLYCOL, TETRAETHYLENE GLYCOL, PENTAETHYLENE GLYCOL, 10 % (W/V) POLYETHYLENE ...Details: CRYSTALS WERE GROWN AT 20C IN 0.1 M MES/IMIDAZOLE, PH 6.5 CONTAINING 0.03 M EACH OF DIETHYLENE GLYCOL, TRIETHYLENE GLYCOL, TETRAETHYLENE GLYCOL, PENTAETHYLENE GLYCOL, 10 % (W/V) POLYETHYLENE GLYCOL 4000, 20% (W/V) GLYCEROL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 10, 2011 / Details: MIRRORS |
Radiation | Monochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.86→50 Å / Num. obs: 46879 / % possible obs: 97 % / Observed criterion σ(I): -3 / Redundancy: 2.8 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 17.4 |
Reflection shell | Resolution: 1.86→1.88 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 1.8 / % possible all: 71.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2H7C Resolution: 1.86→35.78 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.957 / SU B: 5.486 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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: 31.377 Å2
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Refinement step | Cycle: LAST / Resolution: 1.86→35.78 Å
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Refine LS restraints |
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