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- PDB-5a7f: Comparison of the structure and activity of glycosylated and agly... -

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Basic information

Entry
Database: PDB / ID: 5a7f
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 / regulation of bile acid secretion / sterol esterase / sterol ester esterase activity / medium-chain fatty acid metabolic process / carboxylesterase / Physiological factors / carboxylesterase activity ...cholesterol ester hydrolysis involved in cholesterol transport / methylumbelliferyl-acetate deacetylase / methylumbelliferyl-acetate deacetylase activity / regulation of bile acid secretion / sterol esterase / sterol ester esterase activity / medium-chain fatty acid metabolic process / carboxylesterase / Physiological factors / carboxylesterase activity / regulation of bile acid biosynthetic process / cellular response to cholesterol / positive regulation of cholesterol metabolic process / reverse cholesterol transport / Phase I - Functionalization of compounds / carboxylic ester hydrolase activity / cholesterol biosynthetic process / Aspirin ADME / negative regulation of cholesterol storage / cellular response to low-density lipoprotein particle stimulus / positive regulation of cholesterol efflux / Metabolism of Angiotensinogen to Angiotensins / cholesterol metabolic process / lipid catabolic process / lipid droplet / epithelial cell differentiation / cholesterol homeostasis / response to toxic substance / endoplasmic reticulum lumen / endoplasmic reticulum / cytoplasm / cytosol
Similarity search - Function
: / Carboxylesterase type B, active site / Carboxylesterases type-B serine active site. / Carboxylesterase type B, conserved site / Carboxylesterases type-B signature 2. / Carboxylesterase, type B / Carboxylesterase family / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold ...: / Carboxylesterase type B, active site / Carboxylesterases type-B serine active site. / Carboxylesterase type B, conserved site / Carboxylesterases type-B signature 2. / 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
PHOSPHATE ION / Liver carboxylesterase 1 / Isoform 3 of Liver carboxylesterase 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 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 3, 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
Revision 1.4Oct 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)59,0834
Polymers58,6721
Non-polymers4113
Water4,864270
1
A: LIVER CARBOXYLESTERASE 1
hetero molecules

A: LIVER CARBOXYLESTERASE 1
hetero molecules

A: LIVER CARBOXYLESTERASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,25012
Polymers176,0173
Non-polymers1,2339
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area5420 Å2
ΔGint-46.5 kcal/mol
Surface area58900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.715, 114.715, 117.780
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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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: 58672.227 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 21-553
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: P23141-3, UniProt: P23141*PLUS, carboxylesterase, 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: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsN-ACETYL-D-GLUCOSAMINE (NAG): GLYCOSYLATION SITE N79

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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: 293 K / pH: 6.5
Details: CRYSTALS WERE GROWN AT 20C IN 0.1 M MES/IMIDAZOLE, PH 6.5 CONTAINING 0.03 M EACH OF DIETHYLENE GLYCOL, TRIETHYLENE GLYCOL, TETRAETHYLENE GLYCOL, PENTAETHYLENE GLYCOL, 10 % (W/V) POLYETHYLENE ...Details: CRYSTALS WERE GROWN AT 20C IN 0.1 M MES/IMIDAZOLE, PH 6.5 CONTAINING 0.03 M EACH OF DIETHYLENE GLYCOL, TRIETHYLENE GLYCOL, TETRAETHYLENE GLYCOL, PENTAETHYLENE GLYCOL, 10 % (W/V) POLYETHYLENE GLYCOL 4000, 20% (W/V) GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 10, 2011 / 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: 1.86→50 Å / Num. obs: 46879 / % possible obs: 97 % / Observed criterion σ(I): -3 / Redundancy: 2.8 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 17.4
Reflection shellResolution: 1.86→1.88 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 1.8 / % possible all: 71.5

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2H7C

2h7c


Resolution: 1.86→35.78 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.957 / SU B: 5.486 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.18762 2367 5 %RANDOM
Rwork0.15832 ---
obs0.15979 44506 96.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.377 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å2-0.12 Å20 Å2
2---0.12 Å20 Å2
3---0.39 Å2
Refinement stepCycle: LAST / Resolution: 1.86→35.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4130 0 24 270 4424
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0194267
X-RAY DIFFRACTIONr_bond_other_d0.0010.024092
X-RAY DIFFRACTIONr_angle_refined_deg1.631.9765801
X-RAY DIFFRACTIONr_angle_other_deg0.8143.0019453
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7975533
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.46424.74173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.29715717
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.171515
X-RAY DIFFRACTIONr_chiral_restr0.090.2644
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214771
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02926
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_it1.2271.6342129
X-RAY DIFFRACTIONr_mcbond_other1.2261.6332128
X-RAY DIFFRACTIONr_mcangle_it1.9842.4442660
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.9881.8942138
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.9532.7353140
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: 1.863→1.911 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 146 -
Rwork0.257 2584 -
obs--76.15 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.7951-0.3937-0.09070.73870.13620.26720.0213-0.04740.041-0.01120.0155-0.0536-0.0091-0.0276-0.03670.14310.03060.01330.15830.01160.008441.334-14.62332.331
21.43520.1620.00481.0009-0.03810.4545-0.05860.0822-0.0468-0.12230.05470.08740.0211-0.11820.00390.14820.0250.02230.17640.01430.01818.38-12.46928.436
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A21 - 302
2X-RAY DIFFRACTION2A303 - 552

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