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- PDB-3k9b: Crystal structure of human liver carboxylesterase 1 (hCE1) in cov... -

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Basic information

Entry
Database: PDB / ID: 3k9b
TitleCrystal structure of human liver carboxylesterase 1 (hCE1) in covalent complex with the nerve agent Cyclosarin (GF)
ComponentsLiver carboxylesterase 1
KeywordsHYDROLASE / organophosphorus nerve agent / Alternative splicing / Disulfide bond / Endoplasmic reticulum / Glycoprotein / Polymorphism / Serine esterase
Function / homology
Function and homology information


cholesterol ester hydrolysis involved in cholesterol transport / methylumbelliferyl-acetate deacetylase / methylumbelliferyl-acetate deacetylase activity / sterol esterase / sterol ester esterase activity / medium-chain fatty acid metabolic process / regulation of bile acid secretion / carboxylesterase / Physiological factors / carboxylesterase activity ...cholesterol ester hydrolysis involved in cholesterol transport / methylumbelliferyl-acetate deacetylase / methylumbelliferyl-acetate deacetylase activity / sterol esterase / sterol ester esterase activity / medium-chain fatty acid metabolic process / regulation of bile acid secretion / carboxylesterase / Physiological factors / 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
: / Carboxylesterase type B, conserved site / Carboxylesterases type-B signature 2. / Carboxylesterase type B, active site / Carboxylesterases type-B serine active site. / Carboxylesterase, type B / Carboxylesterase family / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold ...: / Carboxylesterase type B, conserved site / Carboxylesterases type-B signature 2. / Carboxylesterase type B, active site / Carboxylesterases type-B serine active site. / Carboxylesterase, type B / Carboxylesterase family / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
cyclohexyl (S)-methylphosphonofluoridoate / Liver carboxylesterase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.1 Å
AuthorsHemmert, A.C. / Redinbo, M.R.
CitationJournal: Mol.Pharmacol. / Year: 2010
Title: Human carboxylesterase 1 stereoselectively binds the nerve agent cyclosarin and spontaneously hydrolyzes the nerve agent sarin.
Authors: Hemmert, A.C. / Otto, T.C. / Wierdl, M. / Edwards, C.C. / Fleming, C.D. / MacDonald, M. / Cashman, J.R. / Potter, P.M. / Cerasoli, D.M. / Redinbo, M.R.
History
DepositionOct 15, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Liver carboxylesterase 1
B: Liver carboxylesterase 1
C: Liver carboxylesterase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,7436
Polymers175,2033
Non-polymers5403
Water1,18966
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Liver carboxylesterase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,5812
Polymers58,4011
Non-polymers1801
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Liver carboxylesterase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,5812
Polymers58,4011
Non-polymers1801
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
C: Liver carboxylesterase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,5812
Polymers58,4011
Non-polymers1801
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.610, 179.880, 200.060
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Liver carboxylesterase 1 / Acyl coenzyme A:cholesterol acyltransferase / ACAT / Monocyte/macrophage serine esterase / HMSE / ...Acyl coenzyme A:cholesterol acyltransferase / ACAT / Monocyte/macrophage serine esterase / HMSE / Serine esterase 1 / Brain carboxylesterase hBr1 / Triacylglycerol hydrolase / TGH / Egasyn / Retinyl ester hydrolase / REH


Mass: 58400.957 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CES1, CES2, SES1 / Plasmid: pBAK / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF21 / References: UniProt: P23141, carboxylesterase
#2: Chemical ChemComp-WW2 / cyclohexyl (S)-methylphosphonofluoridoate / Cyclosarin


Mass: 180.157 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H14FO2P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.86 Å3/Da / Density % sol: 56.93 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 10% PEG 3350, 0.3 M Li2SO4, 0.1 M Citrate pH 5.5, 0.1 M NaCl, 0.1 M LiCl, 5% Glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 24, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→48 Å / Num. all: 37436 / Num. obs: 36488 / % possible obs: 97.5 % / Observed criterion σ(I): 2.1 / Redundancy: 7 % / Biso Wilson estimate: 53.94 Å2 / Rmerge(I) obs: 0.131 / Rsym value: 0.131 / Net I/σ(I): 13.6
Reflection shellResolution: 3.1→3.2 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.481 / Mean I/σ(I) obs: 4.5 / Num. unique all: 2206 / Rsym value: 0.481 / % possible all: 94.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
CNSrefinement
PDB_EXTRACT3.005data extraction
XDSdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1MX1

1mx1


Resolution: 3.1→48 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.756
Isotropic thermal model: anisotropic overall temperature factors
Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 4.5 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.299 3643 9.7 %Random
Rwork0.266 ---
all0.2697 36488 --
obs0.2697 36488 97.5 %-
Solvent computationBsol: 53.94 Å2
Displacement parametersBiso max: 136.48 Å2 / Biso mean: 49.194 Å2 / Biso min: 1 Å2
Baniso -1Baniso -2Baniso -3
1--9.642 Å20 Å20 Å2
2--11.399 Å20 Å2
3----1.758 Å2
Refinement stepCycle: LAST / Resolution: 3.1→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11155 0 30 66 11251
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg1.704
LS refinement shellResolution: 3.1→3.3 Å /
Rfactor% reflection
Rfree0.296 -
Rwork0.268 -
obs-94 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2gfc.par
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param

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