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- PDB-6h19: Crystal structure of ethyl-paraoxon inhibited recombinant human b... -

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Basic information

Entry
Database: PDB / ID: 6h19
TitleCrystal structure of ethyl-paraoxon inhibited recombinant human bile salt activated lipase (aged form)
ComponentsBile salt-activated lipase
KeywordsHYDROLASE / Lipase / alpha-beta hydrolase. / paraoxon inhibition / aged form
Function / homology
Function and homology information


retinyl-palmitate esterase activity / Digestion of dietary lipid / acetylesterase / ceramide catabolic process / sterol esterase / sterol ester esterase activity / pancreatic juice secretion / acetylesterase activity / intestinal cholesterol absorption / triacylglycerol lipase ...retinyl-palmitate esterase activity / Digestion of dietary lipid / acetylesterase / ceramide catabolic process / sterol esterase / sterol ester esterase activity / pancreatic juice secretion / acetylesterase activity / intestinal cholesterol absorption / triacylglycerol lipase / triacylglycerol lipase activity / catalytic activity / lipid metabolic process / heparin binding / hydrolase activity / extracellular space / extracellular exosome / extracellular region / cytoplasm
Similarity search - Function
Mucin-like domain / Mucin-like / : / 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 ...Mucin-like domain / Mucin-like / : / 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
ACETATE ION / Bile salt-activated lipase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.89 Å
AuthorsTouvrey, C. / Brazzolotto, X. / Nachon, F.
Funding support France, 2items
OrganizationGrant numberCountry
French Ministry of Armed ForcesPDH-2-NRBC-3-C-3201 France
French National Research AgencyASTRID CAT-SCAV France
CitationJournal: Toxicology / Year: 2019
Title: X-ray structures of human bile-salt activated lipase conjugated to nerve agents surrogates.
Authors: Touvrey, C. / Courageux, C. / Guillon, V. / Terreux, R. / Nachon, F. / Brazzolotto, X.
History
DepositionJul 11, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 27, 2019Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bile salt-activated lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,96919
Polymers60,8791
Non-polymers1,09018
Water3,639202
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2600 Å2
ΔGint-314 kcal/mol
Surface area21650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.120, 97.810, 110.150
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Bile salt-activated lipase / BAL / Bile salt-stimulated lipase / BSSL / Bucelipase / Carboxyl ester lipase / Cholesterol ...BAL / Bile salt-stimulated lipase / BSSL / Bucelipase / Carboxyl ester lipase / Cholesterol esterase / Pancreatic lysophospholipase / Sterol esterase


Mass: 60878.801 Da / Num. of mol.: 1 / Mutation: N186D, A298D, 534STOP
Source method: isolated from a genetically manipulated source
Details: SPT = serine residue inhibited by ethylparaoxon in its aged form
Source: (gene. exp.) Homo sapiens (human) / Gene: CEL, BAL / Production host: Cricetulus griseus (Chinese hamster)
References: UniProt: P19835, sterol esterase, triacylglycerol lipase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / 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: 2.48 Å3/Da / Density % sol: 50.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 8000, cacodylate, zinc acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Mar 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 1.89→44.7 Å / Num. obs: 49065 / % possible obs: 99.35 % / Redundancy: 3.8 % / CC1/2: 0.995 / Rmerge(I) obs: 0.1196 / Rrim(I) all: 0.1387 / Net I/σ(I): 8.21
Reflection shellResolution: 1.89→1.958 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 1.37 / Num. unique obs: 4813 / CC1/2: 0.639 / % possible all: 98.75

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Processing

Software
NameClassification
XSCALEdata scaling
PHASERphasing
Cootmodel building
PHENIXrefinement
RefinementResolution: 1.89→44.7 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2296 2406 -
Rwork0.193 --
obs-49021 99.26 %
Refinement stepCycle: LAST / Resolution: 1.89→44.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4071 0 39 202 4312

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