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- PDB-6h0v: Crystal structure of tabun surrogate NEDPA inhibited recombinant ... -

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Basic information

Entry
Database: PDB / ID: 6h0v
TitleCrystal structure of tabun surrogate NEDPA inhibited recombinant human bile salt activated lipase
ComponentsBile salt-activated lipase
KeywordsHYDROLASE / Lipase / alpha-beta hydrolase / tabun inhibition
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 / MOLECULAR REPLACEMENT / Resolution: 2.2 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 / struct_conn_type
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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id

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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)61,44110
Polymers60,8781
Non-polymers5639
Water1,33374
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1190 Å2
ΔGint-147 kcal/mol
Surface area21870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.330, 97.750, 110.540
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: 60877.816 Da / Num. of mol.: 1 / Mutation: N186D, A298D, 534STOP
Source method: isolated from a genetically manipulated source
Details: SUN = serine residue inhibited by tabun (already in PDB database please see 2JEZ)
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.: 5 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 2.55 Å3/Da / Density % sol: 51.83 %
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: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jul 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 2.2→48.11 Å / Num. obs: 28933 / % possible obs: 94.42 % / Redundancy: 4 % / Biso Wilson estimate: 33.11 Å2 / Net I/σ(I): 13.52
Reflection shellResolution: 2.2→2.279 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 5.21 / Num. unique obs: 2882 / % possible all: 95.15

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Processing

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

1f6w


Resolution: 2.2→48.11 Å / SU ML: 0.2748 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.0005
RfactorNum. reflection% reflection
Rfree0.2505 1157 4 %
Rwork0.1947 --
obs0.1969 28924 94.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 42.27 Å2
Refinement stepCycle: LAST / Resolution: 2.2→48.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4053 0 21 74 4148
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00774184
X-RAY DIFFRACTIONf_angle_d0.92145688
X-RAY DIFFRACTIONf_chiral_restr0.0541616
X-RAY DIFFRACTIONf_plane_restr0.0063735
X-RAY DIFFRACTIONf_dihedral_angle_d5.26813382
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.30.36671430.27723432X-RAY DIFFRACTION95.82
2.3-2.420.30741480.23233563X-RAY DIFFRACTION97.86
2.42-2.570.27261480.21613540X-RAY DIFFRACTION97.1
2.57-2.770.28591440.21123464X-RAY DIFFRACTION95.88
2.77-3.050.28161440.21453465X-RAY DIFFRACTION94.82
3.05-3.490.26551450.19763466X-RAY DIFFRACTION94.23
3.49-4.40.21261420.16563416X-RAY DIFFRACTION92.08
4.4-48.120.20851430.17453421X-RAY DIFFRACTION88.17

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