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Yorodumi- PDB-2hrr: Crystal structure of Human Liver Carboxylesterase 1 (hCE1) in cov... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2hrr | |||||||||
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Title | Crystal structure of Human Liver Carboxylesterase 1 (hCE1) in covalent complex with the nerve agent Tabun (GA) | |||||||||
Components | Liver carboxylesterase 1Carboxylesterase 1 | |||||||||
Keywords | HYDROLASE / Carboxylesterase / Tabun | |||||||||
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: 2.7 Å | |||||||||
Authors | Fleming, C.D. / Redinbo, M.R. | |||||||||
Citation | Journal: Biochemistry / Year: 2007 Title: Crystal Structures of Human Carboxylesterase 1 in Covalent Complexes with the Chemical Warfare Agents Soman and Tabun. Authors: Fleming, C.D. / Edwards, C.C. / Kirby, S.D. / Maxwell, D.M. / Potter, P.M. / Cerasoli, D.M. / Redinbo, M.R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2hrr.cif.gz | 343.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2hrr.ent.gz | 272.6 KB | Display | PDB format |
PDBx/mmJSON format | 2hrr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hr/2hrr ftp://data.pdbj.org/pub/pdb/validation_reports/hr/2hrr | HTTPS FTP |
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-Related structure data
Related structure data | 2hrqC 1mx1S S: Starting model for refinement 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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Unit cell |
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-Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 58672.227 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CES1 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: Q9UK77, UniProt: P23141*PLUS, carboxylesterase |
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-Sugars , 3 types, 9 molecules
#2: Polysaccharide | #4: Sugar | #5: Sugar | |
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-Non-polymers , 3 types, 835 molecules
#3: Chemical | #6: Chemical | ChemComp-SO4 / #7: Water | ChemComp-HOH / | |
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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: 2.9 Å3/Da / Density % sol: 57.53 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.1 M Citrate pH 5.5, 8-11% PEG 3350, 0.1-0.4M Lithium Sulfate, 0.1M Lithium Chloride, 0.1M Sodium Chloride, 5% Glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 16, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. all: 57407 / Num. obs: 53127 / % possible obs: 91.8 % / Redundancy: 6.4 % / Biso Wilson estimate: 28.8 Å2 / Rsym value: 0.117 / Net I/σ(I): 21.8 |
Reflection shell | Resolution: 2.7→2.87 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 7.7 / Rsym value: 0.292 / % possible all: 91.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB Entry: 1mx1 Resolution: 2.7→41.78 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 72889.76 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 28.9783 Å2 / ksol: 0.350251 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→41.78 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.87 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
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Xplor file |
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