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- PDB-5a7h: Comparison of the structure and activity of glycosylated and agly... -

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Basic information

Entry
Database: PDB / ID: 5a7h
TitleComparison of the structure and activity of glycosylated and aglycosylated Human Carboxylesterase 1
ComponentsLIVER CARBOXYLESTERASE 1
KeywordsHYDROLASE / ESTERASE / AGLYCOSYLATED
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
IODIDE ION / Liver carboxylesterase 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 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 / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LIVER CARBOXYLESTERASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,6149
Polymers58,5991
Non-polymers1,0158
Water3,981221
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)115.470, 115.470, 127.280
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-2221-

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: 58599.172 Da / Num. of mol.: 1 / Mutation: YES [N79Q]
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: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: I
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsSITE MUTATION N79Q

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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: 7.5
Details: CRYSTALS WERE GROWN AT 4C IN 0.1 M BIS-TRIS PROPANE, PH 7.5, CONTAINING 20 % (W/V) POLYETHYLENE GLYCOL 3350, 0.2 M NAI

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 3, 2014 / Details: MIRRORS
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.01→78.63 Å / Num. obs: 41414 / % possible obs: 98.3 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 9.7
Reflection shellResolution: 2.01→2.06 Å / Redundancy: 3 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 1.3 / % possible all: 98

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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: 2.01→30.34 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.944 / SU B: 3.467 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.17 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22163 2034 5 %RANDOM
Rwork0.17897 ---
obs0.18123 38317 95.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.37 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20.03 Å20 Å2
2--0.03 Å20 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 2.01→30.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4125 0 8 221 4354
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0194239
X-RAY DIFFRACTIONr_bond_other_d0.0010.024078
X-RAY DIFFRACTIONr_angle_refined_deg1.4691.9715760
X-RAY DIFFRACTIONr_angle_other_deg0.7843.0019425
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9145532
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.66824.74173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.51315718
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1381515
X-RAY DIFFRACTIONr_chiral_restr0.0830.2638
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214756
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02925
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_it2.724.1752125
X-RAY DIFFRACTIONr_mcbond_other2.7194.1732124
X-RAY DIFFRACTIONr_mcangle_it3.8656.2542655
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.9124.4072114
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.4776.4883140
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: 2.01→2.062 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 110 -
Rwork0.205 2536 -
obs--84.46 %

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