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- PDB-5a7g: Comparison of the structure and activity of glycosylated and agly... -

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Basic information

Entry
Database: PDB / ID: 5a7g
TitleComparison of the structure and activity of glycosylated and aglycosylated Human Carboxylesterase 1
ComponentsLIVER CARBOXYLESTERASE 1
KeywordsHYDROLASE / 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
Liver carboxylesterase 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsArena de Souza, V. / Scott, D.J. / Charlton, M. / Walsh, M.A. / Owen, R.J.
CitationJournal: 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
DepositionJul 4, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1May 15, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
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_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Jan 10, 2024Group: 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)58,8772
Polymers58,6561
Non-polymers2211
Water12,520695
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)115.390, 115.390, 128.140
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-2695-

HOH

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Components

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


Mass: 58656.227 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 21-552 / Mutation: YES
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, 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


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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 695 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSITE MUTATION S221A DISORDERED RESIDUES 315-317

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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: 2.5 Å3/Da / Density % sol: 50.8 % / Description: NONE
Crystal growTemperature: 277 K / pH: 8.5
Details: CRYSTALS WERE GROWN AT 4C IN 0.1 M BICINE/TRIZMA BASE, PH 8.5, CONTAINING 0.03 M EACH OF DIETHYLENE GLYCOL, TRIETHYLENE GLYCOL, TETRAETHYLENE GLYCOL, PENTAETHYLENE GLYCOL, 10 % (W/V) PEG ...Details: CRYSTALS WERE GROWN AT 4C IN 0.1 M BICINE/TRIZMA BASE, PH 8.5, CONTAINING 0.03 M EACH OF DIETHYLENE GLYCOL, TRIETHYLENE GLYCOL, TETRAETHYLENE GLYCOL, PENTAETHYLENE GLYCOL, 10 % (W/V) PEG 4000, 20 % (V/V) GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 18, 2013 / Details: MIRRORS
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.48→53.94 Å / Num. obs: 104388 / % possible obs: 98.4 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 11.1
Reflection shellResolution: 1.48→1.52 Å / Redundancy: 2 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 1 / % possible all: 91.8

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5A7F

5a7f


Resolution: 1.48→46.55 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.974 / SU B: 3.316 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R: 0.062 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.17277 4985 5.1 %RANDOM
Rwork0.12916 ---
obs0.13137 93337 92.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.014 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20.16 Å20 Å2
2--0.16 Å20 Å2
3----0.53 Å2
Refinement stepCycle: LAST / Resolution: 1.48→46.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4107 0 14 695 4816
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0194242
X-RAY DIFFRACTIONr_bond_other_d0.0010.024083
X-RAY DIFFRACTIONr_angle_refined_deg1.511.9745764
X-RAY DIFFRACTIONr_angle_other_deg0.9243.0019430
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.5685531
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.30124.74173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.85315717
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8971515
X-RAY DIFFRACTIONr_chiral_restr0.0930.2641
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214749
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02924
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.3672.6692118
X-RAY DIFFRACTIONr_mcbond_other3.3652.6672117
X-RAY DIFFRACTIONr_mcangle_it4.1134.0232645
X-RAY DIFFRACTIONr_mcangle_other4.1134.0242646
X-RAY DIFFRACTIONr_scbond_it4.2983.0512124
X-RAY DIFFRACTIONr_scbond_other4.2993.0512124
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.9584.4143118
X-RAY DIFFRACTIONr_long_range_B_refined6.4424.4435461
X-RAY DIFFRACTIONr_long_range_B_other5.63322.7525058
X-RAY DIFFRACTIONr_rigid_bond_restr3.58938325
X-RAY DIFFRACTIONr_sphericity_free65.495186
X-RAY DIFFRACTIONr_sphericity_bonded24.36158725
LS refinement shellResolution: 1.48→1.518 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 286 -
Rwork0.234 5418 -
obs--72.49 %

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