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- PDB-4ab1: Recombinant Human Carboxylesterase 1 from whole Cabbage Loopers -

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Basic information

Entry
Database: PDB / ID: 4ab1
TitleRecombinant Human Carboxylesterase 1 from whole Cabbage Loopers
ComponentsLIVER CARBOXYLESTERASE 1Carboxylesterase 1
KeywordsHYDROLASE / WHOLE INSECT EXPRESSION SYSTEMS
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 / positive regulation of cholesterol metabolic process / Physiological factors / carboxylesterase ...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 / positive regulation of cholesterol metabolic process / Physiological factors / carboxylesterase / carboxylesterase activity / reverse cholesterol transport / cellular response to cholesterol / regulation of bile acid biosynthetic process / 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 / Metabolism of Angiotensinogen to Angiotensins / lipid catabolic process / cholesterol metabolic process / epithelial cell differentiation / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
THIOCYANATE ION / Liver carboxylesterase 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsGreenblatt, H.M. / Otto, T.C. / Cerasoli, D.M. / Sussman, J.L.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2012
Title: Structure of Recombinant Human Carboxylesterase 1 Isolated from Whole Cabbage Looper Larvae.
Authors: Greenblatt, H.M. / Otto, T.C. / Kirkpatrick, M.G. / Kovaleva, E. / Brown, S. / Buchman, G. / Cerasoli, D.M. / Sussman, J.L.
History
DepositionDec 6, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 7, 2012Provider: repository / Type: Initial release
Revision 1.1May 30, 2012Group: Other
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LIVER CARBOXYLESTERASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,0685
Polymers58,6721
Non-polymers3954
Water4,342241
1
A: LIVER CARBOXYLESTERASE 1
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)354,40630
Polymers352,0336
Non-polymers2,37324
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_655-x+y+1,y,-z+1/21
crystal symmetry operation12_555x,x-y,-z+1/21
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/21
Buried area21520 Å2
ΔGint-133.5 kcal/mol
Surface area105320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.843, 114.843, 177.100
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-2167-

HOH

21A-2241-

HOH

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Components

#1: Protein LIVER CARBOXYLESTERASE 1 / Carboxylesterase 1 / ACYL-COENZYME A\:CHOLESTEROL ACYLTRANSFERASE / ACAT / BRAIN CARBOXYLESTERASE HBR1 / COCAINE ...ACYL-COENZYME A\:CHOLESTEROL ACYLTRANSFERASE / ACAT / BRAIN CARBOXYLESTERASE HBR1 / COCAINE CARBOXYLESTERASE / EGASYN / HMSE / METHYLUMBELLIFERYL-ACETATE DEACETYLASE 1 / MONOCYTE/MACROPHAGE SERINE ESTERASE / RETINYL ESTER HYDROLASE / REH / SERINE ESTERASE 1 / TRIACYLGLYCEROL HYDROLASE / TGH


Mass: 58672.227 Da / Num. of mol.: 1 / Fragment: RESIDUES 21-553
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Organ: LIVER / Production host: TRICHOPLUSIA NI (cabbage looper)
References: UniProt: P23141, carboxylesterase, methylumbelliferyl-acetate deacetylase
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-SCN / THIOCYANATE ION / Thiocyanate


Mass: 58.082 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CNS
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 241 / 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: 2.83 Å3/Da / Density % sol: 56.14 % / Description: NONE
Crystal growpH: 5.5
Details: DROP WAS 45% PROTEIN SOLUTION (11MG/ML) OF 50 MM TRIS, PH7.6, 150 MM NACL, MIXED WITH 45% 2 M AMMONIUM SULFATE, 0.1 M BIS-TRIS, PH 5.5, AND 10% 2 M NASCN.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 17, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 35646 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 16.8 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 7.6
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 14.1 % / Rmerge(I) obs: 0.65 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2HRQ

2hrq


Resolution: 2.2→47.88 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.922 / SU B: 4.573 / SU ML: 0.118 / Cross valid method: THROUGHOUT / ESU R: 0.202 / ESU R Free: 0.188 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.23578 1846 5.2 %RANDOM
Rwork0.17846 ---
obs0.18141 33751 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.008 Å2
Baniso -1Baniso -2Baniso -3
1-0.85 Å20.43 Å20 Å2
2--0.85 Å20 Å2
3----1.28 Å2
Refinement stepCycle: LAST / Resolution: 2.2→47.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3980 0 23 241 4244
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.024115
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9791.9715603
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3275522
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.27324.5160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.83215643
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8411514
X-RAY DIFFRACTIONr_chiral_restr0.1420.2632
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213107
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2470.22178
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3160.22817
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2148
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2580.261
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2010.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.201→2.258 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 122 -
Rwork0.195 2163 -
obs--98.79 %

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