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- PDB-6h0t: Crystal structure of native recombinant human bile salt activated... -

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Basic information

Entry
Database: PDB / ID: 6h0t
TitleCrystal structure of native recombinant human bile salt activated lipase
ComponentsBile salt-activated lipase
KeywordsHYDROLASE / Lipase / alpha-beta hydrolase.
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 / Developmental Lineage of Pancreatic Acinar Cells / catalytic activity / lipid metabolic process / heparin binding / hydrolase activity / extracellular space / extracellular exosome / extracellular region / membrane / cytoplasm
Similarity search - Function
Mucin-like domain / Mucin-like / : / 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 ...Mucin-like domain / Mucin-like / : / 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
ACETATE ION / Bile salt-activated lipase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 10, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 27, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bile salt-activated lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,59414
Polymers60,7431
Non-polymers85213
Water2,018112
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1770 Å2
ΔGint-243 kcal/mol
Surface area21740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.274, 97.676, 109.640
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: 60742.715 Da / Num. of mol.: 1 / Mutation: N186D, A298D, 534STOP
Source method: isolated from a genetically manipulated source
Details: Crystals with uncleaved tagged enzyme / 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.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.74 Å3/Da / Density % sol: 55.11 %
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: ID23-1 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.9→39.93 Å / Num. obs: 49920 / % possible obs: 99.5 % / Redundancy: 4.5 % / Biso Wilson estimate: 35.21 Å2 / Rmerge(I) obs: 0.08457 / Rpim(I) all: 0.04367 / Rrim(I) all: 0.09572 / Net I/σ(I): 8.07
Reflection shellResolution: 1.9→1.968 Å / Redundancy: 4.7 % / Rmerge(I) obs: 1.231 / Num. unique obs: 4887 / Rpim(I) all: 0.6223 / Rrim(I) all: 1.386 / % possible all: 99.17

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Processing

Software
NameClassification
PHASERphasing
Cootmodel building
PHENIXrefinement
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1f6w

1f6w


Resolution: 1.9→39.93 Å / SU ML: 0.254 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.5616
RfactorNum. reflection% reflection
Rfree0.246 2389 4.79 %
Rwork0.2099 --
obs0.2117 49846 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 46.12 Å2
Refinement stepCycle: LAST / Resolution: 1.9→39.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4019 0 30 112 4161
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00774146
X-RAY DIFFRACTIONf_angle_d0.84785635
X-RAY DIFFRACTIONf_chiral_restr0.0548610
X-RAY DIFFRACTIONf_plane_restr0.0057725
X-RAY DIFFRACTIONf_dihedral_angle_d5.99962434
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.940.42831300.39012748X-RAY DIFFRACTION99.04
1.94-1.980.39831370.34372743X-RAY DIFFRACTION99.38
1.98-2.030.40561550.3312749X-RAY DIFFRACTION99.38
2.03-2.080.33531340.29072759X-RAY DIFFRACTION99.31
2.08-2.130.29051500.26092752X-RAY DIFFRACTION99.9
2.13-2.20.29941450.24572746X-RAY DIFFRACTION99.76
2.2-2.270.25211380.23912781X-RAY DIFFRACTION99.86
2.27-2.350.29081260.23052767X-RAY DIFFRACTION99.69
2.35-2.440.29911280.22842799X-RAY DIFFRACTION99.69
2.44-2.550.27251330.22262784X-RAY DIFFRACTION99.83
2.55-2.690.26851430.2262773X-RAY DIFFRACTION99.66
2.69-2.860.27551240.23012809X-RAY DIFFRACTION99.86
2.86-3.080.26081560.23532812X-RAY DIFFRACTION99.53
3.08-3.390.24671320.21782801X-RAY DIFFRACTION99.39
3.39-3.880.23891540.18722816X-RAY DIFFRACTION99.4
3.88-4.880.1911520.16022849X-RAY DIFFRACTION99.37
4.88-44.620.19881520.17862969X-RAY DIFFRACTION98.86

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