[English] 日本語
Yorodumi- PDB-2dqz: Crystal structure of human carboxylesterase in complex with homat... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2dqz | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of human carboxylesterase in complex with homatropine, coenzyme A, and palmitate | ||||||
Components | Liver carboxylesterase 1Carboxylesterase 1 | ||||||
Keywords | HYDROLASE / cholesterol / esterase | ||||||
Function / homology | Function and homology information cholesterol ester hydrolysis involved in cholesterol transport / methylumbelliferyl-acetate deacetylase / methylumbelliferyl-acetate deacetylase activity / sterol esterase / sterol esterase activity / medium-chain fatty acid metabolic process / regulation of bile acid secretion / Physiological factors / carboxylesterase / carboxylesterase activity ...cholesterol ester hydrolysis involved in cholesterol transport / methylumbelliferyl-acetate deacetylase / methylumbelliferyl-acetate deacetylase activity / sterol esterase / sterol esterase activity / medium-chain fatty acid metabolic process / regulation of bile acid secretion / Physiological factors / carboxylesterase / carboxylesterase activity / cellular response to cholesterol / regulation of bile acid biosynthetic process / positive regulation of cholesterol metabolic process / reverse cholesterol transport / carboxylic ester hydrolase activity / Phase I - Functionalization of compounds / Aspirin ADME / cholesterol biosynthetic process / negative regulation of cholesterol storage / cellular response to low-density lipoprotein particle stimulus / positive regulation of cholesterol efflux / Metabolism of Angiotensinogen to Angiotensins / lipid catabolic process / epithelial cell differentiation / cholesterol metabolic process / lipid droplet / cholesterol homeostasis / response to toxic substance / endoplasmic reticulum lumen / endoplasmic reticulum / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Bencharit, S. / Redinbo, M.R. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2006 Title: Multisite promiscuity in the processing of endogenous substrates by human carboxylesterase 1 Authors: Bencharit, S. / Edwards, C.C. / Morton, C.L. / Howard-Williams, E.L. / Kuhn, P. / Potter, P.M. / Redinbo, M.R. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2dqz.cif.gz | 338.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2dqz.ent.gz | 268.6 KB | Display | PDB format |
PDBx/mmJSON format | 2dqz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dq/2dqz ftp://data.pdbj.org/pub/pdb/validation_reports/dq/2dqz | HTTPS FTP |
---|
-Related structure data
Related structure data | 2dqyC 2dr0C 2h7cC 1mx5S C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 59787.527 Da / Num. of mol.: 3 / Fragment: residues 19-561 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P23141, carboxylesterase |
---|
-Sugars , 2 types, 6 molecules
#2: Sugar | #3: Sugar | |
---|
-Non-polymers , 6 types, 525 molecules
#4: Chemical | ChemComp-SO4 / #5: Chemical | #6: Chemical | #7: Chemical | #8: Chemical | ChemComp-COA / | #9: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.84 Å3/Da / Density % sol: 56.66 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 8% PEG 3350, 0.4M Li2SO4, 0.1M NaCl, 0.1M LiCl, 0.1M citrate (pH 5.5), 5% glycerol , pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 |
---|---|
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Apr 14, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 50837 / % possible obs: 99.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.7 % / Biso Wilson estimate: 47.2 Å2 / Rsym value: 0.123 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 2.8→3 Å / Mean I/σ(I) obs: 2.8 / Rsym value: 0.341 / % possible all: 99.7 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1MX5 Resolution: 2.8→22.6 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2112319.15 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 47.3536 Å2 / ksol: 0.370329 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.5 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→22.6 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.8→2.98 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|